Query gi|254780853|ref|YP_003065266.1| NADH dehydrogenase subunit B [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 185
No_of_seqs 158 out of 603
Neff 4.3
Searched_HMMs 39220
Date Sun May 29 23:46:35 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780853.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01957 nuoB_fam NADH-quinon 100.0 0 0 587.3 9.5 144 37-180 1-146 (146)
2 COG0377 NuoB NADH:ubiquinone o 100.0 0 0 500.0 12.4 155 28-182 11-165 (194)
3 CHL00023 ndhK NADH dehydrogena 100.0 0 0 497.5 12.6 150 33-182 12-162 (225)
4 PRK06411 NADH dehydrogenase su 100.0 0 0 496.6 13.3 155 28-182 16-170 (195)
5 PRK13292 trifunctional NADH de 100.0 0 0 487.3 10.7 145 36-181 1-146 (784)
6 KOG1687 consensus 100.0 0 0 464.6 9.2 154 31-184 10-163 (168)
7 COG3260 Ni,Fe-hydrogenase III 100.0 0 0 334.5 11.6 128 52-179 6-136 (148)
8 pfam01058 Oxidored_q6 NADH ubi 100.0 1.2E-30 3E-35 200.0 8.7 111 63-173 2-124 (124)
9 TIGR03294 FrhG coenzyme F420 h 99.7 3.1E-17 7.9E-22 121.7 7.5 113 63-175 11-142 (228)
10 COG1941 FrhG Coenzyme F420-red 99.6 1.2E-15 3E-20 112.5 6.4 111 63-176 13-153 (247)
11 COG1740 HyaA Ni,Fe-hydrogenase 99.0 1.4E-09 3.5E-14 77.0 7.0 149 24-173 16-205 (355)
12 PRK10468 hydrogenase 2 small s 98.8 1E-08 2.7E-13 71.9 7.1 132 43-175 38-206 (371)
13 TIGR00391 hydA hydrogenase (Ni 95.9 0.012 3.1E-07 36.5 4.4 133 39-174 38-209 (370)
14 pfam00919 UPF0004 Uncharacteri 79.8 3.9 0.0001 21.8 4.7 71 55-131 2-79 (98)
15 cd01980 Chlide_reductase_Y Chl 68.8 6.1 0.00016 20.7 3.3 114 54-177 32-150 (416)
16 TIGR02529 EutJ ethanolamine ut 60.2 13 0.00032 18.9 3.7 48 87-134 163-210 (240)
17 TIGR00705 SppA_67K signal pept 59.1 7 0.00018 20.4 2.2 32 105-136 375-409 (614)
18 PRK11148 cyclic 3',5'-adenosin 49.5 24 0.00061 17.3 4.2 37 88-124 51-91 (275)
19 TIGR02841 spore_YyaC putative 49.2 19 0.00048 17.9 3.1 62 96-158 34-108 (140)
20 COG4820 EutJ Ethanolamine util 49.1 15 0.00037 18.5 2.5 64 71-134 179-242 (277)
21 KOG3586 consensus 48.4 24 0.00062 17.2 3.5 101 64-179 81-188 (437)
22 KOG1111 consensus 47.7 21 0.00053 17.6 3.1 38 141-179 301-338 (426)
23 pfam09565 RE_NgoFVII NgoFVII r 44.9 28 0.00073 16.8 4.8 40 94-133 10-49 (296)
24 TIGR01279 DPOR_bchN light-inde 41.9 32 0.00081 16.6 4.5 67 56-131 26-98 (458)
25 COG4981 Enoyl reductase domain 40.7 20 0.0005 17.8 2.1 33 35-81 452-484 (717)
26 COG0616 SppA Periplasmic serin 39.4 22 0.00056 17.5 2.1 45 102-149 114-167 (317)
27 cd07125 ALDH_PutA-P5CDH Delta( 36.6 39 0.00098 16.1 3.2 100 42-146 293-399 (518)
28 TIGR00396 leuS_bact leucyl-tRN 35.6 12 0.00031 19.0 0.3 13 146-158 558-570 (916)
29 PRK10949 protease 4; Provision 35.6 31 0.00079 16.6 2.4 18 120-137 397-414 (618)
30 TIGR01284 alt_nitrog_alph nitr 33.7 33 0.00083 16.5 2.3 138 11-160 18-177 (468)
31 TIGR00075 hypD hydrogenase exp 30.5 33 0.00083 16.5 1.8 30 145-174 59-93 (384)
32 pfam07796 DUF1638 Protein of u 29.7 50 0.0013 15.4 3.1 33 104-136 12-47 (166)
33 TIGR02306 RNA_lig_DRB0094 RNA 29.5 27 0.00068 17.0 1.3 55 41-98 111-168 (374)
34 TIGR00588 ogg 8-oxoguanine DNA 28.3 14 0.00035 18.7 -0.4 11 146-156 297-307 (379)
35 TIGR01860 VNFD nitrogenase van 28.2 53 0.0014 15.2 3.3 100 60-161 69-169 (461)
36 cd00758 MoCF_BD MoCF_BD: molyb 26.7 57 0.0015 15.1 2.6 76 35-122 13-88 (133)
37 PRK10712 fructose-specific PTS 25.6 60 0.0015 15.0 5.2 30 77-106 25-54 (563)
