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, 1999.
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:

- T0120 DNA repair protein XRCC4, human
- gi|5706612|gb|AAD47298.1|_1:336 (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|4507945|ref|NP_003392.1|_1:334 X-ray repair complementing defective repair in Chinese hamster cells 4 (Homo sapiens)
- gi|1151115|gb|AAC50339.1| (U40622) XRCC4 [Homo sapiens] (Homo sapiens)
- gi|5706611|gb|AAD47297.1| (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|1586944|prf||2205251A XRCC4 gene [Homo sapiens] (Homo sapiens)
- gi|5706612|gb|AAD47298.1|_1:336 (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|4507945|ref|NP_003392.1|_1:334 X-ray repair complementing defective repair in Chinese hamster cells 4 (Homo sapiens)
- gi|1151115|gb|AAC50339.1| (U40622) XRCC4 [Homo sapiens] (Homo sapiens)
- gi|5706611|gb|AAD47297.1| (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|1586944|prf||2205251A XRCC4 gene [Homo sapiens] (Homo sapiens)
- gi|7488950|pir||S72445_48:162 DNA-binding protein WRKY3 - parsley (Petroselinum crispum)
- gi|1432056|gb|AAC49528.1| (U56834) WRKY3 [Petroselinum crispum] (Petroselinum crispum)
- gi|4680251|gb|AAD27591.1|AF121354_1_48:162 (AF121354) transcription factor; sequence specific DNA-binding protein; WRKY3 [Petroselinum crispum] (Petroselinum crispum)
- gi|7491377|pir||T39512_571:664 hypothetical protein SPBC1604.02c - fission yeast (Schizosaccharomyces pombe) (Schizosaccharomyces pombe)
- gi|4007754|emb|CAA22335.1| (AL034433) hypothetical protein [Schizosaccharomyces pombe] (Schizosaccharomyces pombe)
- gi|3183368|sp|O13890|YE35_SCHPO_213:286 HYPOTHETICAL 64.0 KD PROTEIN C20G4.05C IN CHROMOSOME I (Schizosaccharomyces pombe)
- gi|7492060|pir||T38119 hypothetical UPF0061 family protein - fission yeast (Schizosaccharomyces pombe) (Schizosaccharomyces pombe)
- gi|2330761|emb|CAB11255.1| (Z98600) hypothetical UPF0061 family protein [Schizosaccharomyces pombe] (Schizosaccharomyces pombe)
- gi|6606229|gb|AAF19126.1|AF143466_1_34:85 (AF143466) BdrB3 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606211|gb|AAF19114.1|AF143460_1_34:86 (AF143460) BdrC2 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606244|gb|AAF19136.1|AF143471_1_34:86 (AF143471) BdrC4 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606217|gb|AAF19118.1|AF143462_1_34:86 (AF143462) BdrC4 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606199|gb|AAF19106.1|AF143456_1_34:81 (AF143456) BdrC1 [Borrelia parkeri] (Borrelia parkeri)
- gi|3056589|gb|AAC13900.1|_31:171 (AC004255) T1F9.10 [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|6606214|gb|AAF19116.1|AF143461_1_34:97 (AF143461) BdrC3 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606220|gb|AAF19120.1|AF143463_1_34:96 (AF143463) BdrB1 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606247|gb|AAF19138.1|AF143472_1_34:86 (AF143472) BdrC5 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606223|gb|AAF19122.1|AF143464_1_34:85 (AF143464) BdrB2 [Borrelia hermsii] (Borrelia hermsii)
- gi|7294937|gb|AAF50266.1|_157:196 (AE003552) CG3448 gene product [Drosophila melanogaster] (Drosophila melanogaster)
- gi|6606208|gb|AAF19112.1|AF143459_1_34:97 (AF143459) BdrC1 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606241|gb|AAF19134.1|AF143470_1_34:97 (AF143470) BdrC3 [Borrelia hermsii] (Borrelia hermsii)
- gi|6841062|gb|AAF28885.1|AF123078_10_34:97 (AF123078) BdrA [Borrelia hermsii] (Borrelia hermsii)
- gi|6606235|gb|AAF19130.1|AF143468_1_34:97 (AF143468) BdrC1 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606238|gb|AAF19132.1|AF143469_1_34:97 (AF143469) BdrC2 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606259|gb|AAF19146.1|AF143476_1_34:97 (AF143476) BdrC1 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606244|gb|AAF19136.1|AF143471_1_118:162 (AF143471) BdrC4 [Borrelia hermsii] (Borrelia hermsii)
- gi|6606259|gb|AAF19146.1|AF143476_1_129:173 (AF143476) BdrC1 [Borrelia hermsii] (Borrelia hermsii)

