Query psy11033
Match_columns 251
No_of_seqs 194 out of 1477
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 16:24:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11033.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11033hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1894 NuoF NADH:ubiquinone o 100.0 4.2E-68 9.2E-73 494.9 20.7 198 1-250 103-300 (424)
2 PLN03132 NADH dehydrogenase (u 100.0 1.1E-59 2.5E-64 451.4 23.4 206 46-251 117-328 (461)
3 PRK11278 NADH dehydrogenase I 100.0 4.5E-59 9.7E-64 447.4 23.3 204 46-250 94-305 (448)
4 PRK13596 NADH dehydrogenase I 100.0 2.1E-58 4.6E-63 441.4 23.4 205 46-250 86-296 (433)
5 PTZ00304 NADH dehydrogenase [u 100.0 5.3E-58 1.2E-62 440.5 23.0 204 47-250 108-317 (461)
6 KOG2658|consensus 100.0 9.3E-59 2E-63 426.7 14.1 199 1-250 146-344 (478)
7 TIGR01959 nuoF_fam NADH-quinon 100.0 6.5E-57 1.4E-61 429.5 23.1 204 46-250 81-290 (411)
8 TIGR01945 rnfC electron transp 100.0 2E-35 4.3E-40 283.7 17.0 163 47-248 165-334 (435)
9 PRK05035 electron transport co 100.0 3.4E-35 7.4E-40 295.2 18.1 165 47-249 170-341 (695)
10 COG4656 RnfC Predicted NADH:ub 100.0 2E-29 4.3E-34 243.1 15.4 165 46-248 164-335 (529)
11 PF01512 Complex1_51K: Respira 99.9 6.5E-25 1.4E-29 183.6 11.7 109 47-174 37-151 (151)
12 PRK05352 Na(+)-translocating N 99.9 1.1E-22 2.4E-27 196.3 11.0 145 47-248 157-310 (448)
13 TIGR01936 nqrA NADH:ubiquinone 99.9 1.4E-21 3.1E-26 188.5 13.1 146 47-248 154-308 (447)
14 PLN03132 NADH dehydrogenase (u 98.8 3.7E-09 7.9E-14 102.8 4.8 50 1-50 129-178 (461)
15 PTZ00304 NADH dehydrogenase [u 98.8 4.5E-09 9.8E-14 102.3 4.7 49 1-49 119-167 (461)
16 PRK11278 NADH dehydrogenase I 98.6 2.7E-08 5.8E-13 96.7 5.0 51 1-51 106-156 (448)
17 PRK13596 NADH dehydrogenase I 98.6 3.1E-08 6.8E-13 95.9 4.7 51 1-51 98-148 (433)
18 PF10531 SLBB: SLBB domain; I 98.6 1.1E-07 2.5E-12 67.4 5.7 51 196-247 1-58 (59)
19 TIGR01959 nuoF_fam NADH-quinon 98.5 1.2E-07 2.5E-12 91.5 5.0 52 1-52 93-144 (411)
20 PF01512 Complex1_51K: Respira 98.1 2.8E-06 6.2E-11 71.1 3.3 48 1-48 48-95 (151)
21 TIGR01945 rnfC electron transp 97.3 0.00026 5.7E-09 68.7 4.6 45 1-45 176-220 (435)
22 PRK05035 electron transport co 96.5 0.0027 5.9E-08 65.2 4.2 45 1-45 181-225 (695)
23 KOG2658|consensus 96.1 0.0033 7.1E-08 59.7 2.4 38 47-84 135-178 (478)
24 PF11973 NQRA_SLBB: NQRA C-ter 94.9 0.059 1.3E-06 37.5 4.6 46 197-248 2-48 (51)
25 TIGR03027 pepcterm_export puta 90.1 0.66 1.4E-05 39.0 5.3 36 194-230 78-113 (165)
26 COG1894 NuoF NADH:ubiquinone o 89.6 0.23 4.9E-06 48.0 2.3 31 47-77 92-128 (424)
27 TIGR03028 EpsE polysaccharide 85.5 2.1 4.6E-05 38.2 6.0 34 197-231 165-198 (239)
28 TIGR03028 EpsE polysaccharide 85.4 0.95 2.1E-05 40.4 3.7 36 194-230 78-113 (239)
29 COG1596 Wza Periplasmic protei 83.3 1.4 3E-05 39.7 3.7 35 195-230 125-160 (239)
30 COG4656 RnfC Predicted NADH:ub 71.5 3 6.4E-05 41.8 2.5 46 1-46 176-221 (529)
31 PRK15078 polysaccharide export 66.2 12 0.00026 36.0 5.4 37 194-231 170-207 (379)
32 cd03483 MutL_Trans_MLH1 MutL_T 63.9 9.8 0.00021 30.7 3.7 35 20-55 46-80 (127)
33 COG1726 NqrA Na+-transporting 62.1 12 0.00026 36.2 4.5 70 164-249 240-310 (447)
34 PRK15078 polysaccharide export 60.4 15 0.00033 35.3 4.9 35 195-230 255-290 (379)
35 PRK05352 Na(+)-translocating N 58.4 7.3 0.00016 38.4 2.5 29 1-30 168-196 (448)
36 TIGR01936 nqrA NADH:ubiquinone 57.9 7.4 0.00016 38.4 2.4 30 1-31 165-194 (447)
37 PRK15175 Vi polysaccharide exp 43.1 37 0.0008 32.5 4.5 35 195-230 239-274 (355)
38 PF06251 Caps_synth_GfcC: Caps 42.1 43 0.00093 29.6 4.5 33 195-228 129-161 (229)
39 cd03482 MutL_Trans_MutL MutL_T 40.5 31 0.00068 27.5 3.1 31 22-53 44-74 (123)
40 PF01119 DNA_mis_repair: DNA m 37.5 32 0.0007 27.1 2.7 30 22-52 40-69 (119)
41 PF12092 DUF3568: Protein of u 34.8 66 0.0014 26.5 4.2 30 8-37 15-48 (131)
42 PF03361 Herpes_IE2_3: Herpes 30.6 3.5E+02 0.0076 23.2 8.0 25 162-186 69-93 (162)
43 PRK10079 phosphonate metabolis 29.6 45 0.00097 29.3 2.6 61 32-127 14-76 (241)
44 cd03485 MutL_Trans_hPMS_1_like 29.5 57 0.0012 26.2 3.0 31 21-51 48-78 (132)
45 cd00782 MutL_Trans MutL_Trans: 27.2 70 0.0015 24.9 3.1 31 21-52 43-73 (122)
46 COG0323 MutL DNA mismatch repa 26.5 54 0.0012 33.8 2.8 76 20-98 250-330 (638)
47 cd03484 MutL_Trans_hPMS_2_like 26.4 72 0.0016 26.1 3.1 29 22-51 64-92 (142)
48 PRK14983 aldehyde decarbonylas 21.5 78 0.0017 28.3 2.5 55 7-63 107-161 (231)
49 PRK14999 histidine utilization 20.7 86 0.0019 27.5 2.6 61 32-127 14-77 (241)
No 1
>COG1894 NuoF NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]
Probab=100.00 E-value=4.2e-68 Score=494.91 Aligned_cols=198 Identities=58% Similarity=1.047 Sum_probs=193.5
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHHhhhhccCcHhHHhHhHHHHHHHHhcCceEEEEec
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISETLKIWSIHPPWYITVWTHGVAGRAMGAKAAYIYIR 80 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~~~d~~l~~~~~~~i~a~a~gA~~~~I~i~ 80 (251)
|++|||+|||||+||+||+||+++|||||
T Consensus 103 me~dPH~LIEGm~IA~yA~gA~~~YiYiR--------------------------------------------------- 131 (424)
T COG1894 103 MEGDPHLLIEGMIIAAYAVGATKGYIYIR--------------------------------------------------- 131 (424)
T ss_pred HhcCcHHHHHHHHHHHHHhccceeEEEEe---------------------------------------------------
Confidence 78999999999999999999999999999
Q ss_pred cCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEEEcCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCC
Q psy11033 81 GEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMHRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCP 160 (251)
Q Consensus 81 ~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~~~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~P 160 (251)
.||+.+++.|++||+|+|++||||+|||||+|+++|.||.++++|+||||||||+|||||++.||.|||||+..|+||+|
T Consensus 132 gEy~~a~~~l~~AI~eA~~~GlLGknilGSgfdfdl~vh~GAGAYICGEETALl~SLEGkrg~PR~KPPfPa~~GL~G~P 211 (424)
T COG1894 132 GEYPEAIERLQKAIEEAYAAGLLGKNILGSGFDFDLYVHHGAGAYICGEETALLESLEGKRGQPRLKPPFPATSGLYGKP 211 (424)
T ss_pred cchHHHHHHHHHHHHHHHHhCcccccccCCCcceEEEEecCCcceecchHHHHHHHhcCCCCCCCCCCCCccccCccCCC
Confidence 67788889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEeeecccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEe
Q psy11033 161 TTVSNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNISGHVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIP 240 (251)
Q Consensus 161 TvV~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTVsG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~ 240 (251)
|+||||||+++||.++++|..||+++|++.++|||+++|||+|++||+||+|+|+|+++||+++|||+.++| ++|+|++
T Consensus 212 T~INNVET~a~vP~Ii~~G~~wf~~~G~~~s~GTKlf~~sG~V~~pg~~E~pmG~tlrelie~~aGG~r~G~-~lKAv~p 290 (424)
T COG1894 212 TVINNVETLANVPAIIRRGADWFRSIGKPNSRGTKLFSLSGHVKNPGLYEVPMGTTLRELIEDYAGGVRGGW-KLKAVQP 290 (424)
T ss_pred ceeecchhhhhhHHHHHhhHHHHHhcCCCCCCCceEEEeeccccCCceEEecCCCcHHHHHHHhcCCcCCCc-eeEEEee
Confidence 999999999999999999999999999999999999999999999999999999999999988999999996 8999999
Q ss_pred CCCCCCCCCC
Q psy11033 241 GGSSTPLIPK 250 (251)
Q Consensus 241 GGpm~G~l~~ 250 (251)
|||+++++|+
T Consensus 291 GG~s~~~l~~ 300 (424)
T COG1894 291 GGPSGPCLPE 300 (424)
T ss_pred CCCCcccCCH