38 COG3449 DNA gyrase inhibitor [ 25.4 24 0.00062 17.2 0.4 42 39-80 25-69 (154)
39 pfam09897 DUF2124 Uncharacteri 23.4 66 0.0017 14.7 3.2 100 41-158 32-140 (147)
40 TIGR01862 N2-ase-Ialpha nitrog 21.4 64 0.0016 14.8 2.0 109 36-160 42-166 (510)
41 TIGR00706 SppA_dom signal pept 21.3 31 0.00078 16.7 0.3 37 100-137 56-94 (224)
42 TIGR02539 SepCysS Sep-tRNA:Cys 20.8 45 0.0011 15.7 1.1 15 67-81 177-191 (381)
43 TIGR00089 TIGR00089 RNA modifi 20.8 75 0.0019 14.4 5.5 105 56-175 3-118 (455)
44 cd00069 GHB Glycoprotein hormo 20.3 45 0.0012 15.6 1.0 15 148-162 53-67 (102)
No 1
>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit; InterPro: IPR006138 Respiratory-chain NADH dehydrogenase (1.6.5.3 from EC) (also known as complex I or NADH-ubiquinone oxidoreductase) is an oligomeric enzymatic complex located in the inner mitochondrial membrane which also seems to exist in the chloroplast and in cyanobacteria (as a NADH-plastoquinone oxidoreductase). Among the 25 to 30 polypeptide subunits of this bioenergetic enzyme complex there is one with a molecular weight of 20 kDa (in mammals) , which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 4Fe-4S iron-sulphur cluster. The 20 kDa subunit has been found to be nuclear encoded, as a precursor form with a transit peptide in mammals, and in Neurospora crassa. It is mitochondrial encoded in Paramecium (gene psbG) and chloroplast encoded in various higher plants (gene ndhK or psbG).; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0006120 mitochondrial electron transport NADH to ubiquinone.
Probab=100.00 E-value=0 Score=587.32 Aligned_cols=144 Identities=68% Similarity=1.191 Sum_probs=141.5
Q ss_pred CEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCC-EEECCCCCCCCEEEEECCCCHHHHHHHHHHHH
Q ss_conf 76885599998456128834775235465213566336667867648-48706822060799714134556999999998
Q gi|254780853|r 37 GFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFG-FAPRASPRQSDVMIVAGTLTNKMASALRRVYD 115 (185)
Q Consensus 37 ~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG-~~~~~sPRqADvliVtG~vT~km~~~l~~~ye 115 (185)
+|++|++|+++||+|+|||||++||||||+|||||+.+++||++||| +.||+||||||||||+||||+||||+|||+||
T Consensus 1 ~v~~T~~d~~~~WgR~~SLWP~tFGlACCaIEMm~t~~s~yDldRFG~~~fR~SPRQaDvMIvAGT~t~KmAP~lrrlYD 80 (146)
T TIGR01957 1 GVLLTTVDKLLNWGRSNSLWPLTFGLACCAIEMMATGASRYDLDRFGSVVFRASPRQADVMIVAGTVTKKMAPVLRRLYD 80 (146)
T ss_pred CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCEEEECCCCCEEHHHHHHHHHH
T ss_conf 94115489999986311321112236558999999755412631337215877876133344548641004347766875
Q ss_pred HCCCCCEEEEECCCCCCCCCCCCC-CCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 468666199853556688634788-72207722232230674887689899999999999999641
Q gi|254780853|r 116 QMPEPRYVISMGSCANGGGYYHYS-YSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRV 180 (185)
Q Consensus 116 qmpePK~ViA~G~Ca~sGG~f~~s-Y~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~~ 180 (185)
||||||||||||+||+|||+|+++ |+||||+|+||||||||||||||||||++||++||||||++
T Consensus 81 QMPePKwVIsMG~CA~sGG~f~~~~Y~VVqGvDr~~PVDVYiPGCPPRPEAL~~g~~~LQ~KI~~~ 146 (146)
T TIGR01957 81 QMPEPKWVISMGACANSGGPFNESSYSVVQGVDRIVPVDVYIPGCPPRPEALIYGLLKLQKKIKRE 146 (146)
T ss_pred HCCCCCEEEECCCCCCCCCCCCCCCCEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf 378997798517600688554478622761453662255661876883789999999999987049