              10        20        30        40        50          60   
              |         |         |         |         |           |   
   1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDM..AMEK
   2 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDM..AMEK
   3 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDM..AMEK
   4 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDM..AMEK
   5 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDM..AMEK
   6 ---------------------------------AYLSSSSSSETGDTDYR----AVTDV..AVNK
   7 ---------------------------------AYLSSSSSSETGDTDYR----AVTDV..AVNK
   8 -----------------------------------------------------------..----
   9 -----------------------------------------------------------..----
  10 -----------------------------------------------------------..----
  11 -----------------------------------------------------------..----
  12 -----------------------------------------------------------..----
  13 -----------------------------------------------------------..----
  14 -----------------------------------------------------------..----
  15 -----------------------------SRFDISVTDGSFTWTCNATEEEQPNSVYGFsdAIEG
  16 -----------------------------------------------------------..----
  17 -----------------------------------------------------------..----
  18 -----------------------------------------------------------..----
  19 -----------------------------------------------------------..----
  20 -----------------------------------------------------------..----
  21 -----------------------------------------------------------..----
  22 -----------------------------------------------------------..----
  23 -----------------------------------------------------------..----
  24 -----------------------------------------------------------..----
  25 -----------------------------------------------------------..----
  26 -----------------------------------------------------------..----
  27 -----------------------------------------------------------..----
  28 -----------------------------------------------------------..----


           70        80        90            100       110        120  
           |         |         |              |         |          |  
   1 GKYVGELRKALLSGAGPADVYTFNFSKESCYFFFE.....KNLKDVSFRLGSFNLE.KVENPAEV
   2 GKYVGELRKALLSGAGPADVYTFNFSKESCYFFFE.....KNLKDVSFRLGSFNLE.KVENPAEV
   3 GKYVGELRKALLSGAGPADVYTFNFSKESCYFFFE.....KNLKDVSFRLGSFNLE.KVENPAEV
   4 GKYVGELRKALLSGAGPADVYTFNFSKESCYFFFE.....KNLKDVSFRLGSFNLE.KVENPAEV
   5 GKYVGELRKALLSGAGPADVYTFNFSKESCYFFFE.....KNLKDVSFRLGSFNLE.KVENPAEV
   6 FKKFISL--------------------------LD.....KN--------------.--------
   7 FKKFISL--------------------------LD.....KN--------------.--------
   8 -----------------------------------.....-------ALLYSFKVS.DVDDSHFS
   9 -----------------------------------.....------WIRIGTFDLQ.GINNQIES
  10 -----------------------------------.....----------------.--------
  11 -----------------------------------.....----------------.--------
  12 -----------------------------------.....----------------.--------
  13 -----------------------------------.....----------------.--------
  14 -----------------------------------.....----------------.--------
  15 SKR-----------------LSWTFEKEGTKLEWRwk6psDDSKKITVRILDFLMEaNIRLSEEV
  16 -----------------------------------.....----------------.--------
  17 -----------------------------------.....----------------.--------
  18 -----------------------------------.....----------------.--------
  19 -----------------------------------.....----------------.--------
  20 -----------------------------------.....----------------.--------
  21 -----------------------------------.....----------------.--------
  22 -----------------------------------.....----------------.--------
  23 -----------------------------------.....----------------.--------
  24 -----------------------------------.....----------------.--------
  25 -----------------------------------.....----------------.--------
  26 -----------------------------------.....----------------.--------
  27 -----------------------------------.....----------------.--------
  28 -----------------------------------.....----------------.--------


             130           140       150       160       170       180 
              |             |         |         |         |         | 
   1 IRE..LICYCL....DTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFI
   2 IRE..LICYCL....DTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFI
   3 IRE..LICYCL....DTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFI
   4 IRE..LICYCL....DTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFI
   5 IRE..LICYCL....DTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFI
   6 ---..------....------------------------------------------RTGHARFR
   7 ---..------....------------------------------------------RTGHARFR
   8 FRSqiLICWCYyrlnDFKSLIQHTNNLLQSNNASLLRR-------LAATLYRIQIRENNGYKRVL
   9 LRK..LADYCL....NFVLKDGFHGGDTGNRYEKLLRD---VAYRNAKTVAKWQAY---------
  10 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  11 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  12 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  13 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  14 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  15 VNK..TR----....--------SFEKMKSEAERCLAQ-------GEKLCDEKTEFENATYAKFL
  16 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  17 ---..------....---------------------------YYRNELTHKDIEYLETTFNLKLE
  18 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  19 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  20 ---..------....--------------------LAE-------YEKYVRDSKLKEEELLKKFL
  21 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  22 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  23 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  24 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  25 ---..------....---------------------------YYRNELTYKDIGYLETTFNLKLE
  26 ---..------....---------------------------YYRNELTYKDIEYLETTFNLKLE
  27 ---..------....-----------------------------------NKIDAVENNLNIKID
  28 ---..------....-----------------------------------NKIDTVENNLNIKID


