a2m2html output for 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:

- T0538
- gi|17231646|ref|NP_488194.1|_9:61 hypothetical protein asr4154 [Nostoc sp. PCC 7120]
- gi|17133289|dbj|BAB75853.1| asr4154 [Nostoc sp. PCC 7120]
- gi|75906974|ref|YP_321270.1|_9:61 hypothetical protein Ava_0751 [Anabaena variabilis ATCC 29413]
- gi|75700699|gb|ABA20375.1| conserved hypothetical protein [Anabaena variabilis ATCC 29413]
- gi|186683772|ref|YP_001866968.1|_10:61 proto-chlorophyllide reductase 57 kD subunit [Nostoc punctiforme PCC 73102]
- gi|186466224|gb|ACC82025.1| Proto-chlorophyllide reductase 57 kD subunit [Nostoc punctiforme PCC 73102]
- gi|16331202|ref|NP_441930.1|_7:58 hypothetical protein ssr3304 [Synechocystis sp. PCC 6803]
- gi|1653696|dbj|BAA18608.1| ssr3304 [Synechocystis sp. PCC 6803]
- gi|284052849|ref|ZP_06383059.1|_9:61 proto-chlorophyllide reductase 57 kD subunit [Arthrospira platensis str. Paraca]
- gi|291571397|dbj|BAI93669.1| hypothetical protein [Arthrospira platensis NIES-39]
- gi|67925604|ref|ZP_00518930.1|_24:74 hypothetical protein CwatDRAFT_0913 [Crocosphaera watsonii WH 8501]
- gi|67852558|gb|EAM47991.1| hypothetical protein CwatDRAFT_0913 [Crocosphaera watsonii WH 8501]
- gi|209523303|ref|ZP_03271859.1|_9:61 Proto-chlorophyllide reductase 57 kD subunit [Arthrospira maxima CS-328]
- gi|209496454|gb|EDZ96753.1| Proto-chlorophyllide reductase 57 kD subunit [Arthrospira maxima CS-328]
- gi|218249083|ref|YP_002374454.1|_11:61 Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 8801]
- gi|257062170|ref|YP_003140058.1| Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 8802]
- gi|218169561|gb|ACK68298.1| Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 8801]
- gi|256592336|gb|ACV03223.1| Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 8802]
- gi|166363206|ref|YP_001655479.1|_10:61 hypothetical protein MAE_04650 [Microcystis aeruginosa NIES-843]
- gi|166085579|dbj|BAG00287.1| hypothetical protein [Microcystis aeruginosa NIES-843]
- gi|159030304|emb|CAO91199.1|_10:61 unnamed protein product [Microcystis aeruginosa PCC 7806]
- gi|254410548|ref|ZP_05024327.1|_10:61 Proto-chlorophyllide reductase 57 kD subunit superfamily [Microcoleus chthonoplastes PCC 7420]
- gi|196182754|gb|EDX77739.1| Proto-chlorophyllide reductase 57 kD subunit superfamily [Microcoleus chthonoplastes PCC 7420]
- gi|158334266|ref|YP_001515438.1|_10:61 hypothetical protein AM1_1085 [Acaryochloris marina MBIC11017]
- gi|158304507|gb|ABW26124.1| conserved domain protein [Acaryochloris marina MBIC11017]
- gi|218439948|ref|YP_002378277.1|_20:69 Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 7424]