No 2
>COG0377 NuoB NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]
Probab=100.00 E-value=0 Score=499.99 Aligned_cols=155 Identities=70% Similarity=1.169 Sum_probs=150.1
Q ss_pred HHHHHHHHCCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCHHHH
Q ss_conf 76675410876885599998456128834775235465213566336667867648487068220607997141345569
Q gi|254780853|r 28 RISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMA 107 (185)
Q Consensus 28 ~~~~~~~~~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~km~ 107 (185)
....+...++++.|++|+++||+|++||||+|||||||+|||++++++|||+||||+.|++||||||+|||+||+|+|||
T Consensus 11 ~~~~~~~~~~~~~t~~~~l~~W~r~~SLWp~~fg~aCC~vEm~~~~~~r~D~eRfG~~~r~SPRQaDvmIvaGt~t~Kma 90 (194)
T COG0377 11 DPVEALLSKGVLLTKVDKLINWGRKNSLWPVTFGLACCAVEMMATFASRYDLERFGEVPRASPRQADLMIVAGTLTNKMA 90 (194)
T ss_pred CHHHHHHCCCEEEECHHHHHHHHHHCCCCHHHHCCHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCEEEEECCCHHHHH
T ss_conf 04777631474652318888665314542566511368888787406655788717677899651357999353328788
Q ss_pred HHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999984686661998535566886347887220772223223067488768989999999999999964126
Q gi|254780853|r 108 SALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGN 182 (185)
Q Consensus 108 ~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~~~~ 182 (185)
|+|+++||||||||||||||+||++||+||+||++|+|+|++||||+|||||||||||+++||++||+||++++.
T Consensus 91 p~lr~~YdQMPePK~VIsMGsCa~~GG~f~~sYsvV~g~D~~vPVDvyIPGCPPrPEAl~~gi~~Lq~KI~~~~~ 165 (194)
T COG0377 91 PALRRVYDQMPEPKWVISMGSCANSGGMYWNSYSVVQGVDRVVPVDVYIPGCPPRPEALLYGILLLQEKIRREGR 165 (194)
T ss_pred HHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCEEEECCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 999999971899837997455116887323553134056426765366489888879999999999999985156
No 3
>CHL00023 ndhK NADH dehydrogenase subunit K
Probab=100.00 E-value=0 Score=497.54 Aligned_cols=150 Identities=47% Similarity=0.912 Sum_probs=145.3
Q ss_pred HHHCCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf 41087688559999845612883477523546521356633666786764848706822060799714134556999999
Q gi|254780853|r 33 ITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRR 112 (185)
Q Consensus 33 ~~~~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~km~~~l~~ 112 (185)
...+|+++|++|+++||+|++||||++||||||+|||||+.+||||+||||+.+++||||||+|||+|+||+||+++|++
T Consensus 12 ~~~~nvi~t~ld~~~nWaR~~SLWpl~fgtaCC~IEmma~~~~ryD~eRFG~~~raSPRqADlliVtGtVT~kMa~~l~r 91 (225)
T CHL00023 12 TTSNSVISTTLNDLSNWSRLSSLWPLLYGTSCCFIEFASLIGSRFDFDRYGLVPRSSPRQADLILTAGTVTMKMAPSLVR 91 (225)
T ss_pred CCCCCEEEEEHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHCCCEECCCCCCCCEEEEECCCCHHHHHHHHH
T ss_conf 67787798428997545531776504665246898898622664245441101238975023799803161867999999
Q ss_pred HHHHCCCCCEEEEECCCCCCCCCCC-CCCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9984686661998535566886347-887220772223223067488768989999999999999964126
Q gi|254780853|r 113 VYDQMPEPRYVISMGSCANGGGYYH-YSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGN 182 (185)
Q Consensus 113 ~yeqmpePK~ViA~G~Ca~sGG~f~-~sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~~~~ 182 (185)
+||||||||||||||+||++||+|+ |||++++|+|++||||+|||||||||||||+||++||+||++|..