Confidence 9999999985
No 2
>PLN03132 NADH dehydrogenase (ubiquinone) flavoprotein 1; Provisional
Probab=100.00 E-value=1.1e-59 Score=451.40 Aligned_cols=206 Identities=70% Similarity=1.164 Sum_probs=199.1
Q ss_pred HhhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEE
Q psy11033 46 TLKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMH 119 (251)
Q Consensus 46 ~~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~ 119 (251)
.-||++.+|++||+.+|| .|+|+++||+++|||||+||+.+++.+++||++++++||||+||||++|+++|+|+
T Consensus 117 E~EPg~~kDr~Lm~~~Ph~vieG~~iaa~avgA~~~~IyIr~ey~~~~~~l~~Ai~ea~~~g~lG~nilg~~~~~~I~V~ 196 (461)
T PLN03132 117 ESEPGTCKDREIMRHDPHKLLEGCLIAGVGMRARAAYIYIRGEYVNERLNLERARHEAYAAGLLGKNACGSGYDFDVYIH 196 (461)
T ss_pred CCCccchhcHHHHhHCHHHHHHHHHHHHHHhCCCEEEEEEccCCHHHHHHHHHHHHHHHHcCCccccccCCCCCceEEEE
Confidence 368999999999999998 67899999999999999999999999999999999999999999999999999999
Q ss_pred EcCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceeecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEe
Q psy11033 120 RGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVSNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNI 199 (251)
Q Consensus 120 ~~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTV 199 (251)
.++++|||||||+||+|+||+++.||.|||+|+++|+||+||+||||||+++|+.++++|.+||+++|++.++|||++||
T Consensus 197 ~g~g~Y~~GeEtaLi~sleG~~~~pr~kpp~Pa~~Gl~g~PTvVnNVETla~v~~i~~~G~~~f~~~G~~~~~gtkl~tv 276 (461)
T PLN03132 197 YGAGAYICGEETALLESLEGKQGKPRLKPPFPANVGLYGCPTTVTNVETVAVSPTILRRGPEWFASFGRKNNAGTKLFCI 276 (461)
T ss_pred ECCCcCcCCHHHHHHHHHhCCccCCCCCCCCCccccccCCCceeecHHHHHHHHHHHHhChHHHHhcCCCCCCceEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCCCCC
Q psy11033 200 SGHVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLIPKR 251 (251)
Q Consensus 200 sG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l~~~ 251 (251)
||+|++|++||+|+|||++|||+++|||+..+|+++++|++||+++++++++
T Consensus 277 SG~V~~Pg~~Evp~Gt~l~eli~~~~GG~~~g~~~~~~vi~GG~s~~~l~~~ 328 (461)
T PLN03132 277 SGHVNKPCTVEEEMSIPLKELIERHCGGVRGGWDNLLAIIPGGSSVPLLPKK 328 (461)
T ss_pred ecccCCCeeEEEeCCCCHHHHHHHHcCCCCCCccccceEEECCCCcccccHH
Confidence 9999999999999999999999878999988755789999999999999863
No 3
>PRK11278 NADH dehydrogenase I subunit F; Provisional
Probab=100.00 E-value=4.5e-59 Score=447.40 Aligned_cols=204 Identities=40% Similarity=0.738 Sum_probs=195.5
Q ss_pred HhhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEE
Q psy11033 46 TLKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMH 119 (251)
Q Consensus 46 ~~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~ 119 (251)
.-||++.+|++||+++|| .|+|+++||+++|||||+||+++++.|++||+|++++||||+||||++|+++|+|+
T Consensus 94 E~EP~~~kDr~Lm~~~p~~vieG~~i~a~a~gA~~~~I~i~~~~~~ai~~l~~Ai~e~~~~g~lg~~i~g~~~~~~i~v~ 173 (448)
T PRK11278 94 EMEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVH 173 (448)
T ss_pred CCCCccccCHHHHhHCHHHHHHHHHHHHHHhCCCEEEEEeccCCHHHHHHHHHHHHHHHHcCcccccccCCCCcceEEEE
Confidence 368999999999999997 66899999999999999999999999999999999999999999999999999999
Q ss_pred EcCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceeecHHHHHHHHHHHHcCHHHHHhcCC--CCCCCceEE
Q psy11033 120 RGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVSNVETVAVAPEICRRGGAWFASLGR--PRNSGTKLF 197 (251)
Q Consensus 120 ~~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~NVeTla~V~~a~r~G~pw~~~~g~--~~~~GtrLv 197 (251)
.++++|||||||+||+++||+++.||.|||+|+++|+||+||+||||||+++|+.++++|.+||+++|+ ..++|+|++
T Consensus 174 ~~~~~Y~~GeEtaLi~sl~G~~~~pr~kpp~P~~~G~~g~PT~V~NVeTla~v~~iv~~G~~~~~~~G~~~~~~~Gtklv 253 (448)
T PRK11278 174 TGAGRYICGEETALINSLEGRRANPRSKPPFPATSGVWGKPTCVNNVETLCNVPAILANGVEWYQNISKGKSKDAGTKLM 253 (448)
T ss_pred ECCCCCcCCHHHHHHHHHcCCcCCCCCCCCCcccccCcCCCceeeCHHHHHHHHHHHHhChHHHHhcCcCCCCCCccEEE
Confidence 999999999999999999999999999999999999999999999999999999999999999999999 677999999
Q ss_pred EeeecccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCCCC
Q psy11033 198 NISGHVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLIPK 250 (251)
Q Consensus 198 TVsG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l~~ 250 (251)
||||+|++|++||+|+|||+++||+++|||+..+ .++++|++||||||++++
T Consensus 254 tVsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~-~~~k~vi~GGp~~g~~~~ 305 (448)
T PRK11278 254 GFSGRVKNPGLWELPFGTTAREILEDYAGGMRDG-LKFKAWQPGGAGTDFLTE 305 (448)
T ss_pred EEecccCCCeeEEEeCCCcHHHHHHHHcCCCCCC-CceeEEEECCCccCccCH
Confidence 9999999999999999999999998679998876 357799999999999875
No 4
>PRK13596 NADH dehydrogenase I subunit F; Provisional
Probab=100.00 E-value=2.1e-58 Score=441.38 Aligned_cols=205 Identities=67% Similarity=1.168 Sum_probs=198.0
Q ss_pred HhhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEE
Q psy11033 46 TLKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMH 119 (251)
Q Consensus 46 ~~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~ 119 (251)
.-||++.+|++||+++|| .|+|+++||+++|||||++|+++++.|++||++++++||||+|||||+|+++|+|+
T Consensus 86 E~EP~~~kDr~Lm~~~p~~vieG~~i~a~avgA~~~~I~ir~~~~~~i~~l~~ai~~~~~~~~lg~~i~g~~~~~~i~v~ 165 (433)
T PRK13596 86 ESEPGTCKDRDILRHDPHKLIEGCLIASFAMGAHAAYIYIRGEFIREREALQAAIDEAYEAGLIGKNACGSGWDFDIYVH 165 (433)
T ss_pred CCCccchhhHHHHHHCHHHHHHHHHHHHHHhCCCeEEEEECcCCHHHHHHHHHHHHHHHhcCccccccccCCCCceEEEE
Confidence 368999999999999997 66899999999999999999999999999999999999999999999999999999
Q ss_pred EcCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceeecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEe
Q psy11033 120 RGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVSNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNI 199 (251)
Q Consensus 120 ~~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTV 199 (251)
.++++|||||||+||+++||+++.||.|||+|+++|+||+||+||||||+++|++++++|.+||+++|++.++|+|++||
T Consensus 166 ~~~~~Y~~GeEtaLi~sleG~~~~pr~~Pp~P~~~G~~g~Pt~V~NVeT~a~v~~~v~~G~~~~~~~G~~~~~gtklvtV 245 (433)
T PRK13596 166 HGAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGAAWFASIGRPNNTGTKLFCI 245 (433)
T ss_pred ECCCcCCCCHHHHHHHHHcCCcCCCCCCCCCcccccCcCCCceeecHHHHHHHHHHHHhChHHHhhcCCCCCCccEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCCCC
Q psy11033 200 SGHVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLIPK 250 (251)
Q Consensus 200 sG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l~~ 250 (251)
||+|++|++||+|+|||+++||+++|||+..+|+++++|++||++++++++
T Consensus 246 sG~V~~Pg~~evp~Gt~l~~li~~~~GG~~~g~~~~~~vi~GG~s~~~l~~ 296 (433)
T PRK13596 246 SGHVNKPCNVEEAMGIPFRELIEKHAGGVRGGWDNLLAVIPGGSSVPLIPA 296 (433)
T ss_pred ecccCCCeeEEEeCCCCHHHHHHHHcCCCCCCCccccEEEECCCCCCCcCH
Confidence 999999999999999999999986799998765568999999999999985
No 5
>PTZ00304 NADH dehydrogenase [ubiquinone] flavoprotein 1; Provisional
Probab=100.00 E-value=5.3e-58 Score=440.48 Aligned_cols=204 Identities=73% Similarity=1.216 Sum_probs=197.4
Q ss_pred hhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEEE
Q psy11033 47 LKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMHR 120 (251)
Q Consensus 47 ~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~~ 120 (251)
-||++.||++||+.+|| .|+|+++||+++|||||+||+++++.|++||+|++++||||+||+|++++++|+++.
