a2m2html output for file tmp.a2m

Citations (SAM, SAM-T99, HMMs)

R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.

Sequence numbers correspond to the following labels:

- YGR229C SMI1 SGDID:S0003461, Chr VII from 949374-950891, reverse complement
- gi|6321668|ref|NP_011745.1|_1:505 Protein involved in (1,3)-beta-glucan synthesis, possibly through regulation of cell wall glucan and chitin synthesis; chromatin binding protein; Smi1p [Saccharomyces cerevisiae]
- gi|417781 sp|P32566|SMI1_YEAST SMI1 PROTEIN (KILLER TOXIN RESISTANT PROTEIN 4)
- gi|1078065|pir||A55923 KNR4 protein - yeast (Saccharomyces cerevisiae)
- gi|295663|gb|AAA35053.1| MAR inhibitor suppressor
- gi|311113|gb|AAA67469.1| k9 killer toxin resistant gene
- gi|886922|emb|CAA61178.1| ORF 505 [Saccharomyces cerevisiae]
- gi|1323413|emb|CAA97257.1| ORF YGR229c [Saccharomyces cerevisiae]
- gi|729636 sp|P38678|GS1_NEUCR_89:532 Glucan synthase-1 (1,3-beta-glucan synthase) (UDP-glucose-1,3-beta-D-glucan glucosyltransferase)
- gi|11282399|pir||T46649 1,3-beta-glucan synthase (EC 2.4.1.34) 1 [imported] - Neurospora crassa
- gi|493030|gb|AAA50440.1| glucan synthase-1
- gi|11595725|emb|CAC18203.1| 1, 3-beta-glucan synthase [Neurospora crassa]
- gi|19113060|ref|NP_596268.1|_76:503 putative glucan synthase [Schizosaccharomyces pombe]
- gi|7492592|pir||T40179 probable glucan synthase - fission yeast (Schizosaccharomyces pombe)
- gi|2276366|emb|CAB10812.1| putative glucan synthase regulator (PMID 7937796); possibly involved in beta-1,3 glucan biosynthesis; possibly involved in cell wall organization and biogenesis; similar to S. cerevisiae SMI1; similar to N. crassa GS-1 [Schizosaccharomyces pombe]
- gi|15965547|ref|NP_385900.1|_6:184 HYPOTHETICAL PROTEIN [Sinorhizobium meliloti]
- gi|15074728|emb|CAC46373.1| HYPOTHETICAL PROTEIN [Sinorhizobium meliloti]
- gi|15807885|ref|NP_285544.1|_1:168 glucan synthase 1-related protein [Deinococcus radiodurans]
- gi|7471933|pir||F75574 glucan synthase 1-related protein - Deinococcus radiodurans (strain R1)
- gi|6460707|gb|AAF12412.1|AE001863_37 glucan synthase 1-related protein [Deinococcus radiodurans]
- gi|21223354|ref|NP_629133.1|_132:346 putative bifunctional protein [Streptomyces coelicolor A3(2)]
- gi|14285275|emb|CAC40594.1| putative bifunctional protein [Streptomyces coelicolor A3(2)]
- gi|18390613|ref|NP_563759.1|_73:246 F-box protein family; protein id: At1g06110.1, supported by cDNA: gi_16930490, supported by cDNA: gi_20466210 [Arabidopsis thaliana]
- gi|8810473|gb|AAF80134.1|AC024174_16 Contains similarity to a F-box protein FBA from Mus musculus gb|AF233226. ESTs gb|AV536237, gb|AV541425, gb|AV542477, gb|AV543534, gb|AV536862, gb|AI100662, gb|Z27285, gb|Z29939, gb|T21404, gb|T44511, gb|H37689 come from this gene. [Arabidopsis thaliana]
- gi|16930491|gb|AAL31931.1|AF419599_1 At1g06110/T21E18_13 [Arabidopsis thaliana]
- gi|20466211|gb|AAM20423.1| unknown protein [Arabidopsis thaliana]
- gi|12835784|dbj|BAB23360.1|_91:314 data source:MGD, source key:MGI:1929084, evidence:ISS~f-box only protein 3~putative [Mus musculus]
- gi|10181216|ref|NP_065618.1|_91:273 f-box only protein 3; F-box protein FBA [Mus musculus]
- gi|7677412|gb|AAF67156.1|AF233226_1 F-box protein FBA [Mus musculus]
- gi|13124239 sp|Q9UK99|FBX3_HUMAN_90:281 F-box only protein 3
- gi|7023521|dbj|BAA91991.1| unnamed protein product [Homo sapiens]
- gi|15812186|ref|NP_036307.2|_91:281 F-box only protein 3 isoform 1; F-box protein FBX3 [Homo sapiens]
- gi|12859828|dbj|BAB31793.1|_91:314 data source:MGD, source key:MGI:1929084, evidence:ISS~f-box only protein 3~putative [Mus musculus]
- gi|12052776|emb|CAB66560.1|_91:281 hypothetical protein [Homo sapiens]
- gi|9630133|ref|NP_046560.1|_40:107 unknown [Bacteriophage SPBc2]
- gi|16079218|ref|NP_390042.1| similar to hypothetical proteins from B. subtilis [Bacillus subtilis]
- gi|7514651|pir||T12772 conserved hypothetical yokH protein - Bacillus subtilis phage SPBc2
- gi|2634579|emb|CAB14077.1| similar to hypothetical proteins from B. subtilis [Bacillus subtilis]
- gi|3025486|gb|AAC12981.1| unknown [Bacteriophage SPBc2]
- gi|16078961|ref|NP_389782.1|_19:80 similar to hypothetical proteins from B. subtilis [Bacillus subtilis]
- gi|7474665|pir||D69899 conserved hypothetical protein yobM - Bacillus subtilis
- gi|2619041|gb|AAB84465.1| spore coat protein [Bacillus subtilis]
- gi|2634294|emb|CAB13793.1| similar to hypothetical proteins from B. subtilis [Bacillus subtilis]
- gi|16307347|gb|AAH10212.1|_1:201 Unknown (protein for MGC:7209) [Mus musculus]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MDLFKRKVKEWVYSLSTDDHYAEYNPDETPTFNMGKRLNSNNGQVNPSQMHLNSVDEEMSM.GFQ
   2 MDLFKRKVKEWVYSLSTDDHYAEYNPDETPTFNMGKRLNSNNGQVNPSQMHLNSVDEEMSM.GFQ
   3 ---------------------------------YSPGLVSQRQSVHQDAFDVHSPTGEIPMqNFQ
   4 ----------------------------------------LPNSSNTSQVGLNNIS-PAPV.GYV
   5 -------------------------------------------------------------.---
   6 -------------------------------------------------------------.---
   7 -------------------------------------------------------------.---
   8 -------------------------------------LWRESFRMY---------------.---
   9 -------------------------------------------------------------.---
  10 -------------------------------------------------------------.---
  11 -------------------------------------------------------------.---
  12 -------------------------------------------------------------.---
  13 -------------------------------------------------------------.---
  14 -------------------------------------------------------------.---
  15 -------------------------------------------------------------.---
  16 -------------------------------------------------------------.---
  17 -------------------------------------------------------------.---