T Consensus 92 ~YeQMPePK~VIAmGaCA~sGG~F~~dsYsvv~GvD~iIPVDVyIPGCPPrPEAiidaI~kLqkKi~~e~~ 162 (225)
T CHL00023 92 LYEQMPEPKYVIAMGACTITGGMFSTDSYSTVRGVDKLIPVDVYLPGCPPKPEAIIDAITKLRKKISREIY 162 (225)
T ss_pred HHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCEEECCEECCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 99857998569985664578874457985011577721451367689886989999999999999976658
No 4
>PRK06411 NADH dehydrogenase subunit B; Validated
Probab=100.00 E-value=0 Score=496.65 Aligned_cols=155 Identities=70% Similarity=1.162 Sum_probs=148.1
Q ss_pred HHHHHHHHCCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCHHHH
Q ss_conf 76675410876885599998456128834775235465213566336667867648487068220607997141345569
Q gi|254780853|r 28 RISSEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMA 107 (185)
Q Consensus 28 ~~~~~~~~~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~km~ 107 (185)
....+..++|+++|++|+++||+|++||||++||||||+|||+++++|+||+||||+.|++||||||+|||+|+||+||+
T Consensus 16 ~~~~~~~~~~~~~t~~d~~~nW~r~~SlWp~~fg~aCC~IE~~a~~~pryD~eRfG~~~~aSPRqADvliVtG~vT~km~ 95 (195)
T PRK06411 16 DPLEEELDKGVVLTTLDDLLNWARKNSLWPMTFGLACCAVEMMAAGTSRYDLDRFGMVFRASPRQADLMIVAGTLTNKMA 95 (195)
T ss_pred CCHHHHCCCCEEEEEHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCHHHHH
T ss_conf 82345325876986799986466607843577761428998987448854777705256058752447897052318889
Q ss_pred HHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999984686661998535566886347887220772223223067488768989999999999999964126
Q gi|254780853|r 108 SALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGN 182 (185)
Q Consensus 108 ~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~~~~ 182 (185)
++|+++||||||||||||||+||++||+|++||+|++|+|++||||+|||||||||||||+||++||+||+..++
T Consensus 96 ~~l~~~YeqmPePK~VIA~G~Ca~sGG~f~~sY~v~~gvd~~iPVDvyVPGCPPrPEAil~gi~~Lq~kI~~~~r 170 (195)
T PRK06411 96 PALRRLYDQMPEPKWVISMGSCANSGGMYHYSYSVVRGVDKIVPVDVYVPGCPPRPEALLYGIMKLQKKIQGVRR 170 (195)
T ss_pred HHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCEEECCEECCCCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 999999985899707998455557786346886111688760234567889886989999999999999843344
No 5
>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional
Probab=100.00 E-value=0 Score=487.25 Aligned_cols=145 Identities=53% Similarity=1.031 Sum_probs=141.2
Q ss_pred CCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCE-EECCCCCCCCEEEEECCCCHHHHHHHHHHH
Q ss_conf 8768855999984561288347752354652135663366678676484-870682206079971413455699999999
Q gi|254780853|r 36 KGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGF-APRASPRQSDVMIVAGTLTNKMASALRRVY 114 (185)
Q Consensus 36 ~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~-~~~~sPRqADvliVtG~vT~km~~~l~~~y 114 (185)
.|+++|++|+++||+|+|||||+|||||||++|||++++|+||++|||. .+++||||||+|||+||||+||||+++++|
T Consensus 1 ~~~~~~~~d~~~~w~~k~SlWp~~f~~aCc~vE~~~~~~~~yD~~R~G~e~~~~~pRqadl~iv~Gtvt~Kma~~~~~~y 80 (784)
T PRK13292 1 QNIILASLDDLINWGRANSLWPMFFGLSCCFVEMMTSFTSRYDVSRFGAEVLRGTPREADLMVIAGTVFKKMAPSILRLY 80 (784)
T ss_pred CCEEHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHH
T ss_conf 95202316877422320552418875157877777501677678884743367996434479993531798899999999
Q ss_pred HHCCCCCEEEEECCCCCCCCCCCCCCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 8468666199853556688634788722077222322306748876898999999999999996412
Q gi|254780853|r 115 DQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVG 181 (185)
Q Consensus 115 eqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~~~ 181 (185)
||||+||||||||+||++||+| ++|+|++|+|+++|||+|||||||||||+|+||++||+||.++.