T Consensus 108 ~EP~~~kDr~Lm~~~P~~vieG~~i~a~a~gA~~~~I~Ir~e~~~~~~~l~~Ai~e~~~~g~lg~n~~~~~~~~~i~v~~ 187 (461)
T PTZ00304 108 SEPGTCKDREIMRHDPHKLVEGALLAGFAMRARAAYIYIRGEFYNEARALQQAIDEAYKKGFLGKNACGSGYDFDVYVHR 187 (461)
T ss_pred CCccchhcHHHHhHCHHHHHHHHHHHHHHhCCCEEEEEEccCcHHHHHHHHHHHHHHHHcCcccccccCCCCCeEEEEEE
Confidence 58999999999999998 668999999999999999999999999999999999999999999999999999999
Q ss_pred cCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceeecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEee
Q psy11033 121 GAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVSNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNIS 200 (251)
Q Consensus 121 ~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTVs 200 (251)
++++|||||||+||+++||+++.||.|||+|+++|+||+||+||||||+++|+.++++|..||+++|++.++|+|++|||
T Consensus 188 gag~Y~~GeEtaLi~sleG~~~~pr~kpp~Pa~~Gl~g~PTvVnNVeTla~v~~i~~~G~~w~~~~G~p~~~gtkl~tVS 267 (461)
T PTZ00304 188 GAGAYICGEETALIESIEGKPGKPRLKPPFPANVGLYGCPTTVTNVETVAVSPTILRRGPQWFASFGRPNNAGTKLFCIS 267 (461)
T ss_pred CCCcCCCCHHHHHHHHHhCCcCCCCCCCCCccccCccCCCCeeecHHHHHHHHHHHHhhHHHHHhCCCCCCCceEEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCCCC
Q psy11033 201 GHVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLIPK 250 (251)
Q Consensus 201 G~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l~~ 250 (251)
|+|++|++||+|+|||+++||+++|||+..+++++++|++||++++++++
T Consensus 268 G~V~~Pg~~evp~Gtpl~eli~~~aGG~~~g~~~~~~vi~GG~s~~~l~~ 317 (461)
T PTZ00304 268 GHVNNPCTVEEEMSIPLRELIERHCGGVRGGWDNLLCVIPGGSSVPLIPK 317 (461)
T ss_pred cccCCCeeEEEeCCCCHHHHHHHHcCCCCCCCCcccEEEECCCCCCccCH
Confidence 99999999999999999999986899998875577999999999999885
No 6
>KOG2658|consensus
Probab=100.00 E-value=9.3e-59 Score=426.69 Aligned_cols=199 Identities=86% Similarity=1.476 Sum_probs=192.5
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHHhhhhccCcHhHHhHhHHHHHHHHhcCceEEEEec
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISETLKIWSIHPPWYITVWTHGVAGRAMGAKAAYIYIR 80 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~~~d~~l~~~~~~~i~a~a~gA~~~~I~i~ 80 (251)
|||+||+|||||+|+++||+|+++|||||+||+|++.+
T Consensus 146 lRHdPHKliEG~liagram~a~aayiyIR~efynEa~n------------------------------------------ 183 (478)
T KOG2658|consen 146 LRHDPHKLIEGCLIAGRAMGASAAYIYIRGEFYNEACN------------------------------------------ 183 (478)
T ss_pred hccCcHHhhhhhhhhhhhcccceeEEEehhhhHHHHHH------------------------------------------
Confidence 79999999999999999999999999999988887664
Q ss_pred cCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEEEcCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCC
Q psy11033 81 GEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMHRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCP 160 (251)
Q Consensus 81 ~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~~~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~P 160 (251)
|++||.|+|++||||+|.||++++|++.||.++++|+|||||+||+|++|+.+.||.|||||+++|+||.|
T Consensus 184 ---------lq~ai~eAY~agllGkn~cGtg~~fdv~vhrGagaYicGEEtAlIesLeGk~gkPr~kppf~a~~G~Fg~P 254 (478)
T KOG2658|consen 184 ---------LQKAIIEAYAAGLLGKNACGTGYDFDVFVHRGAGAYICGEETALIESLEGKQGKPRLKPPFPADSGLFGCP 254 (478)
T ss_pred ---------HHHHHHHHHHhcccccccccCCcCeeEEEecCCcceeeccHHHHHHHhhccCCCCCCCCCCccccccccCC
Confidence 66777777899999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEeeecccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEe
Q psy11033 161 TTVSNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNISGHVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIP 240 (251)
Q Consensus 161 TvV~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTVsG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~ 240 (251)
|+|.||||++..|++||.|..||+++|.+.+.|||||++||+|++||.+|..+..|++||||.+|||+.+||+++-+||+
T Consensus 255 t~V~NvETVav~PtI~rrG~~wfasfGR~~N~GTKLf~iSG~Vn~PctVEeeMSiPlKdLIErhaGGV~GGWdnLlaiiP 334 (478)
T KOG2658|consen 255 TTVTNVETVAVSPTICRRGGKWFASFGRPRNRGTKLFCISGHVNNPCTVEEEMSIPLKDLIERHAGGVRGGWDNLLAIIP 334 (478)
T ss_pred ceeeeeeeeecchHHHhccchhhhhcCCCCCCCceEEEeccccCCCcchHHHhCCcHHHHHHHhcCCcccchhheeeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCC
Q psy11033 241 GGSSTPLIPK 250 (251)
Q Consensus 241 GGpm~G~l~~ 250 (251)
||++++.+|.
T Consensus 335 GG~stpli~k 344 (478)
T KOG2658|consen 335 GGSSTPLIPK 344 (478)
T ss_pred CCCCCCCcCh
Confidence 9999999986
No 7
>TIGR01959 nuoF_fam NADH-quinone oxidoreductase, F subunit. This model describes the F chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2.
Probab=100.00 E-value=6.5e-57 Score=429.46 Aligned_cols=204 Identities=54% Similarity=0.951 Sum_probs=196.3
Q ss_pred HhhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEE
Q psy11033 46 TLKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMH 119 (251)
Q Consensus 46 ~~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~ 119 (251)
.-||++.+|++||+++|| .|+|+++||+++|||||+||+++++.|++|+++++++||+|+||||++++++|+++
T Consensus 81 E~EP~~~~D~~lm~~~p~~vieG~~i~~~a~gA~~~~i~i~~~~~~~i~~l~~ai~~~~~~~llg~~i~g~~~~~~i~~~ 160 (411)
T TIGR01959 81 ESEPGTCKDRDLMEFDPHQLIEGMIIAAYAIGAHRGYIYIRGEFIKEAENLEAAIAEAYAAGLLGKNILGSGFDFELFVH 160 (411)
T ss_pred CCCccchhhHHHHHHCHHHHHHHHHHHHHHhCCCEEEEEEccCCHHHHHHHHHHHHHHHHcCCccccccCCCCceEEEEE
Confidence 358999999999999997 66899999999999999999999999999999999999999999999999999999
Q ss_pred EcCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceeecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEe
Q psy11033 120 RGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVSNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNI 199 (251)
Q Consensus 120 ~~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTV 199 (251)
.++++||||||++||++++|+++.|+.+||+|+++|+||+||+||||||+++|++++++|.+|++++|+..++|+|++||
T Consensus 161 ~~~~~Y~~Gee~~Li~~l~G~~~~p~~~pp~p~~~G~~g~Pt~V~NveT~~~v~~~v~~G~~~~~~~g~~~~~gtr~vtV 240 (411)
T TIGR01959 161 RGAGAYICGEETALLESLEGKRGQPRLKPPFPAVFGLYGKPTVINNVETLASVPAILRRGADWYRKLGKEKSPGTKLFSV 240 (411)
T ss_pred ECCCcCCCCHHHHHHHHHcCCcCCCCCCCCCchhccCcCCCceeecHHHHHHHHHHHHhCHHHHHhcCCCCCCCeEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCCCC
Q psy11033 200 SGHVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLIPK 250 (251)
Q Consensus 200 sG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l~~ 250 (251)
||+|++|++|++|+|||+++||+++|||++.+ .++++|++||||||++++
T Consensus 241 sG~V~~Pg~~evp~Gt~l~~li~~~~GG~~~~-~~~~~vi~GGp~~g~~~~ 290 (411)
T TIGR01959 241 SGHVNKPGNYELPLGTPLRELLEDYAGGMRGG-WKLKAVIPGGSSTPVLPA 290 (411)
T ss_pred ecccCCCceEEEeCCCCHHHHHHHHcCCCCCC-CcceEEEECCCCCCcccH
Confidence 99999999999999999999998679999876 357899999999999984
No 8
>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the C subunit.
Probab=100.00 E-value=2e-35 Score=283.69 Aligned_cols=163 Identities=19% Similarity=0.274 Sum_probs=151.5
Q ss_pred hhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEEE
Q psy11033 47 LKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMHR 120 (251)
Q Consensus 47 ~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~~ 120 (251)
-||++.+|++||+.+|+ .++++++||+++||+|+++|+++++.|++++++. +++|+.
T Consensus 165 ~EP~~~~D~~lm~~~~~~i~~G~~~~~~~~~a~~~~i~i~~~~~~~i~~l~~~~~~~-----------------~i~v~~ 227 (435)
T TIGR01945 165 CEPYLTCDDRLMRERAEEIIGGIRILLKILGVKKVVIGIEDNKPEAIAALKKALGGY-----------------NIKVRV 227 (435)
T ss_pred CCcchhhhHHHHhHCHHHHHHHHHHHHHHhCCCEEEEEEeCCCHHHHHHHHHHHhhC-----------------CeEEEE
Confidence 48999999999999997 5789999999999999999999999999998763 589999
Q ss_pred cCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceeecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEee
Q psy11033 121 GAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVSNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNIS 200 (251)
Q Consensus 121 ~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTVs 200 (251)
++++||||+|++||++++|++ +|++ ++|.+.|+ +|+||||+++|++++++|.||+ +|++|||
T Consensus 228 ~~~~Yp~G~e~~li~~l~G~~-~p~~--~~p~~~G~-----~V~Nv~T~~~i~~~~~~G~p~~----------~r~vtVs 289 (435)
T TIGR01945 228 LPTKYPQGGEKQLIYALTGRE-VPSG--GLPADIGV-----VVQNVGTAFAIYEAVVNGKPLI----------ERVVTVT 289 (435)
T ss_pred CCCcccCCHHHHHHHHHhCCc-cCCC--CCchhcCe-----EEEcHHHHHHHHHHHHcCcccE----------EEEEEEe
Confidence 999999999999999999998 7776 49999999 9999999999999999999999 8999999
Q ss_pred ec-ccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCC
Q psy11033 201 GH-VNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLI 248 (251)
Q Consensus 201 G~-V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l 248 (251)
|+ +++|++|++++|||+++||+ .|||...+ ..+||+||||||+.
T Consensus 290 G~~v~~p~~~~v~iGt~~~~li~-~~gg~~~~---~~~vi~GGpm~G~~ 334 (435)
T TIGR01945 290 GDAIRRPKNLWVLIGTPVSDILA-FCGGFREK---PERLIMGGPMMGLA 334 (435)
T ss_pred CCccCCCceEEEeCCCCHHHHHH-HcCCCCCC---CcEEEECCCCCccc
Confidence 97 89999999999999999998 79998764 46799999999985
No 9
>PRK05035 electron transport complex protein RnfC; Provisional
Probab=100.00 E-value=3.4e-35 Score=295.25 Aligned_cols=165 Identities=21% Similarity=0.276 Sum_probs=152.2
Q ss_pred hhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEEE
Q psy11033 47 LKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMHR 120 (251)
Q Consensus 47 ~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~~ 120 (251)
-||++..|.+||+.+++ .|+++++|++++||+|++|++++++.|++++.+. .+|+|+.