          70            80           90       100       110       120  
          |             |            |         |         |         |  
   1 NGVPSNE....DINIDEFTSTES...NDGVSETLLAWRHIDFWTSEHNPDLNATLSDPCTQNDIT
   2 NGVPSNE....DINIDEFTSTES...NDGVSETLLAWRHIDFWTSEHNPDLNATLSDPCTQNDIT
   3 NGGP---....-----------P...PPPVAS---SWEKIDRWAEENYPELFDQLGEGCTVNDLN
   4 PGSKTNElannSMEMQEISPNGSaslPPPVSE---SWRRIDRWAEENYYELYCQLCYGATVADVD
   5 -------....------------...-----EPVLALKRIDTWVARHHPDRLPFVRPGADCGTIQ
   6 -------....------------...---MSEISAIWERIEAWHAAN--DQTENLNPGATAEALA
   7 -------....---LPEAVPGAL...PAPSADPAL----LERTLRERLPDAV-----GATEAEIA
   8 -------....-----------P...WNLVKRVRLCWDNLKQWLTLNFPEAKATLRKGVTEDDLQ
   9 -------....------------...-DHYAAIKKAWRDLKKYLEPRCPRMVLSLKEGAREEDLD
  10 -------....------------...-DHYAAIKKAWRDLKKYLEPRCPRMVLSLKEGAREEDLD
  11 -------....------------...IDHYAAIKKAWDDLKKYLEPRCPRMVLSLKEGAREEDLD
  12 -------....------------...-DHYAAIKKAWDDLKKYLEPRCPRMVLSLKEGAREEDLD
  13 -------....------------...-DHYAAIKKAWRDLKKYLEPRCPRMVLSLKEGAREEDLD
  14 -------....------------...-DHYAAVKRAWDDLKKYLEPRCPRMVLSLKEGAREEDLD
  15 -------....------------...----------------------P-------DKATLNDIQ
  16 -------....------------...-------------------------------KATLNDIQ
  17 -------....------------...------------------------MVLSLKEGAREEDLD