T Consensus 81 eQM~~PK~Vi~mGsC~~~GG~~-~~Y~vv~g~d~i~PVd~~vpGCPP~Pea~l~gi~~lq~kI~~~e 146 (784)
T PRK13292 81 EQMAEPKWVISMGSCANSGGMY-DVYSVVQGVNQILPVDVYIPGCPPRPEAFLQGLMLLQEKIRREE 146 (784)
T ss_pred HHCCCCCEEEEECCCCCCCCCC-CCEEECCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCC
T ss_conf 7489984799844412578876-64354247761356536737988797999999999999985143
No 6
>KOG1687 consensus
Probab=100.00 E-value=0 Score=464.64 Aligned_cols=154 Identities=71% Similarity=1.265 Sum_probs=149.0
Q ss_pred HHHHHCCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCHHHHHHH
Q ss_conf 75410876885599998456128834775235465213566336667867648487068220607997141345569999
Q gi|254780853|r 31 SEITHKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASAL 110 (185)
Q Consensus 31 ~~~~~~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~km~~~l 110 (185)
+..+..+++.+++||+.||+|++|+||++||+|||++|||++.+||||++|||++||+||||||++||+||+|.||||+|
T Consensus 10 ~~ss~~e~~~a~ldDl~Nwar~~SlWPltfGlaCCavEmmh~~a~RyD~DRyGvvfRaSPRQaD~iivAGTlTnKMAPaL 89 (168)
T KOG1687 10 NPSSKAEYVLARLDDLLNWARRGSLWPLTFGLACCAVEMMHLAAPRYDMDRYGVVFRASPRQADLIIVAGTLTNKMAPAL 89 (168)
T ss_pred CCCCCCEEEHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCCCCCCEEEEECCCHHHHCHHH
T ss_conf 96542203022178777577516743145405899999997525534630022453389762457999321111015899
Q ss_pred HHHHHHCCCCCEEEEECCCCCCCCCCCCCCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99998468666199853556688634788722077222322306748876898999999999999996412645
Q gi|254780853|r 111 RRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRRVGNVK 184 (185)
Q Consensus 111 ~~~yeqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~~~~~~ 184 (185)
+++|||||||||||+||+||++||.|+.||+|++|+|++||||+|||||||++||+|+|+++||+||+|++..+
T Consensus 90 rkvYdQMPEpr~VisMGsCangGGyyhysYSvvRGcDriiPVDiYvPGCPPtaEAllygilqLqkKi~R~r~~q 163 (168)
T KOG1687 90 RKVYDQMPEPRWVISMGSCANGGGYYHYSYSVVRGCDRIIPVDIYVPGCPPTAEALLYGILQLQKKIKRIRPLQ 163 (168)
T ss_pred HHHHHHCCCCEEEEEECCCCCCCCEEEEEEHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99986089970699852302688558886543317662245546658988978999999999999997752555
No 7
>COG3260 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]
Probab=100.00 E-value=0 Score=334.50 Aligned_cols=128 Identities=41% Similarity=0.845 Sum_probs=120.4
Q ss_pred CCCCEEEEECC-CC--CCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf 28834775235-46--5213566336667867648487068220607997141345569999999984686661998535
Q gi|254780853|r 52 TGSLMWMTFGL-AC--CAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGS 128 (185)
Q Consensus 52 ~~Slwp~~fg~-aC--C~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~ 128 (185)
+.|+|.++.-+ +| |+||+.++++|+||+||||+.+++||||||+|||||+||++|+++|+++||+|||||.|||+|+
T Consensus 6 ~rS~~v~~VdsG~CNgCdIEi~a~~sP~YDaErfgI~~v~sPRhADiLlVTG~vT~~~~e~lkk~Yea~PePKiViA~Ga 85 (148)
T COG3260 6 KRSLHVYHVDSGGCNGCDIEILAALSPRYDAERFGIKVVNSPRHADILLVTGAVTRQMREPLKKAYEAMPEPKIVIAVGA 85 (148)
T ss_pred CCCEEEEEECCCCCCCEEEEEEECCCCCCCHHHHEEEEECCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECC
T ss_conf 66359999426886765688754258534367811688479864338999521658889999999973899817999755
Q ss_pred CCCCCCCCCCCCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 566886347887220772223223067488768989999999999999964
Q gi|254780853|r 129 CANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179 (185)
Q Consensus 129 Ca~sGG~f~~sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~ 179 (185)
||+|||+|+++|+|.+|+|++||||++||||||||++||+|++.+..|..+
T Consensus 86 Ca~~GGIf~~~~~v~gpvd~viPVDv~IPGCPP~P~~il~g~~~al~~~~k 136 (148)
T COG3260 86 CALSGGIFKDSYSVWGPVDKVIPVDVEIPGCPPRPEAILAGLVAALGKLEK 136 (148)
T ss_pred CCCCCCEECCCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 435776632565100465534574547279987979999999999888887
No 8
>pfam01058 Oxidored_q6 NADH ubiquinone oxidoreductase, 20 Kd subunit.