T Consensus 170 cEP~~t~D~~Lm~e~~~~ii~Gi~il~~~~~a~~~~I~Ie~nkp~ai~~l~~a~~~~----------------~~i~V~~ 233 (695)
T PRK05035 170 CEPYITADDRLMRERADEIIEGIRILAHLLQPKEVLIGIEDNKPEAIAALRAALAGA----------------DDIRVRV 233 (695)
T ss_pred CCCCCcchHHHHhHhHHHHHHHHHHHHHHhCCCEEEEEEeCCCHHHHHHHHHHHhcC----------------CCEEEEE
Confidence 48999999999999997 6789999999999999999999999999998762 3699999
Q ss_pred cCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceeecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEee
Q psy11033 121 GAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVSNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNIS 200 (251)
Q Consensus 121 ~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTVs 200 (251)
+++.||+|+|++||++|+|+. +|.++ +|.+.|+ +|+||+|+++|++++++|.||+ +|++|||
T Consensus 234 ~p~~YP~G~ek~LI~~ltGr~-vP~g~--~P~~~Gv-----vV~NV~T~~aI~~av~~G~Pl~----------~RiVTVt 295 (695)
T PRK05035 234 IPTKYPSGGEKQLIQILTGKE-VPSGG--RPADIGV-----LMQNVGTAYAIKRAVIDGEPLI----------ERVVTLT 295 (695)
T ss_pred CCCCCCCCcHHHHHHHHhCCc-CCCCC--CCCcCCe-----EEEcHHHHHHHHHHHHcCCcce----------EEEEEEE
Confidence 999999999999999999997 67664 8999999 9999999999999999999999 8999999
Q ss_pred ec-ccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCCC
Q psy11033 201 GH-VNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLIP 249 (251)
Q Consensus 201 G~-V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l~ 249 (251)
|+ |++|+||++++|||+++||+ +|||.... ...||+||||||+..
T Consensus 296 G~~v~~P~nv~v~iGTpv~~Ll~-~~G~~~~~---~~rvI~GGPmmG~~~ 341 (695)
T PRK05035 296 GEAVARPGNVWARLGTPVRHLLN-QAGFKPDA---DQRVIMGGPMMGFTL 341 (695)
T ss_pred CcccCCCceEEEeCCCCHHHHHH-hcCCCCCC---CceEEECCCCcCccc
Confidence 97 89999999999999999998 79987653 468999999999864
No 10
>COG4656 RnfC Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion]
Probab=99.96 E-value=2e-29 Score=243.05 Aligned_cols=165 Identities=21% Similarity=0.307 Sum_probs=152.2
Q ss_pred HhhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEE
Q psy11033 46 TLKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMH 119 (251)
Q Consensus 46 ~~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~ 119 (251)
.-||++..|.+||++++. +|+++.++.++++|+++++||++++.++.++.+. .+|.++
T Consensus 164 ecEp~~~~d~~LM~e~a~eI~~Gi~il~~i~~~~~vvIaied~kp~ai~~l~~a~~~~----------------~~i~I~ 227 (529)
T COG4656 164 ECEPYITADDRLMREHAEEIVKGIQILRKILKPKEVVIAIEDNKPEAIAALRAALFGD----------------RDIKIH 227 (529)
T ss_pred ccCccccHhHHHHHHHHHHHHHHHHHHHHhcccceeEEEEecCCHHHHHHHHHHhccC----------------CceEEE
Confidence 458999999999999996 6789999999999999999999999999998863 269999
Q ss_pred EcCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceeecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEe
Q psy11033 120 RGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVSNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNI 199 (251)
Q Consensus 120 ~~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTV 199 (251)
.++++||+|.|.+|+..++||. +|.+. +|.++|+ +|+||+|+++|++++.+|.|++ +|.+||
T Consensus 228 ~lp~kYP~g~~k~li~~ltgr~-vP~g~--lp~~vgv-----lv~NV~T~~aV~~AIv~~~Pli----------er~vTl 289 (529)
T COG4656 228 VLPTKYPSGGEKQLIKILTGRE-VPKGG--LPSDVGV-----LVQNVGTAYAVKRAIVDGKPLI----------ERVVTL 289 (529)
T ss_pred EcCCCCCCchHHHHHHHHhCCc-CCCCC--CCccccE-----EEechHHHHHHHHHHhcCCCeE----------EEEEEe
Confidence 9999999999999999999997 66664 8999999 9999999999999999999999 899999
Q ss_pred ee-cccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCC
Q psy11033 200 SG-HVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLI 248 (251)
Q Consensus 200 sG-~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l 248 (251)
+| .+++|++++|++|||+++||+ .|||.... ...||+||||||+.
T Consensus 290 tG~av~~p~nv~VrIGTP~~~lL~-~~G~~~~~---~~~vi~gGPmmG~~ 335 (529)
T COG4656 290 TGDAVKRPKNVWVRIGTPVSQLLN-EAGGIDTK---PYRVIMGGPMMGFK 335 (529)
T ss_pred ecccccCCccEEEECCCcHHHHHH-HcCCCCCC---CceEEeCCCccccc
Confidence 99 689999999999999999998 69998763 56799999999975
No 11
>PF01512 Complex1_51K: Respiratory-chain NADH dehydrogenase 51 Kd subunit; InterPro: IPR011538 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Thie entry represents the 51 kDa subunit from NADH:ubiquinone oxidoreductase []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 51 kDa (in mammals), which is the second largest subunit of complex I and is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind to NAD, FMN, and a 2Fe-2S cluster. The 51 kDa subunit and the bacterial hydrogenase alpha subunit contain three regions of sequence similarities. The first one most probably corresponds to the NAD-binding site, the second to the FMN-binding site, and the third one, which contains three cysteines, to the iron-sulphur binding region.; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0051539 4 iron, 4 sulfur cluster binding; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1.
Probab=99.92 E-value=6.5e-25 Score=183.56 Aligned_cols=109 Identities=35% Similarity=0.473 Sum_probs=87.0
Q ss_pred hhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEEE
Q psy11033 47 LKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMHR 120 (251)
Q Consensus 47 ~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~~ 120 (251)
-||++.+|.+||+.+|+ .++++++||++++|+|+++|+++++.|++|+++...+|+ ++|+|+.
T Consensus 37 ~EP~~~~D~~Lm~~~~~~il~G~~i~~~a~ga~~~iI~i~~~~~~~~~~l~~al~~~~~~~~-----------~~i~v~~ 105 (151)
T PF01512_consen 37 CEPYLTKDRRLMREHPHEILEGIKIAAKALGAKKIIIAIEENKPEAIEALREALAEARNAGL-----------FDIEVVA 105 (151)
T ss_dssp -STT--SHHHHHHH-HHHHHHHHHHHHHHTTESEEEEEE-TT-HHHHHHHHHHHHHHHHTTS-----------BEEEEEE
T ss_pred CCchhHHHHHHHHHhHHHHHHHHHHHHHhcCCCEEEEEEccCcHHHHHHHHHHHHHHHhcCC-----------CeEEEEE
Confidence 47999999999999997 668999999999999999999999999999999876554 4799999
Q ss_pred cCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceeecHHHHHHHHH
Q psy11033 121 GAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVSNVETVAVAPE 174 (251)
Q Consensus 121 ~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~NVeTla~V~~ 174 (251)
++++||||+|++||++++|+ .+|+++ .|.|+|+ +|+||||+++|++
T Consensus 106 ~~~~Yp~G~e~~Li~~l~G~-~~p~~~--~P~~~G~-----~v~NveT~~~v~~ 151 (151)
T PF01512_consen 106 VPDRYPQGEEKALIRALTGR-EVPRGR--LPADVGV-----LVNNVETLAAVYR 151 (151)
T ss_dssp --S-GGGGSHHHHHHHHTTS------S--SSTTSBG-----EEEEHHHHHHH--
T ss_pred CcCcccCChHHHHHHHHhCC-CCCCCc--CCCCCCe-----EEECHHHHHHhcC
Confidence 99999999999999999999 588877 5799999 9999999999985
No 12
>PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional
Probab=99.88 E-value=1.1e-22 Score=196.31 Aligned_cols=145 Identities=18% Similarity=0.176 Sum_probs=124.1
Q ss_pred hhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEEE
Q psy11033 47 LKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMHR 120 (251)
Q Consensus 47 ~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~~ 120 (251)
-+|++-.|.+||+.++. .+.++++|++ ++|+++++ ++++ . ++ ..+|+|+.
T Consensus 157 ceP~l~~d~~lm~~~~~~i~~Gi~~l~kl~~~~-~~I~ie~~--~ai~---~--~~----------------~~~i~v~~ 212 (448)
T PRK05352 157 TNPLAADPEVIIAEQEEAFQAGLTVLSRLTDGK-VHVCKAPG--ASLP---G--EN----------------LKNVEVHT 212 (448)
T ss_pred CCcccCChHHHHHHhHHHHHHHHHHHHHHhCCc-EEEEECcc--cccc---c--cc----------------CCCEEEEE
Confidence 48999999999999996 6789999997 99999986 2332 0 11 12699999
Q ss_pred cCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCcee--ecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEE
Q psy11033 121 GAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTV--SNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFN 198 (251)
Q Consensus 121 ~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV--~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvT 198 (251)
+++.||+|.|++||+.++ |.+.|. +| +||+|+++|+++++.|.|.+ +|++|
T Consensus 213 ~~~~YP~G~e~~lI~~l~------------P~~~G~-----vV~~~nv~tv~aI~~a~~~G~p~~----------eR~VT 265 (448)
T PRK05352 213 FSGPHPAGLVGTHIHFLD------------PVSAGK-----TVWTIGYQDVIAIGKLFLTGELYT----------ERVVA 265 (448)
T ss_pred CCCCCCCCchHhheEEec------------CCCCCc-----EEEEeCHHHHHHHHHHHHcCCCce----------eEEEE
Confidence 999999999999999983 668887 77 99999999999999999998 89999
Q ss_pred eee-cccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCC
Q psy11033 199 ISG-HVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLI 248 (251)
Q Consensus 199 VsG-~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l 248 (251)
|+| .+++|+++.+++|||+++||+ .+ ... +...+|.||||||+.
T Consensus 266 VtG~~v~~p~nv~v~iGTpi~~ll~-~~--~~~---~~~rvI~GGPMmG~~ 310 (448)
T PRK05352 266 LAGPAVKKPRLVRTRLGASLSELTA-GE--LKA---GDNRVISGSVLTGRT 310 (448)
T ss_pred EECcccCCCceEEEeCCCCHHHHHh-cc--ccC---CCCEEEECCCCcCcC
Confidence 999 689999999999999999998 44 232 245799999999975
No 13
>TIGR01936 nqrA NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit. This model represents the NqrA subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump.