           130       140       150            160       170       180  
            |         |         |              |         |         |  
   1 HAEEDLEVSFPNPVKASFKIHDGQEDLESMTGTSGLF.....YGFQLMTLDQVVAMTQAWRNVA.
   2 HAEEDLEVSFPNPVKASFKIHDGQEDLESMTGTSGLF.....YGFQLMTLDQVVAMTQAWRNVA.
   3 ELEYQLDCTLPQDLRQSLQIHDGQERGGLPTG---II.....FSSMLLDCEEMVQEWENWKTVNq
   4 SLEYELECTLPRDVRESLYIHDGQDRGGQPTG---IL.....FGVTLLDIEEIEEESELWRRVA.
   5 RVEAKFGRRLPPDIRRLYAAHDGQ-----PAGSPALY.....LNQRWLPLDLVL---IAWEDLC.
   6 QAEKDMGLTFPPEMRESLLRHDGSVDDSWPTG-----.....---ELLSLERMADERKVWMDL-.
   7 EAQTRLGVTLPDELKALYRVV--RARWQDWRGDYAAQer6daVGCELLPLDQLY----------.
   8 EFETSLKVKLPLPTRLLYRFVDGQ-ELSSPNGLDGSLg12hdVNVYLLPLKEVMRETKE-----.
   9 AVEAQIGCKLPDDYRCSYRIHNGQKLV--VPGLLGSMal6hyRSEDLLDVDTAAGGFQQRQGLKy
  10 AVEAQIGCKLPDDYRCSYRIHNGQKLV--VPGLLGSMal6hyRSEDLLDVDTAAGGFQQRQGLKy
  11 AVEAQIGCKLPDDYRCSYRIHNGQKLV--VPGLLGSMtl6hyRSEDLLDVDTAAGGFQQRQGLKy
  12 AVEAQIGCKLPDDYRCSYRIHNGQKLV--VPGLLGSMal6hyRSEDLLDVDTAAGGFQQRQGLKy
  13 AVEAQIGCKLPDDYRCSYRIHNGQKLV--VPGLLGSMal6hyRSEDLLDVDTAAGGFQQRQGLKy
  14 AVEAQIGCKLPDDYRCSYRIHNGQKLV--VPGLLGSMal6hyRSEDLLDVDTAAGGFQQRQGLKy
  15 SFEAKHQLSLPEDYQKFITLHNGAKIFEILSDGENIG.....GGLQLFSLEEIEEELKY-EDLF.
  16 SFEAKHQLTLPQDYQKFMTLHNGAKIFEILSDGENIG.....GGLQLFSLEEIEEELKY-----.
  17 AVEAQIGCKLPDDYRCSYRIHNGQKLV--VPGLLGSMal6hyRSEDLLDVDTAAGGFQQRQGLKy