Probab=99.97 E-value=1.2e-30 Score=200.03 Aligned_cols=111 Identities=39% Similarity=0.697 Sum_probs=101.6
Q ss_pred CCCCHHHHHHCCCCCCH-----HHCCEEECCCCC----CCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCC
Q ss_conf 46521356633666786-----764848706822----060799714134556999999998468666199853556688
Q gi|254780853|r 63 ACCAVEMMQASMPRYDL-----ERFGFAPRASPR----QSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGG 133 (185)
Q Consensus 63 aCC~iE~~a~~~p~yD~-----eRfG~~~~~sPR----qADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sG 133 (185)
..|.+||.++..+.||+ .+|+..+.+++| |+|+++|+|.||++|++.++++|++++++|+|||+|+||++|
T Consensus 2 ~GC~~s~~~~~~~~~dil~~~~~~y~~~~~~~~~~~~~~~dillVeG~v~~~~~~~~~~~~e~~~~ak~vIAvG~CA~~G 81 (124)
T pfam01058 2 TGCSISLLALHPPLLDLLDLISLRYHIPLMADPREIPEGADVLLVEGAVTRKPKEALERLYELAPKAKYVIAVGTCAAFG 81 (124)
T ss_pred CCCHHHHHHCCCCHHHHHHHCCHHCCCEECCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCC
T ss_conf 78069997539817778740002308734048787887830899970178887899999998642146389961342568
Q ss_pred CCCC--CCCCE-ECCCCCCCCCEEECCCCCCCHHHHHHHHHHH
Q ss_conf 6347--88722-0772223223067488768989999999999
Q gi|254780853|r 134 GYYH--YSYSV-VRGCDRIVPVDIYVPGCPPTAEALIYGILLL 173 (185)
Q Consensus 134 G~f~--~sY~v-~~g~d~~iPVDvyVPGCPPrPeail~gl~~L 173 (185)
|+|. ..+++ ++++++++|||+|||||||+||.|+++|+.|
T Consensus 82 Gi~~~~~~~~~~~~~~~~~v~VDi~IpGCPp~Pe~i~~~l~~l 124 (124)
T pfam01058 82 GIPAAGNNPSYGVRPVLGVVPVDINIPGCPPHPEWILGTLLAL 124 (124)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHC
T ss_conf 6444468875233463446871599739899999999999869
No 9
>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma. This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein contains two 4Fe-4S cluster binding domains (pfam00037) and scores above the trusted cutoff to model pfam01058 for the "NADH ubiquinone oxidoreductase, 20 Kd subunit" family.
Probab=99.70 E-value=3.1e-17 Score=121.69 Aligned_cols=113 Identities=25% Similarity=0.508 Sum_probs=81.6
Q ss_pred CC--CCHHHHHHCCCCCC-HHHC-CEEE---CCCCC---CCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCC
Q ss_conf 46--52135663366678-6764-8487---06822---06079971413455699999999846866619985355668
Q gi|254780853|r 63 AC--CAVEMMQASMPRYD-LERF-GFAP---RASPR---QSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANG 132 (185)
Q Consensus 63 aC--C~iE~~a~~~p~yD-~eRf-G~~~---~~sPR---qADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~s 132 (185)
+| |.+.+..+..--.| ++++ -+.+ ..+-+ ..|+-+|.|.|+.+-.+.+.++-+---.-|+|||+|+||+.