- gi|218172676|gb|ACK71409.1| Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 7424]
- gi|220905691|ref|YP_002481002.1|_10:61 Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 7425]
- gi|219862302|gb|ACL42641.1| Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 7425]
- gi|37523536|ref|NP_926913.1|_17:68 hypothetical protein gsr3967 [Gloeobacter violaceus PCC 7421]
- gi|35214540|dbj|BAC91908.1| gsr3967 [Gloeobacter violaceus PCC 7421]
- gi|196255846|ref|ZP_03154384.1|_15:64 Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 7822]
- gi|196203026|gb|EDX97843.1| Proto-chlorophyllide reductase 57 kD subunit [Cyanothece sp. PCC 7822]
- gi|126657719|ref|ZP_01728873.1|_11:61 hypothetical protein CY0110_26008 [Cyanothece sp. CCY0110]
- gi|126620936|gb|EAZ91651.1| hypothetical protein CY0110_26008 [Cyanothece sp. CCY0110]
- gi|172037053|ref|YP_001803554.1|_15:65 hypothetical protein cce_2138 [Cyanothece sp. ATCC 51142]
- gi|171698507|gb|ACB51488.1| unknown [Cyanothece sp. ATCC 51142]
- gi|119489868|ref|ZP_01622623.1|_12:61 hypothetical protein L8106_30440 [Lyngbya sp. PCC 8106]
- gi|119454296|gb|EAW35447.1| hypothetical protein L8106_30440 [Lyngbya sp. PCC 8106]
- gi|170079242|ref|YP_001735880.1|_11:61 hypothetical protein SYNPCC7002_A2648 [Synechococcus sp. PCC 7002]
- gi|169886911|gb|ACB00625.1| conserved hypothetical protein [Synechococcus sp. PCC 7002]
- gi|87125057|ref|ZP_01080904.1|_3:52 hypothetical protein RS9917_03608 [Synechococcus sp. RS9917]
- gi|86167377|gb|EAQ68637.1| hypothetical protein RS9917_03608 [Synechococcus sp. RS9917]
- gi|86606400|ref|YP_475163.1|_6:55 light-independent protochlorophyllide reductase, B subunit, truncation [Synechococcus sp. JA-3-3Ab]
- gi|86554942|gb|ABC99900.1| light-independent protochlorophyllide reductase, B subunit, truncation [Synechococcus sp. JA-3-3Ab]
- gi|254430670|ref|ZP_05044373.1|_3:52 Proto-chlorophyllide reductase 57 kD subunit superfamily [Cyanobium sp. PCC 7001]
- gi|197625123|gb|EDY37682.1| Proto-chlorophyllide reductase 57 kD subunit superfamily [Cyanobium sp. PCC 7001]
- gi|56751303|ref|YP_172004.1|_1:53 hypothetical protein syc1294_d [Synechococcus elongatus PCC 6301]
- gi|81299029|ref|YP_399237.1| hypothetical protein Synpcc7942_0218 [Synechococcus elongatus PCC 7942]
- gi|56686262|dbj|BAD79484.1| hypothetical protein [Synechococcus elongatus PCC 6301]
- gi|81167910|gb|ABB56250.1| conserved hypothetical protein [Synechococcus elongatus PCC 7942]
- gi|254424890|ref|ZP_05038608.1|_5:55 Proto-chlorophyllide reductase 57 kD subunit superfamily [Synechococcus sp. PCC 7335]