             190       200       210        220       230       240    
              |         |         |          |         |         |    
   1 .KNLNKRSQQGLSHVTSTGSSSSMERLNGNK.FKLPNIPDQKSIPPNAVQPVYAHPAWIPLITDN
   2 .KNLNKRSQQGLSHVTSTGSSSSMERLNGNK.FKLPNIPDQKSIPPNAVQPVYAHPAWIPLITDN
   3 eFMLDPVLVKRQSQAFAAQASSSKDAPNRNQnWRQELLNKQDSVPPAAIQKAYAHPAWIPLVRDW
   4 .-------------------QSYAEATLAGK.IDQAVASRQASFPPGAVQCVYAHPGWIPLAKDF
   5 .--------------LRYGGEVYPSRGDGRQ.F---------------LGTMVWSPNWLPLFGSP
   6 .----------LQDGTFDGNASHNES-----.-------------SEALQPGWWNPAWIPLDADG
   7 .-VADARSRPCLWQFAATDAAV---------.----------TAPDAAVQGLVGSPGWIAFGDNG
   8 .--------------------SFMRDLGFSS.---------------------------------
   9 cLPLTFCIHTGLSQYIAVEAAEGRNK---NE.-VFYQCPDQMARNPAAIDM--------------
  10 cLPLTFCIHTGLSQYIAVEAAEGRNK---NE.-VFYQCPDQMARNPAAIDM--------------
  11 cLPLTFCIHTGLSQYIAVEAAEGRNK---NE.-VFYQCPDQMARNPAAIDM--------------
  12 cLPLTFCIHTGLSQYIAVEAAEGRNK---NE.-VFYQCPDQMARNPAAIDM--------------
  13 cLPLTFCIHTGLSQYIAVEAAEGRN---KNEvF--YQCP-----------------------DKM
  14 cLPLTFCIHTGLSQYIAVEAAEGRNK---NE.-VFYQCPGQMARNPAA-----------------
  15 .------------------------------.---------------------------------
  16 .------------------------------.---------------------------------
  17 cLPLTFCIHTGLSQYIAVEAAEGRNK---NE.-VFYQCPDQMARNPAAIDM--------------


         250       260       270       280       290       300       31
          |         |         |         |         |         |         
   1 AGNHIGVDLAPGPNGKYAQIITFGRDFDTKFVIAENWGEFLLSFANDLEAGNWYLVDDNDDYFSG
   2 AGNHIGVDLAPGPNGKYAQIITFGRDFDTKFVIAENWGEFLLSFANDLEAGNWYLVDDNDDYFSG
   3 GGNNLAVDLAPGPKGHWGQIILFGRDYDTKYVVARSWAHFLAMVAEDLSSGRWFVDEDTN-----
   4 VGNNIAIDLAPGPAGQWGQVILFGRDQDTKYVVARSWADFLAIVAYDMENGKWLVDEDDN-----
   5 RGDHYCIDLRPELTNGYGQIIWFLYDEADRPVVAQSIAELLSRIANGVSTGRWALDDGYD-----
   6 GGNGAVIDLAPGPQGTVGQVIDMDHEVGPSGPKYVSLAAYLEAMLERLS----------------
   7 GGDRLALDLTPGPGGHTGQVVMIGHE--------DSIGAGLL-----------------------
   8 -----RL---------------------DLIVMAASVVASLKIFLLDCTTGQLFTGTSNRQLLPC
   9 ------------------------------FIIGATFTDWFTSYVNNVVSGGFPIIRDQIFRYIH
  10 ------------------------------FIIGATFTDWFTSYVNNVVSGGFPIIRDQIFRYIH
  11 ------------------------------FIIGATFTDWFTSYVKNVVSGGFPIIRDQIFRYVH
  12 ------------------------------FIIGATFTDWFTSYVKNVVSGGFPIIRDQIFRYVH
  13 ARNPAAIDM---------------------FIIGATFTDWFTSYVNNVVSGGFPIIRDQIFRYIH
  14 ------IDM---------------------LIIGATFTDWFTSYVKNVVSGGFPIIRDQIFRYVH
  15 -----------------------------------------------------------------
  16 -----------------------------------------------------------------
  17 ------------------------------FIIGATFTDWFTSYVNNVVSGGFPIIRDQIFRYIH