T Consensus 11 gC~GC~lSllD~~E~Lldll~~v~divy~~~l~d~ke~pe~DValVEGsV~~~~e~~le~ikeiRekskilVA~GaCA~~ 90 (228)
T TIGR03294 11 GCTGCLVSLTDNYEGLLDILDNIADLVYCQTLADAREIPEMDVALVEGSVCLQDEHSLEEIKELREKAKVVVALGACAAT 90 (228)
T ss_pred CCCCHHHHHHCCHHHHHHHHHHHHEEEECHHHCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCEEEEEECCCCC
T ss_conf 76653774650315799999752324744011157658885189995501578677799999999868889996412102
Q ss_pred CCCCCC---------CCCEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf 863478---------8722077222322306748876898999999999999
Q gi|254780853|r 133 GGYYHY---------SYSVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQK 175 (185)
Q Consensus 133 GG~f~~---------sY~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ 175 (185)
||+-+. .+..+.++.++|+||+|||||||.||.|...+..|.+
T Consensus 91 GGI~~~~~ggq~~~P~~e~~~Pi~~vV~VD~~iPGCPP~pe~I~~~~~all~ 142 (228)
T TIGR03294 91 GNFTRYSRGGQQAQPQHESFVPITDVIDVDLAIPGCPPSPEAIRNVCVALLN 142 (228)
T ss_pred CCCCEECCCCCCCCCCCCCCCCHHHEEEECEECCCCCCCHHHHHHHHHHHHC
T ss_conf 8820002588778887555256014476167827998498999999999973
No 10
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Probab=99.61 E-value=1.2e-15 Score=112.46 Aligned_cols=111 Identities=26% Similarity=0.494 Sum_probs=82.9
Q ss_pred CC--CCHHHHHHCCCCCCHHHCC-EE-------ECCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCC
Q ss_conf 46--5213566336667867648-48-------70682206079971413455699999999846866619985355668
Q gi|254780853|r 63 AC--CAVEMMQASMPRYDLERFG-FA-------PRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANG 132 (185)
Q Consensus 63 aC--C~iE~~a~~~p~yD~eRfG-~~-------~~~sPRqADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~s 132 (185)
+| |.+-+.-+.---+|+-.+- +. -+--|- .|+.+|.|.|. -.+-|..+-|.--.-|+|||+|+||.+
T Consensus 13 gC~GC~~slldl~E~L~dll~~~div~~~~l~D~keiPE-vDValVEGsV~--~ee~lE~v~ElRekakivVA~GsCA~~ 89 (247)
T COG1941 13 GCSGCHMSLLDLYEKLLDLLEDADIVYCPTLVDEKEIPE-VDVALVEGSVC--DEEELELVKELREKAKIVVALGSCAVT 89 (247)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHCEEEEECCCCCCCCCC-CCEEEEECCCC--CHHHHHHHHHHHHHCCEEEEEECCHHC
T ss_conf 565136678769999997652101787100135564876-43899854327--688899999999738489997523530
Q ss_pred CCCCC-----------CCC---------CEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf 86347-----------887---------220772223223067488768989999999999999
Q gi|254780853|r 133 GGYYH-----------YSY---------SVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKK 176 (185)
Q Consensus 133 GG~f~-----------~sY---------~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~k 176 (185)
||+-. ..| ..+.++.++|+||.+||||||+||.|.+++..|.+.