Probab=99.86 E-value=1.4e-21 Score=188.50 Aligned_cols=146 Identities=15% Similarity=0.122 Sum_probs=125.3
Q ss_pred hhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCCCCCcccEEEEE
Q psy11033 47 LKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACGSGYDFDVFMHR 120 (251)
Q Consensus 47 ~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g~~~~~~I~v~~ 120 (251)
=+|++-.|..+|+.++. .+.+++++ ++++|++++|. +.+.+ . ..+|+|+.
T Consensus 154 ceP~~t~d~~lm~e~~~~~~~Gi~il~kl~~-~kv~i~ie~n~----~~~~~----~---------------~~~i~v~~ 209 (447)
T TIGR01936 154 TRPLAPDPEVVLAEFSSAFVVGLDALAKLFT-GKVHVCKKDRL----SLPTQ----L---------------LSNAEIHT 209 (447)
T ss_pred CCcccCCcHHHHHHHHHHHHHHHHHHHHHhC-CcEEEEEcCCh----hhhhh----c---------------cCCcEEEE
Confidence 37889999999999996 67899999 99999999883 22221 1 12699999
Q ss_pred cCccccCChHHHHHHHHcCCCCCCCCCCCCCcccCCCCCCceee--cHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEE
Q psy11033 121 GAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVS--NVETVAVAPEICRRGGAWFASLGRPRNSGTKLFN 198 (251)
Q Consensus 121 ~~~~Yp~GeE~aLi~sl~G~~~~P~~kpp~P~~~G~~g~PTvV~--NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvT 198 (251)
.++.||+|.|++||+.++ |.+.|. +|. ||+|+++|++++++|.|++ +|++|
T Consensus 210 ~~~~YP~G~ek~lI~~l~------------P~~~G~-----iV~~inv~tv~aI~~a~~~G~pl~----------eRvVT 262 (447)
T TIGR01936 210 FSGPHPAGLPGTHIHFIA------------PIGNGK-----VVWTLNYQDVIAIGHLFLTGELLT----------ERVIA 262 (447)
T ss_pred CCCCCCCCChhhhheEec------------CCCCCc-----EEEeCCHHHHHHHHHHHHcCCCcc----------eEEEE
Confidence 999999999999999994 678998 999 9999999999999999999 89999
Q ss_pred eeec-ccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCC
Q psy11033 199 ISGH-VNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLI 248 (251)
Q Consensus 199 VsG~-V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l 248 (251)
|||+ +++|+++++++|||+++||+ .++ ... +...+|.||||||+-
T Consensus 263 VtG~~v~~P~nv~v~iGTpi~~ll~-~~~-~~~---~~~riI~GGpMmG~~ 308 (447)
T TIGR01936 263 LAGPAVKKPRYVRTTKGANLSQLFP-GEL-TSE---GENRLISGSVLTGRK 308 (447)
T ss_pred EECcccCCCCcEEEECCCcHHHHHh-hcC-cCC---CCCeEEECCCCcCcC
Confidence 9995 79999999999999999998 443 332 246799999999964
No 14
>PLN03132 NADH dehydrogenase (ubiquinone) flavoprotein 1; Provisional
Probab=98.81 E-value=3.7e-09 Score=102.82 Aligned_cols=50 Identities=60% Similarity=0.960 Sum_probs=47.8
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHHhhhh
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISETLKIW 50 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~ 50 (251)
|+++||+||||++|+++|+||+++|||||+||.+.+.+|+.||+|+|+-.
T Consensus 129 m~~~Ph~vieG~~iaa~avgA~~~~IyIr~ey~~~~~~l~~Ai~ea~~~g 178 (461)
T PLN03132 129 MRHDPHKLLEGCLIAGVGMRARAAYIYIRGEYVNERLNLERARHEAYAAG 178 (461)
T ss_pred HhHCHHHHHHHHHHHHHHhCCCEEEEEEccCCHHHHHHHHHHHHHHHHcC
Confidence 68999999999999999999999999999999999999999999999843
No 15
>PTZ00304 NADH dehydrogenase [ubiquinone] flavoprotein 1; Provisional
Probab=98.79 E-value=4.5e-09 Score=102.27 Aligned_cols=49 Identities=73% Similarity=1.091 Sum_probs=47.3
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHHhhh
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISETLKI 49 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~ 49 (251)
|+++||+||||++|+++++||+++|||||+||.+.+.+|++||+|+|+-
T Consensus 119 m~~~P~~vieG~~i~a~a~gA~~~~I~Ir~e~~~~~~~l~~Ai~e~~~~ 167 (461)
T PTZ00304 119 MRHDPHKLVEGALLAGFAMRARAAYIYIRGEFYNEARALQQAIDEAYKK 167 (461)
T ss_pred HhHCHHHHHHHHHHHHHHhCCCEEEEEEccCcHHHHHHHHHHHHHHHHc
Confidence 6899999999999999999999999999999999999999999999865
No 16
>PRK11278 NADH dehydrogenase I subunit F; Provisional
Probab=98.64 E-value=2.7e-08 Score=96.73 Aligned_cols=51 Identities=39% Similarity=0.602 Sum_probs=48.2
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHHhhhhc
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISETLKIWS 51 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~ 51 (251)
|+++||+||||++|+++++||+++|||||+||...+.+|+.||+|+|+-.+
T Consensus 106 m~~~p~~vieG~~i~a~a~gA~~~~I~i~~~~~~ai~~l~~Ai~e~~~~g~ 156 (448)
T PRK11278 106 MEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGL 156 (448)
T ss_pred HhHCHHHHHHHHHHHHHHhCCCEEEEEeccCCHHHHHHHHHHHHHHHHcCc
Confidence 789999999999999999999999999999999999999999999986544
No 17
>PRK13596 NADH dehydrogenase I subunit F; Provisional
Probab=98.62 E-value=3.1e-08 Score=95.90 Aligned_cols=51 Identities=61% Similarity=0.983 Sum_probs=48.0
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHHhhhhc
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISETLKIWS 51 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~ 51 (251)
|+++||+||||++|+++++||+++|||||+||.....+|++||+|+|+-.+
T Consensus 98 m~~~p~~vieG~~i~a~avgA~~~~I~ir~~~~~~i~~l~~ai~~~~~~~~ 148 (433)
T PRK13596 98 LRHDPHKLIEGCLIASFAMGAHAAYIYIRGEFIREREALQAAIDEAYEAGL 148 (433)
T ss_pred HHHCHHHHHHHHHHHHHHhCCCeEEEEECcCCHHHHHHHHHHHHHHHhcCc
Confidence 688999999999999999999999999999999999999999999987443
No 18
>PF10531 SLBB: SLBB domain; InterPro: IPR019554 The soluble ligand-binding beta-grasp domain (SLBB) contains a beta-grasp fold. They are found in a diverse set of proteins that include the animal vitamin B12 uptake proteins; transcobalamin, intrinsic factor and the bacterial polysaccharide export proteins []. Some proteins may be part of a membrane complex involved in electron transport, others are probably involved in the export of the extracellular polysaccharide colanic acid from the cell to medium.; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1 2W8I_E 2W8H_E 2J58_D.
Probab=98.59 E-value=1.1e-07 Score=67.41 Aligned_cols=51 Identities=29% Similarity=0.371 Sum_probs=38.4
Q ss_pred EEEeeecccCceeEEecccCcHHHHHHhhcCCCCCCCc-------ccceEEeCCCCCCC
Q psy11033 196 LFNISGHVNTPCTVEEEMSIPLKELIQRHAGDVIGGWD-------NLLAIIPGGSSTPL 247 (251)
Q Consensus 196 LvTVsG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~-------~~~~vi~GGpm~G~ 247 (251)
.++|+|+|++|+.|+++.|+++.|+|+ .|||+..... ..+.+++||+||++
T Consensus 1 ~V~V~G~V~~PG~~~~~~g~tl~~~i~-~AGG~~~~a~~~~i~v~R~~~vi~gG~~~~~ 58 (59)
T PF10531_consen 1 TVTVSGEVNRPGTYELPPGTTLSDAIA-QAGGLTPRADLRRIEVIRKNPVIDGGPMMGV 58 (59)
T ss_dssp EEEEECSBSS-EEEEEETT-BHHHHHH-CTTSBBTTBETTSEEEEESSEEE-SSSSS--
T ss_pred CEEEEEEeCCCEEEEECCCCcHHHHHH-HhCCCCCCcccccccccccceecCCCccCCc
Confidence 479999999999999999999999998 7999986411 12358889999986
No 19
>TIGR01959 nuoF_fam NADH-quinone oxidoreductase, F subunit. This model describes the F chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2.
Probab=98.50 E-value=1.2e-07 Score=91.46 Aligned_cols=52 Identities=48% Similarity=0.830 Sum_probs=49.0
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHHhhhhcc
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISETLKIWSI 52 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~~ 52 (251)
|+++||+||||++|+++++||+++|||||+||.+...+|++|++|+|+-.+.
T Consensus 93 m~~~p~~vieG~~i~~~a~gA~~~~i~i~~~~~~~i~~l~~ai~~~~~~~ll 144 (411)
T TIGR01959 93 MEFDPHQLIEGMIIAAYAIGAHRGYIYIRGEFIKEAENLEAAIAEAYAAGLL 144 (411)
T ss_pred HHHCHHHHHHHHHHHHHHhCCCEEEEEEccCCHHHHHHHHHHHHHHHHcCCc
Confidence 6899999999999999999999999999999999999999999999876544
No 20
>PF01512 Complex1_51K: Respiratory-chain NADH dehydrogenase 51 Kd subunit; InterPro: IPR011538 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Thie entry represents the 51 kDa subunit from NADH:ubiquinone oxidoreductase []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 51 kDa (in mammals), which is the second largest subunit of complex I and is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind to NAD, FMN, and a 2Fe-2S cluster. The 51 kDa subunit and the bacterial hydrogenase alpha subunit contain three regions of sequence similarities. The first one most probably corresponds to the NAD-binding site, the second to the FMN-binding site, and the third one, which contains three cysteines, to the iron-sulphur binding region.; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0051539 4 iron, 4 sulfur cluster binding; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1.
Probab=98.06 E-value=2.8e-06 Score=71.06 Aligned_cols=48 Identities=31% Similarity=0.499 Sum_probs=42.4
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHHhh
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISETLK 48 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~~~ 48 (251)
|+++||+|++|+.++++++||++++|+|+.++...+..|++|+.+...