      0       320        330       340         350       360       370 
     |         |          |         |           |         |         | 
   1 DGELVFRDKKSN.GPIQDYFEVLKRRTWIKYQENLRSQQQK..SQPDTSLQEQKYVPASQKKVAA
   2 DGELVFRDKKSN.GPIQDYFEVLKRRTWIKYQENLRSQQQK..SQPDTSLQEQKYVPASQKKVAA
   3 --ELKLREFKAT.RVEPSYFEILRWRMDQKYGRTANKRKSMapSMASASGMRSPPTPGSPYQSPT
   4 ---SLRLIYGPP.REQWSYLDILKYRARKAERRKFKKRDGK..-------RTTRPIPKSIAKEDV
   5 ------------.----------------------------..----------------------
   6 ------------.----------------------------..----------------------
   7 ------------.----------------------------..-----------------AESLT
   8 VPDALVRSVHD-.----------------------------..----------------------
   9 DPECVATTGDITvSVSTSFLPELSSVHPPHYFFTYRIRIEM..----------------------
  10 ------------.----------------------------..----------------------
  11 DPECVATT----.----------------------------..----------------------
  12 DPECVATT----.----------------------------..----------------------
  13 DPECVATTGDITvSVSTSFLPELSSVHPPHYFFTYRIRIEM..----------------------
  14 DPECVATT----.----------------------------..----------------------
  15 ------------.----------------------------..----------------------
  16 ------------.----------------------------..----------------------
  17 DPECVATTGDITvSVSTSFLPELSSVHPPHYFFTYRIRIEM..----------------------


                 380       390         400       410         420       
                  |         |           |         |           |       
   1 EQ.....PSTLNAESIKGEDSGSADVQSVQD..HESVKIVKTEPSEAETT..TVNTESLGQAE..
   2 EQ.....PSTLNAESIKGEDSGSADVQSVQD..HESVKIVKTEPSEAETT..TVNTESLGQAE..
   3 EHne...PRGRSLHRLTGTSPMSSPIRPGYG..KPSP--LARVAEEAPPT..TSLTASNASLEa1
   4 TNsa6taPSTGTTVLDDGLDNNYEDIPLYGP..SKDEELIKKEELEADTDlgLINTSEINQPA..
   5 --.....------------------------..-----------------..-----------..
   6 --.....------------------------..-----------------..-----------..
   7 DM.....VVNGRAEWHPGRDWDRPPVVARLNvlGDDVSAVARPELE----..-----------..
   8 --.....------------------------..-----------------..-----------..
   9 --.....------------------------..-----------------..-----------..
  10 --.....------------------------..-----------------..-----------..
  11 --.....------------------------..-----------------..-----------..
  12 --.....------------------------..-----------------..-----------..
  13 --.....------------------------..-----------------..-----------..
  14 --.....------------------------..-----------------..-----------..
  15 --.....------------------------..-----------------..-----------..
  16 --.....------------------------..-----------------..-----------..
  17 --.....------------------------..-----------------..-----------..


           430        440       450       460       470       480      
            |          |         |         |         |         |      
   1 ...HEIKADNVDI.KQESERKEDEKQPKVEEKEHVENEHVTESAKKDDDVNKQTEEMNKKEENEI
   2 ...HEIKADNVDI.KQESERKEDEKQPKVEEKEHVENEHVTESAKKDDDVNKQTEEMNKKEENEI
   3 6tsGEHSKEDIKV.NEDSPAKERTSEDKEKKPETEANGKATESKGKQTTV---------------
   4 ...NLPDEPTAETsNPVSATTVEAVTTTADNKDEEKNDHVTEDVSQNSTIAEASSLQAQEEEKEI
   5 ...----------.---------------------------------------------------
   6 ...----------.---------------------------------------------------
   7 ...----------.---------------------------------------------------
   8 ...----------.---------------------------------------------------
   9 ...----------.---------------------------------------------------
  10 ...----------.---------------------------------------------------
  11 ...----------.---------------------------------------------------
  12 ...----------.---------------------------------------------------
  13 ...----------.---------------------------------------------------
  14 ...----------.---------------------------------------------------
  15 ...----------.---------------------------------------------------
  16 ...----------.---------------------------------------------------
  17 ...----------.---------------------------------------------------


       490       500     
        |         |     
   1 RSDDAKVEEAREEFENIAL
   2 RSDDAKVEEAREEFENIAL
   3 --------EDAEDMKDIEI
   4 ETTSVKQ------------
   5 -------------------
   6 -------------------
   7 -------------------
   8 -------------------
   9 -------------------
  10 -------------------
  11 -------------------
  12 -------------------
  13 -------------------
  14 -------------------
  15 -------------------
  16 -------------------
  17 -------------------