- gi|196192379|gb|EDX87343.1| Proto-chlorophyllide reductase 57 kD subunit superfamily [Synechococcus sp. PCC 7335]
- gi|170076702|ref|YP_001733340.1|_3:50 hypothetical protein SYNPCC7002_A0067 [Synechococcus sp. PCC 7002]
- gi|169884371|gb|ACA98084.1| conserved hypothetical protein [Synechococcus sp. PCC 7002]
- gi|119511120|ref|ZP_01630238.1|_5:49 protochlorophillide reductase 57 kD subunit [Nodularia spumigena CCY9414]
- gi|119464215|gb|EAW45134.1| protochlorophillide reductase 57 kD subunit [Nodularia spumigena CCY9414]
- gi|16330112|ref|NP_440840.1|_34:79 protochlorophillide reductase 57 kD subunit [Synechocystis sp. PCC 6803]
- gi|1652599|dbj|BAA17520.1| protochlorophillide reductase 57 kD subunit [Synechocystis sp. PCC 6803]

              10        20        30        40        50    
              |         |         |         |         |    
   1 MNLRWTSEAKTKLKNIPFFARSQAKARIEQLARQAEQDIVTPELVEQARLEFGQ
   2 -NLRWTSEAKTKLKNIPFFARSQAKARIEQLARQAEQDIVTPELVEQARLEFGQ
   3 -NLRWTSEAKTKLKNIPFFARSQAQARIEQLARQAEQDIVTPELVEQARLEFGQ
   4 --LRWTPEAKEKLQNIPFFVRSQAKARIEQLAREAGQEIVTGDLVEQARLEFGQ
   5 --LPWTPEARQKLKNIPYFARVQARQRIEQLARQADLDEVTVDLVEQARLEFGQ
   6 -NLKWQPEATAKLKNIPYFVRGQARQRIEQLAREADQEEVTVELVEQARLEFGQ
   7 ---RWTQDAEKKLKNIPFFVRTQARQRIEDLARAANSDEITVEMVEQARLEFGQ
   8 -NLKWQPEATAKLKNIPYFVRGQARQRIEQLAREADQEEVTVELVEQARLEFGQ
   9 ---RWTPEAQVKLKNIPFFVRTQARQRIEELAREAGSDEVTVEMVEQARLEFGQ
  10 --LQWTAEAKAKLKNIPYFVRSQARQRIEELARHAGSDRVTVEMVEQARIEFGQ
  11 --LQWTAEAKAKLKNIPYFVRSQARQRIEELARHAGSDRVTLEMVEQARIEFGQ
  12 --LDWTPEAKAKLKKIPYFVRTQARQRIEHLAREADLDVVTVDIVEQARIEFGQ
  13 --LQWTSTAEAKLKNIPFFARSQARQKIEAIARESNLDVVTVELVELARLEFGQ
  14 ----WTPEAKAKLKQIPFFVRTQARQRIEELARAAGSDEVTVEIVEQARVEFGQ
  15 --LSWTPEATLKLRNIPFFARAQARQRIERLARDNDLETVTLELVEQARQEFGQ
  16 --LVWTPEALVKLRKIPYFVRSQARLRIEELARASEVDLITVELVQKARLEFGQ
  17 ----WTPQAKAKLKQIPFFVRTQARQRIEELARAAGMDEVTVEIVEQARVEFGQ
  18 ---RWTQEAQRKLKNIPFFVRTQARQRIEELARAADSDEVTVEMVEQARLEFGQ
  19 ---RWTQEAQRKLKNIPFFVRTQARQRIEELARATDSEEVTVEMVEQARLEFGQ
  20 ----WTPEAKAKLQKIPYFVRSQARKRIEQLAREGDFEEITVELVEKARVEFGQ
  21 ---PWTEEAKTKYKNIPFYARSQARQTIEELAREEEVEEITAELVMRAQQKFGK
  22 ----WTSEAEQALKEVPFFVRPAVRKRIEAMARESKRDPIDLSFYTEARARFGQ
  23 ---EWTPEAEARLKEIPFFVRPAARKKIEQFAREAGIQKITVAVYEQAKQKFG-
  24 ----WTSAAEQRLKEVPFFVRPAVRRRIEAMAADAGLEQIDEAFYGEARVQFGQ
  25 MPMNWTPAAEQCLKEIPFFVRPAARKKIEKFASDRGITEIDEEVYKQAKAQFG-
  26 --IEWTAQAEALLKEIPFFVRPAARKKIEKFAREREISEISESVYREAKQQFG-
  27 ----WIDEAKELFKKIPFFVRPFAKKKIEKLAEEMGAKIIDKEIYIQAKAQF--
  28 --IKWTADAEAKLKEIPFFVRPFARKKIETYAEENNISLITLEIYEA-------
  29 ---SWTAEATERLKEIPFFVRPAARKKIENFAREAGITEITETVYEQAK-----