T Consensus 48 m~~~~~~il~G~~i~~~a~ga~~~iI~i~~~~~~~~~~l~~al~~~~~ 95 (151)
T PF01512_consen 48 MREHPHEILEGIKIAAKALGAKKIIIAIEENKPEAIEALREALAEARN 95 (151)
T ss_dssp HHH-HHHHHHHHHHHHHHTTESEEEEEE-TT-HHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHhcCCCEEEEEEccCcHHHHHHHHHHHHHHHh
Confidence 578999999999999999999999999999999999999999999854
No 21
>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the C subunit.
Probab=97.29 E-value=0.00026 Score=68.66 Aligned_cols=45 Identities=18% Similarity=0.279 Sum_probs=42.7
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHH
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISE 45 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~ 45 (251)
|+++||++++|+.+++++++|+++||||+++|....+.|+.|+++
T Consensus 176 m~~~~~~i~~G~~~~~~~~~a~~~~i~i~~~~~~~i~~l~~~~~~ 220 (435)
T TIGR01945 176 MRERAEEIIGGIRILLKILGVKKVVIGIEDNKPEAIAALKKALGG 220 (435)
T ss_pred HhHCHHHHHHHHHHHHHHhCCCEEEEEEeCCCHHHHHHHHHHHhh
Confidence 688999999999999999999999999999999999999999877
No 22
>PRK05035 electron transport complex protein RnfC; Provisional
Probab=96.47 E-value=0.0027 Score=65.21 Aligned_cols=45 Identities=18% Similarity=0.304 Sum_probs=42.7
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHH
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISE 45 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~ 45 (251)
|+++||+|++|+.|++++++++++||+|++++-...+.|+.++.+
T Consensus 181 m~e~~~~ii~Gi~il~~~~~a~~~~I~Ie~nkp~ai~~l~~a~~~ 225 (695)
T PRK05035 181 MRERADEIIEGIRILAHLLQPKEVLIGIEDNKPEAIAALRAALAG 225 (695)
T ss_pred HhHhHHHHHHHHHHHHHHhCCCEEEEEEeCCCHHHHHHHHHHHhc
Confidence 789999999999999999999999999999998889999999887
No 23
>KOG2658|consensus
Probab=96.12 E-value=0.0033 Score=59.71 Aligned_cols=38 Identities=50% Similarity=0.636 Sum_probs=35.5
Q ss_pred hhhhccCcHhHHhHhHH------HHHHHHhcCceEEEEeccCcH
Q psy11033 47 LKIWSIHPPWYITVWTH------GVAGRAMGAKAAYIYIRGEFY 84 (251)
Q Consensus 47 ~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I~i~~~~~ 84 (251)
-||..+||+.+||+.|| .|+++++||..+|||||++|.
T Consensus 135 gepGtcKDReilRHdPHKliEG~liagram~a~aayiyIR~efy 178 (478)
T KOG2658|consen 135 GEPGTCKDREILRHDPHKLIEGCLIAGRAMGASAAYIYIRGEFY 178 (478)
T ss_pred CCCCccccHHHhccCcHHhhhhhhhhhhhcccceeEEEehhhhH
Confidence 58999999999999998 779999999999999999984
No 24
>PF11973 NQRA_SLBB: NQRA C-terminal domain; InterPro: IPR022615 This domain is found in bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration []. The function of this domain has not been characterised.; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=94.87 E-value=0.059 Score=37.54 Aligned_cols=46 Identities=22% Similarity=0.376 Sum_probs=37.5
Q ss_pred EEeee-cccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCCCCCCCC
Q psy11033 197 FNISG-HVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGGSSTPLI 248 (251)
Q Consensus 197 vTVsG-~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GGpm~G~l 248 (251)
++|+| .+++|..+.+.+|.++.+|++ |-...+ ...+|.|.+++|.-
T Consensus 2 IAlaG~~v~~p~y~rt~~Ga~i~~l~~---g~~~~~---~~RiIsG~vLtG~~ 48 (51)
T PF11973_consen 2 IALAGPGVKNPRYVRTRIGASISDLLA---GNLKED---NVRIISGSVLTGRK 48 (51)
T ss_pred EEecCccCCcccEEEEeCCcCHHHHhC---cccCCC---CcEEEEcCCCCCeE
Confidence 68899 579999999999999999996 224432 56899999999853
No 25
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=90.09 E-value=0.66 Score=39.02 Aligned_cols=36 Identities=11% Similarity=0.286 Sum_probs=33.1
Q ss_pred ceEEEeeecccCceeEEecccCcHHHHHHhhcCCCCC
Q psy11033 194 TKLFNISGHVNTPCTVEEEMSIPLKELIQRHAGDVIG 230 (251)
Q Consensus 194 trLvTVsG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~ 230 (251)
++.++|.|.|++|+.|...-+.++.++|. .|||+..
T Consensus 78 ~~~V~V~GeV~~PG~y~~~~~~tl~~ai~-~AGG~~~ 113 (165)
T TIGR03027 78 SEQIRVVGAAANPQALPYREGMTLLDVMI-AVGGLTD 113 (165)
T ss_pred CcEEEEEEEeCCCceeeeCCCCcHHHHHH-HcCCCCc
Confidence 46789999999999999999999999998 7999986
No 26
>COG1894 NuoF NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]
Probab=89.60 E-value=0.23 Score=48.05 Aligned_cols=31 Identities=23% Similarity=0.163 Sum_probs=28.7
Q ss_pred hhhhccCcHhHHhHhHH------HHHHHHhcCceEEE
Q psy11033 47 LKIWSIHPPWYITVWTH------GVAGRAMGAKAAYI 77 (251)
Q Consensus 47 ~~~~~~~d~~l~~~~~~------~i~a~a~gA~~~~I 77 (251)
-||..+||+-+|+..|| .|+++|+||.++||
T Consensus 92 ~ePGTfkDR~ime~dPH~LIEGm~IA~yA~gA~~~Yi 128 (424)
T COG1894 92 GEPGTFKDRLIMEGDPHLLIEGMIIAAYAVGATKGYI 128 (424)
T ss_pred CCCcccccHHHHhcCcHHHHHHHHHHHHHhccceeEE
Confidence 58999999999999998 67999999999997
No 27
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=85.53 E-value=2.1 Score=38.17 Aligned_cols=34 Identities=21% Similarity=0.366 Sum_probs=31.3
Q ss_pred EEeeecccCceeEEecccCcHHHHHHhhcCCCCCC
Q psy11033 197 FNISGHVNTPCTVEEEMSIPLKELIQRHAGDVIGG 231 (251)
Q Consensus 197 vTVsG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~ 231 (251)
+.|.|.|++|+.|+..-++++.++|. .+||+...
T Consensus 165 v~v~G~V~~pg~~~~~~~~tl~~al~-~aGG~~~~ 198 (239)
T TIGR03028 165 FYIYGEVQRPGAYRLERNMTVMQALA-QGGGLTPR 198 (239)
T ss_pred EEEEeEccCCeEEEeCCCCCHHHHHH-hcCCCCcc
Confidence 78999999999999999999999998 79999753
No 28
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=85.43 E-value=0.95 Score=40.40 Aligned_cols=36 Identities=22% Similarity=0.304 Sum_probs=32.8
Q ss_pred ceEEEeeecccCceeEEecccCcHHHHHHhhcCCCCC
Q psy11033 194 TKLFNISGHVNTPCTVEEEMSIPLKELIQRHAGDVIG 230 (251)
Q Consensus 194 trLvTVsG~V~~Pgv~evpiGtpl~~LI~~~aGG~~~ 230 (251)
..-++|+|.|++|+.|...-++++.++|. .|||++.
T Consensus 78 ~~~V~V~GeV~~PG~~~l~~~~tl~~ai~-~AGG~~~ 113 (239)
T TIGR03028 78 GQQVSVLGQVNRPGRYPLETAGRVSDVLA-LAGGVTP 113 (239)
T ss_pred ceEEEEEEEecCCceEEcCCCCcHHHHHH-HcCCCCc
Confidence 35689999999999999999999999998 7999875
No 29
>COG1596 Wza Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]
Probab=83.26 E-value=1.4 Score=39.65 Aligned_cols=35 Identities=23% Similarity=0.280 Sum_probs=32.1
Q ss_pred eEEEeeecccCceeEEecc-cCcHHHHHHhhcCCCCC
Q psy11033 195 KLFNISGHVNTPCTVEEEM-SIPLKELIQRHAGDVIG 230 (251)
Q Consensus 195 rLvTVsG~V~~Pgv~evpi-Gtpl~~LI~~~aGG~~~ 230 (251)
+-+.|+|+|++|+-|.... +.++.+.|. .+||+..
T Consensus 125 ~~v~V~GeV~~PG~y~~~~~~~tv~~ai~-~AGG~~~ 160 (239)
T COG1596 125 QKVFVSGEVKTPGQYPLTPRGLTVLDAIA-LAGGLTP 160 (239)
T ss_pred cEEEEeeecCCCceEEecCCccHHHHHHH-HcCCCCc
Confidence 4489999999999999999 999999998 8999976
No 30
>COG4656 RnfC Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion]
Probab=71.51 E-value=3 Score=41.85 Aligned_cols=46 Identities=17% Similarity=0.275 Sum_probs=38.7
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHH
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISET 46 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~ 46 (251)
|+++++++++|+.|..++++++.++|+|++-+--...-|+.|+...
T Consensus 176 M~e~a~eI~~Gi~il~~i~~~~~vvIaied~kp~ai~~l~~a~~~~ 221 (529)
T COG4656 176 MREHAEEIVKGIQILRKILKPKEVVIAIEDNKPEAIAALRAALFGD 221 (529)
T ss_pred HHHHHHHHHHHHHHHHHhcccceeEEEEecCCHHHHHHHHHHhccC
Confidence 6788999999999999999999999999976666666666666655
No 31
>PRK15078 polysaccharide export protein Wza; Provisional
Probab=66.20 E-value=12 Score=35.96 Aligned_cols=37 Identities=16% Similarity=0.253 Sum_probs=32.0
Q ss_pred ceEEEeeecccCceeEEecc-cCcHHHHHHhhcCCCCCC
Q psy11033 194 TKLFNISGHVNTPCTVEEEM-SIPLKELIQRHAGDVIGG 231 (251)
Q Consensus 194 trLvTVsG~V~~Pgv~evpi-Gtpl~~LI~~~aGG~~~~ 231 (251)
+.-++|.|.|++|+.|.+.- +.++.++|. .+||+...
T Consensus 170 s~~V~V~GeV~~PG~~~l~~~~~tlldaIa-~AGG~~~~ 207 (379)
T PRK15078 170 SQKAYVTGEVNKSGQQAITNVPLTILDAIN-AAGGLTDD 207 (379)
T ss_pred ceEEEEEceecCCeEEEecCCCccHHHHHH-HccCCCcc
Confidence 45699999999999999864 789999998 79998753
No 32
>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.