            190            200       210       220       230       240 
             |              |         |         |         |         | 
   1 LVLNEKKTKIRSLHNKL.....LNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQT
   2 LVLNEKKTKIRSLHNKL.....LNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQT
   3 LVLNEKKTKIRSLHNKL.....LNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQT
   4 LVLNEKKTKIRSLHNKL.....LNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQT
   5 LVLNEKKTKIRSLHNKL.....LNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQT
   6 RGPVQEKTGVEMLVNPI.....QNQIQNHGSDGFQ------------------------------
   7 RGPVQEKTGVEMLVNPI.....QNQIQNHGSDGFQ------------------------------
   8 LDRLRKKAILRAFPSRT.....LN-----------------------------------------
   9 -----------GFMNGV.....LNT----------------------------------------
  10 KLEASLKSDIRDLDNKV.....DNVRNELKSDIR-------------------------------
  11 KVEASLKSDIKDLDNKI.....DNVRNELKSDIKD------------------------------
  12 KVGASLKSDIKDLDNKI.....DNVRNELKSDIKD------------------------------
  13 KVEASLKSDIKDLDNKI.....DNVRNELKSDIKD------------------------------
  14 KVEANLKSDIKDLDNKI.....DNVENNLN-----------------------------------
  15 SVLNAKKAKLRAVRDK-.....-------------------------------------------
  16 KVGASLKSDIKDLDNKId11kiDNVRNELKSDIKD------------------------------
  17 KLEASLKSDIRDLDNKId11kiDNVRNELKSDIK-------------------------------
  18 KVGASLKSDIKDLDNKI.....DNVRNELKSDIKD------------------------------
  19 KLEASLKSDIRDLDNKI.....DNVRNELKSDIR-------------------------------
  20 LLLNSKKAHIRDLESQL.....-------------------------------------------
  21 KVGASLKSDIKDLDNKId11kiDNVRNELKSDIKD------------------------------
  22 KVEASLKSDIKDLDNKId11kiDNVRNELKSDIKD------------------------------
  23 KLEASLKSDIRDLDNKId11kiDNVRNELKSDIKD------------------------------
  24 KVEASLKSDIKDLDNKId11kiDNVRNELKSDIKD------------------------------
  25 KVEASLKSDIKDLDNKId11kiDNVRNELKSDIKD------------------------------
  26 KVGASLKSDIKDIDNKId11kiDNVRNELKSDIKD------------------------------
  27 NVRNELKSDIKDLDNKI.....DNVRNELKSDIKD------------------------------
  28 NVRNELKSDIKDLDNKI.....DNVRNELKSDIKD------------------------------


            250       260       270       280       290       300      
             |         |         |         |         |         |      
   1 DLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKENSRPDSSLP
   2 DLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKENSRPDSSLP
   3 DLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKE--KPDSSLP
   4 DLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKENSRPDSSLP
   5 DLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKE--KPDSSLP
   6 ----------------------------------VYRPTAVHPVQPVQPVQIQPVQLVQPVQRLP
   7 ----------------------------------VYRPTAVHPVQPVQPVQIQPVQLVQPVQRLP
   8 -----------------------------------------------------------------
   9 -----------------------------------------------------------------
  10 -----------------------------------------------------------------
  11 -----------------------------------------------------------------
  12 -----------------------------------------------------------------
  13 -----------------------------------------------------------------
  14 -----------------------------------------------------------------
  15 -----------------------------------------------------------------
  16 -----------------------------------------------------------------
  17 -----------------------------------------------------------------
  18 -----------------------------------------------------------------
  19 -----------------------------------------------------------------
  20 -----------------------------------------------------------------
  21 -----------------------------------------------------------------
  22 -----------------------------------------------------------------
  23 -----------------------------------------------------------------
  24 -----------------------------------------------------------------
  25 -----------------------------------------------------------------
  26 -----------------------------------------------------------------
  27 -----------------------------------------------------------------
  28 -----------------------------------------------------------------


       310       320       330      
        |         |         |      
   1 ETSKKEHISAENMSLETLRNSSPEDLFDEI
   2 ETSKKEHISAENMSLETLRNSSPEDLFDEI
   3 ETSKKEHISAENMSLETLRNSSPEDLFDEI
   4 ETSKKEHISAENMSLETLRNSSPEDLFDEI
   5 ETSKKEHISAENMSLETLRNSSPEDLFDEI
   6 PVPKKENIS---------------------
   7 PVPKKENIS---------------------
   8 ------------------------------
   9 ------------------------------
  10 ------------------------------
  11 ------------------------------
  12 ------------------------------
  13 ------------------------------
  14 ------------------------------
  15 ------------------------------
  16 ------------------------------
  17 ------------------------------
  18 ------------------------------
  19 ------------------------------
  20 ------------------------------
  21 ------------------------------
  22 ------------------------------
  23 ------------------------------
  24 ------------------------------
  25 ------------------------------
  26 ------------------------------
  27 ------------------------------
  28 ------------------------------