Probab=63.85 E-value=9.8 Score=30.66 Aligned_cols=35 Identities=11% Similarity=0.113 Sum_probs=29.8
Q ss_pred CCCeEEEEEeccccchhHHHHHHHHHHhhhhccCcH
Q psy11033 20 GAKAAYIYIRGEFYNEASNMQVAISETLKIWSIHPP 55 (251)
Q Consensus 20 ~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~~~d~ 55 (251)
+-+.-|+||+|.+++. +.|..||.++|+.++-+++
T Consensus 46 ~~~~q~~fVNgR~V~~-~~l~~aI~~~Y~~~l~~~~ 80 (127)
T cd03483 46 KKIIFILFINNRLVEC-SALRRAIENVYANYLPKGA 80 (127)
T ss_pred CCceEEEEEcCCEecC-HHHHHHHHHHHHHhCcCCC
Confidence 4567899999999986 7899999999999876654
No 33
>COG1726 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion]
Probab=62.14 E-value=12 Score=36.23 Aligned_cols=70 Identities=21% Similarity=0.329 Sum_probs=57.9
Q ss_pred ecHHHHHHHHHHHHcCHHHHHhcCCCCCCCceEEEeee-cccCceeEEecccCcHHHHHHhhcCCCCCCCcccceEEeCC
Q psy11033 164 SNVETVAVAPEICRRGGAWFASLGRPRNSGTKLFNISG-HVNTPCTVEEEMSIPLKELIQRHAGDVIGGWDNLLAIIPGG 242 (251)
Q Consensus 164 ~NVeTla~V~~a~r~G~pw~~~~g~~~~~GtrLvTVsG-~V~~Pgv~evpiGtpl~~LI~~~aGG~~~~~~~~~~vi~GG 242 (251)
.|-+.+-+|.+....|.=|. +|+++++| .|+.|..+....|.++++|+. |-...+ ...+|.|-
T Consensus 240 inyQDViaIG~LF~tG~l~~----------erVvaLAGp~v~~prlvrT~~GAsls~L~~---~~l~~g---~nrlISGs 303 (447)
T COG1726 240 INYQDVIAIGKLFLTGELLT----------ERVVALAGPQVNKPRLVRTVLGASLSQLTA---GELKSG---ENRLISGS 303 (447)
T ss_pred eehhhhhhhhhhhhcceeeh----------hhheecccCCCCCceEEEEeccCCHHHhcc---ccccCC---CceEEecC
Confidence 48889999999998887766 89999999 469999999999999999985 334443 35799999
Q ss_pred CCCCCCC
Q psy11033 243 SSTPLIP 249 (251)
Q Consensus 243 pm~G~l~ 249 (251)
+.+|.+.
T Consensus 304 vL~G~~~ 310 (447)
T COG1726 304 VLTGRLA 310 (447)
T ss_pred cccCccc
Confidence 9999764
No 34
>PRK15078 polysaccharide export protein Wza; Provisional
Probab=60.35 E-value=15 Score=35.27 Aligned_cols=35 Identities=17% Similarity=0.221 Sum_probs=30.7
Q ss_pred eEEEeeecccCceeEEec-ccCcHHHHHHhhcCCCCC
Q psy11033 195 KLFNISGHVNTPCTVEEE-MSIPLKELIQRHAGDVIG 230 (251)
Q Consensus 195 rLvTVsG~V~~Pgv~evp-iGtpl~~LI~~~aGG~~~ 230 (251)
.-++|.|.|++|+.|..+ -+.++.|.|. .+||+..
T Consensus 255 ~~v~V~GeV~~Pg~~~~~~~~~TL~~Al~-~AGGl~~ 290 (379)
T PRK15078 255 LKVFVMGEVKKQSTLKMDRSGMTLTEALG-NAEGIDQ 290 (379)
T ss_pred cEEEEeeecccceEEecCCCCCCHHHHHH-hcCCCCc
Confidence 458999999999999995 5899999998 7999874
No 35
>PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional
Probab=58.43 E-value=7.3 Score=38.37 Aligned_cols=29 Identities=14% Similarity=0.146 Sum_probs=27.1
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEec
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRG 30 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~ 30 (251)
|++++.++++|+.+.+++++++ ++|.|++
T Consensus 168 m~~~~~~i~~Gi~~l~kl~~~~-~~I~ie~ 196 (448)
T PRK05352 168 IAEQEEAFQAGLTVLSRLTDGK-VHVCKAP 196 (448)
T ss_pred HHHhHHHHHHHHHHHHHHhCCc-EEEEECc
Confidence 6789999999999999999998 9999984
No 36
>TIGR01936 nqrA NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit. This model represents the NqrA subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump.
Probab=57.94 E-value=7.4 Score=38.36 Aligned_cols=30 Identities=7% Similarity=0.047 Sum_probs=27.8
Q ss_pred CCCCchhHhHHHHHHHHHhCCCeEEEEEecc
Q psy11033 1 MRHDPHKLVEGCLVAGRAMGAKAAYIYIRGE 31 (251)
Q Consensus 1 ~~~~~~~~~~g~~~~~~~~~a~~~~i~i~~e 31 (251)
|++++.++++|+.+.+++++ ++++|.|++.
T Consensus 165 m~e~~~~~~~Gi~il~kl~~-~kv~i~ie~n 194 (447)
T TIGR01936 165 LAEFSSAFVVGLDALAKLFT-GKVHVCKKDR 194 (447)
T ss_pred HHHHHHHHHHHHHHHHHHhC-CcEEEEEcCC
Confidence 67899999999999999999 9999999954
No 37
>PRK15175 Vi polysaccharide export protein VexA; Provisional
Probab=43.14 E-value=37 Score=32.51 Aligned_cols=35 Identities=9% Similarity=0.075 Sum_probs=30.4
Q ss_pred eEEEeeecccCceeEE-ecccCcHHHHHHhhcCCCCC
Q psy11033 195 KLFNISGHVNTPCTVE-EEMSIPLKELIQRHAGDVIG 230 (251)
Q Consensus 195 rLvTVsG~V~~Pgv~e-vpiGtpl~~LI~~~aGG~~~ 230 (251)
+.++|-|.+.+|+.++ ..-+.++.+.|. .+||+..
T Consensus 239 ~~v~V~Gavg~p~~~~~~~~~lTL~eALa-~aGGl~~ 274 (355)
T PRK15175 239 EYVNVLGAAGVQGKHALVQRHSSVVDALA-LAKGLND 274 (355)
T ss_pred CEEEEEEeecCccccccCCCCCCHHHHHH-HcCCCCc
Confidence 4589999999999887 578999999998 7999875
No 38
>PF06251 Caps_synth_GfcC: Capsule biosynthesis GfcC; InterPro: IPR010425 This entry represents uncharacterised bacterial proteins that contain a central beta-grasp like domain related to the SLBB domain [].; PDB: 3P42_B.
Probab=42.08 E-value=43 Score=29.57 Aligned_cols=33 Identities=18% Similarity=0.405 Sum_probs=23.1
Q ss_pred eEEEeeecccCceeEEecccCcHHHHHHhhcCCC
Q psy11033 195 KLFNISGHVNTPCTVEEEMSIPLKELIQRHAGDV 228 (251)
Q Consensus 195 rLvTVsG~V~~Pgv~evpiGtpl~~LI~~~aGG~ 228 (251)
.-++|.|.|..||.+.-..|.++++.|+ .||..
T Consensus 129 ~~V~V~G~V~~p~~~~~~~g~sv~dYl~-~~g~~ 161 (229)
T PF06251_consen 129 NTVSVLGAVQNPTSVPYQPGLSVSDYLD-SAGPT 161 (229)
T ss_dssp SEEEEEESBTT-EEEE--TT--HHHHHT-TS-B-
T ss_pred CEEEEEEccCCcceeeccCCCCHHHHHH-hCCCc
Confidence 3489999999999999999999999998 68743
No 39
>cd03482 MutL_Trans_MutL MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.
Probab=40.49 E-value=31 Score=27.54 Aligned_cols=31 Identities=13% Similarity=0.253 Sum_probs=26.5
Q ss_pred CeEEEEEeccccchhHHHHHHHHHHhhhhccC
Q psy11033 22 KAAYIYIRGEFYNEASNMQVAISETLKIWSIH 53 (251)
Q Consensus 22 ~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~~~ 53 (251)
+.-|+||+|.+++. +.|..||.++|+-.+..
T Consensus 44 ~~q~ifVN~R~V~~-~~l~~ai~~~y~~~~~~ 74 (123)
T cd03482 44 DIQYFYVNGRMVRD-KLISHAVRQAYSDVLHG 74 (123)
T ss_pred CcEEEEEcCcEECC-hHHHHHHHHHHHHhccC
Confidence 56799999999985 77999999999987654
No 40
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=37.54 E-value=32 Score=27.07 Aligned_cols=30 Identities=17% Similarity=0.302 Sum_probs=24.1
Q ss_pred CeEEEEEeccccchhHHHHHHHHHHhhhhcc
Q psy11033 22 KAAYIYIRGEFYNEASNMQVAISETLKIWSI 52 (251)
Q Consensus 22 ~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~~ 52 (251)
+.-|+||++.++... .|..||.++|+..+-
T Consensus 40 ~~q~ifVN~R~V~~~-~l~~~I~~~y~~~~~ 69 (119)
T PF01119_consen 40 DRQFIFVNGRPVENK-ALSKAINEAYRERLP 69 (119)
T ss_dssp TCEEEEETTEEE--H-HHHHHHHHHHHCTTC
T ss_pred CcEEEEeCCCeEeCh-HHHHHHHHHHhhccc
Confidence 578999999999996 899999999995444
No 41
>PF12092 DUF3568: Protein of unknown function (DUF3568); InterPro: IPR021952 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 130 amino acids in length.
Probab=34.80 E-value=66 Score=26.50 Aligned_cols=30 Identities=23% Similarity=0.440 Sum_probs=20.7
Q ss_pred HhHHHHHHHHHhCC----CeEEEEEeccccchhH
Q psy11033 8 LVEGCLVAGRAMGA----KAAYIYIRGEFYNEAS 37 (251)
Q Consensus 8 ~~~g~~~~~~~~~a----~~~~i~i~~e~~~~~~ 37 (251)
.+-||..++-++|+ .-.+.|++|||.-.+.
T Consensus 15 ~L~sC~~~al~~G~aa~g~g~~~Yv~G~~~~~~~ 48 (131)
T PF12092_consen 15 SLSSCGVAALVAGGAAAGGGTVAYVNGEYSANYP 48 (131)
T ss_pred HHhhhhhhhhhcccccccCceEEEEeeEEEEEcC
Confidence 45677667777772 3359999999966644
No 42
>PF03361 Herpes_IE2_3: Herpes virus intermediate/early protein 2/3; InterPro: IPR005028 This domain of unknown function is found in the intermediate/early proteins of the Herpes virus. Many of these proteins play a role in transcriptional regulation.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=30.57 E-value=3.5e+02 Score=23.22 Aligned_cols=25 Identities=32% Similarity=0.321 Sum_probs=21.1
Q ss_pred eeecHHHHHHHHHHHHcCHHHHHhc
Q psy11033 162 TVSNVETVAVAPEICRRGGAWFASL 186 (251)
Q Consensus 162 vV~NVeTla~V~~a~r~G~pw~~~~ 186 (251)
++++.+|..++.++|+.|.+..-++
T Consensus 69 ~~h~p~t~~~~~~a~~~g~~~~wd~ 93 (162)
T PF03361_consen 69 RPHDPETVRRFSEACRQGVKAVWDL 93 (162)
T ss_pred cCCCHHHHHHHHHHHHhCchhHhhc
Confidence 7889999999999999997655444
No 43
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=29.57 E-value=45 Score=29.28 Aligned_cols=61 Identities=10% Similarity=0.209 Sum_probs=40.8
Q ss_pred ccchhHHHHHHHHHHhhhhcc--CcHhHHhHhHHHHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCCC
Q psy11033 32 FYNEASNMQVAISETLKIWSI--HPPWYITVWTHGVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNACG 109 (251)
Q Consensus 32 ~~~~~~~~~~a~~~~~~~~~~--~d~~l~~~~~~~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~g 109 (251)
|...+..|+.-|...|+|... ..+.|++.+. -....+++|+++..+.||+
T Consensus 14 Y~qi~~~L~~~I~~~~~~G~~LPsE~eLa~~~~----------------------VSR~TVR~Al~~L~~eGli------ 65 (241)
T PRK10079 14 YQEIAAKLEQELRQHYRCGDYLPAEQQLAARYE----------------------VNRHTLRRAIDQLVEKGWV------ 65 (241)
T ss_pred HHHHHHHHHHHHhcccCCCCcCCCHHHHHHHHC----------------------CCHHHHHHHHHHHHHCCCE------
Confidence 455667777777767777766 5666665543 2344578899988888874
Q ss_pred CCCcccEEEEEcCccccC
Q psy11033 110 SGYDFDVFMHRGAGAYIC 127 (251)
Q Consensus 110 ~~~~~~I~v~~~~~~Yp~ 127 (251)
.-..+.|.|+.
T Consensus 66 -------~r~~G~GtfV~ 76 (241)
T PRK10079 66 -------QRRQGVGVLVL 76 (241)
T ss_pred -------EEecCCEEEEe
Confidence 45566667764
No 44
>cd03485 MutL_Trans_hPMS_1_like MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition.
Probab=29.53 E-value=57 Score=26.21 Aligned_cols=31 Identities=3% Similarity=0.034 Sum_probs=27.0
Q ss_pred CCeEEEEEeccccchhHHHHHHHHHHhhhhc
Q psy11033 21 AKAAYIYIRGEFYNEASNMQVAISETLKIWS 51 (251)
Q Consensus 21 a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~ 51 (251)
-+.-|+||.+.++..-+.+..||.++|+..+
T Consensus 48 ~~~q~~fVN~R~v~~~~~l~k~i~~~y~~~~ 78 (132)
T cd03485 48 SDGKFISVNSRPVSLGKDIGKLLRQYYSSAY 78 (132)
T ss_pred CCcEEEEECCeecccchHHHHHHHHHHHHHh
Confidence 3567999999999865889999999999877
No 45
>cd00782 MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot synd
Probab=27.24 E-value=70 Score=24.89 Aligned_cols=31 Identities=13% Similarity=0.303 Sum_probs=26.5
Q ss_pred CCeEEEEEeccccchhHHHHHHHHHHhhhhcc
Q psy11033 21 AKAAYIYIRGEFYNEASNMQVAISETLKIWSI 52 (251)
Q Consensus 21 a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~~ 52 (251)
-+.-|+||.+.++. .+.|..||.++|+-.+.
T Consensus 43 ~~~q~~fVN~R~v~-~~~l~~ai~~~y~~~~~ 73 (122)
T cd00782 43 KDRQFLFVNGRPVR-DKLLSKAINEAYRSYLP 73 (122)
T ss_pred CccEEEEECCeEec-CHHHHHHHHHHHHHhCc
Confidence 35679999999999 57899999999998775
No 46
>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]
Probab=26.55 E-value=54 Score=33.83 Aligned_cols=76 Identities=14% Similarity=0.137 Sum_probs=46.4
Q ss_pred CCCeEEEEEeccccchhHHHHHHHHHHhhhhccCcHh-----HHhHhHHHHHHHHhcCceEEEEeccCcHHHHHHHHHHH
Q psy11033 20 GAKAAYIYIRGEFYNEASNMQVAISETLKIWSIHPPW-----YITVWTHGVAGRAMGAKAAYIYIRGEFYNEASNMQVAI 94 (251)
Q Consensus 20 ~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~~~d~~-----l~~~~~~~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai 94 (251)
..+.-|+||+|.++... .|..||+++|...+..|++ .++..|+.+=-..=-+ |--|-+.++ ....+.+.++|
T Consensus 250 ~~~~q~~fVNgR~V~~~-~l~~Ai~~aY~~~L~~~r~P~~vL~l~l~p~~vDVNVHP~-K~EVrf~~~-~~i~~~I~~~I 326 (638)
T COG0323 250 SRDYQYLFVNGRPVRDK-LLNHALREAYADYLPRGRYPVFVLFLELDPELVDVNVHPA-KKEVRFSDE-RLVHDLIYEAI 326 (638)
T ss_pred CccceEEEECCCEeccH-HHHHHHHHHHHhhccCCCCcEEEEEEeeChhhcccccCCC-cceEEecCH-HHHHHHHHHHH
Confidence 34567999999999885 7999999999998877653 1233333222222222 222333322 34566667777
Q ss_pred HHHH
Q psy11033 95 SEAY 98 (251)
Q Consensus 95 ~e~~ 98 (251)
.++.
T Consensus 327 ~~~L 330 (638)
T COG0323 327 KEAL 330 (638)
T ss_pred HHHH
Confidence 6653
No 47
>cd03484 MutL_Trans_hPMS_2_like MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2). hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome.
Probab=26.43 E-value=72 Score=26.13 Aligned_cols=29 Identities=21% Similarity=0.383 Sum_probs=25.6
Q ss_pred CeEEEEEeccccchhHHHHHHHHHHhhhhc
Q psy11033 22 KAAYIYIRGEFYNEASNMQVAISETLKIWS 51 (251)
Q Consensus 22 ~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~ 51 (251)
+.-|+||.+.++.. +.|+.||.++|+..+
T Consensus 64 ~~q~~fVN~R~V~~-~~l~~aI~~~y~~~~ 92 (142)
T cd03484 64 DRQFFYINGRPVDL-KKVAKLINEVYKSFN 92 (142)
T ss_pred CcEEEEECCeecCC-HHHHHHHHHHHHHhc
Confidence 45799999999986 779999999999976
No 48
>PRK14983 aldehyde decarbonylase; Provisional
Probab=21.47 E-value=78 Score=28.32 Aligned_cols=55 Identities=13% Similarity=0.243 Sum_probs=47.3
Q ss_pred hHhHHHHHHHHHhCCCeEEEEEeccccchhHHHHHHHHHHhhhhccCcHhHHhHhHH
Q psy11033 7 KLVEGCLVAGRAMGAKAAYIYIRGEFYNEASNMQVAISETLKIWSIHPPWYITVWTH 63 (251)
Q Consensus 7 ~~~~g~~~~~~~~~a~~~~i~i~~e~~~~~~~~~~a~~~~~~~~~~~d~~l~~~~~~ 63 (251)
.||.+++|-+.|+-|=+.||-|-+.| .++.-+..++..|.-+-+-..||.+++..
T Consensus 107 LlIQaLiIE~FAIaAYniYIpVAD~F--ARkITegVVkDEY~HLN~Ge~WLk~~f~~ 161 (231)
T PRK14983 107 LLIQALIIEAFAIAAYNIYIPVADPF--ARKITEGVVKDEYLHLNFGEEWLKANFET 161 (231)
T ss_pred HHHHHHHHHHHHHHHHhhccccccHH--HHHHHHhHHhhHHHhcchHHHHHHHHHHH
Confidence 57889999999999999999998877 34556778899999999999999999984
No 49
>PRK14999 histidine utilization repressor; Provisional
Probab=20.69 E-value=86 Score=27.48 Aligned_cols=61 Identities=10% Similarity=0.198 Sum_probs=39.5
Q ss_pred ccchhHHHHHHHHH-Hhhhhcc--CcHhHHhHhHHHHHHHHhcCceEEEEeccCcHHHHHHHHHHHHHHHHcCccCcCCC
Q psy11033 32 FYNEASNMQVAISE-TLKIWSI--HPPWYITVWTHGVAGRAMGAKAAYIYIRGEFYNEASNMQVAISEAYQAGLIGKNAC 108 (251)
Q Consensus 32 ~~~~~~~~~~a~~~-~~~~~~~--~d~~l~~~~~~~i~a~a~gA~~~~I~i~~~~~~a~~~l~~ai~e~~~~g~~g~~~~ 108 (251)
|...+..|+..|.+ .|+|... +.+.|++.+.- ...-+++|+++..+.|+
T Consensus 14 y~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gV----------------------SR~TVR~Al~~L~~eGl------ 65 (241)
T PRK14999 14 YETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGF----------------------SRMTINRALRELTDEGW------ 65 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCC----------------------CHHHHHHHHHHHHHCCC------
Confidence 44455666666655 6777765 67777766542 33457788888777776
Q ss_pred CCCCcccEEEEEcCccccC
Q psy11033 109 GSGYDFDVFMHRGAGAYIC 127 (251)
Q Consensus 109 g~~~~~~I~v~~~~~~Yp~ 127 (251)
|.-+.+.|.|+.
T Consensus 66 -------i~r~~GkGTfV~ 77 (241)
T PRK14999 66 -------LVRLQGVGTFVA 77 (241)
T ss_pred -------EEEecCcEEEEC
Confidence 455566777765
Done!