T Consensus 90 Ggv~~~~~~s~~e~l~~~y~~~~~~~~~~~v~Pl~evI~VD~~IpGCPP~~e~I~~al~all~g 153 (247)
T COG1941 90 GGVQGLRNKSGEELLRPVYGDAKSTFNEESVVPLGEVIDVDYAIPGCPPSPEEIARALTALLEG 153 (247)
T ss_pred CCCHHHHHCCCCCCCHHHHHCCCCCCCCCCEEECCCEEEEEEECCCCCCCHHHHHHHHHHHHCC
T ss_conf 8864463335320004565304577876515770032651154689885989999999999769
No 11
>COG1740 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion]
Probab=98.99 E-value=1.4e-09 Score=77.01 Aligned_cols=149 Identities=17% Similarity=0.299 Sum_probs=94.9
Q ss_pred HHHHHHHHHHHHCCEEEEEHHHHHHH----HHC-CCCEEEEECCCCCCHHHHHHCCCCCC--HHHC-CEEE-----CCCC
Q ss_conf 25777667541087688559999845----612-88347752354652135663366678--6764-8487-----0682
Q gi|254780853|r 24 ADFSRISSEITHKGFLVTSVDQLVTW----ART-GSLMWMTFGLACCAVEMMQASMPRYD--LERF-GFAP-----RASP 90 (185)
Q Consensus 24 ~~~~~~~~~~~~~~~i~t~~d~l~nW----~R~-~Slwp~~fg~aCC~iE~~a~~~p~yD--~eRf-G~~~-----~~sP 90 (185)
.+|-+....+...-++.++..-.+-+ +-+ .-+|-.-....||..-+.....|-.+ +..| -..+ .++=
T Consensus 16 r~f~k~~~~~~a~l~L~~~~~~~~~~a~e~~~~~~viWLhg~eCTGcteSfLrs~~P~~~~li~~~IsL~Yhetlmaa~G 95 (355)
T COG1740 16 RDFLKLCGALAASLGLSASYAPEIAKALENKPRTPVIWLHGLECTGCTESFLRSEHPTANDLILELISLEYHETLMAASG 95 (355)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 88999999999875367201699999985587784698704555677688760479979999999875422035544122
Q ss_pred C--------------CCCEEEEECCCCHH---------HHHHHHHHHHHCCCCCEEEEECCCCCCCCCCC--CCCCEECC
Q ss_conf 2--------------06079971413455---------69999999984686661998535566886347--88722077
Q gi|254780853|r 91 R--------------QSDVMIVAGTLTNK---------MASALRRVYDQMPEPRYVISMGSCANGGGYYH--YSYSVVRG 145 (185)
Q Consensus 91 R--------------qADvliVtG~vT~k---------m~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~--~sY~v~~g 145 (185)
- --+||+|.|.|... -.+.+..+-+.-..-++|||+|+||+.||+-. -..+..++
T Consensus 96 ~~aee~l~~~i~~~kg~yILvVEG~v~~~~~G~y~~vgg~~~~e~l~kaA~~A~aIiAvG~CAs~GgI~AA~pnps~a~~ 175 (355)
T COG1740 96 TQAEELLEDAILKYKGKYILVVEGAVPLGENGMYCIVGGEPFKEILRKAAEGASAIIAVGTCASWGGIQAAKPNPTGAGP 175 (355)
T ss_pred HHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEEECCCCCCEECCCCCCCCCCC
T ss_conf 26899999999743785599980676679985179876802899999986137669998604245883036779977655
Q ss_pred CCCCC---CCEEECCCCCCCHHHHHHHHHHH
Q ss_conf 22232---23067488768989999999999
Q gi|254780853|r 146 CDRIV---PVDIYVPGCPPTAEALIYGILLL 173 (185)
Q Consensus 146 ~d~~i---PVDvyVPGCPPrPeail~gl~~L 173 (185)
+++++ || +.||||||.|+-|+--|...
T Consensus 176 i~ev~~~kpV-INiPGCPp~pd~iv~tl~~~ 205 (355)
T COG1740 176 LSEVIKDKPV-INIPGCPPNPDWIVATLLHI 205 (355)
T ss_pred CEECCCCCCE-EECCCCCCCCHHHHHHHHHH
T ss_conf 0000268855-65899989810579999999
No 12
>PRK10468 hydrogenase 2 small subunit; Provisional
Probab=98.84 E-value=1e-08 Score=71.90 Aligned_cols=132 Identities=19% Similarity=0.385 Sum_probs=88.5
Q ss_pred HHHHHHHHHCCCCEEEEEC-CCCCCHHHHHHCCCCCCH---HHCCEEECCC-----CCC--------------CCEEEEE
Q ss_conf 9999845612883477523-546521356633666786---7648487068-----220--------------6079971
Q gi|254780853|r 43 VDQLVTWARTGSLMWMTFG-LACCAVEMMQASMPRYDL---ERFGFAPRAS-----PRQ--------------SDVMIVA 99 (185)
Q Consensus 43 ~d~l~nW~R~~Slwp~~fg-~aCC~iE~~a~~~p~yD~---eRfG~~~~~s-----PRq--------------ADvliVt 99 (185)
+.+.+.-+.+.++-++++. .++|.+-++.+..|..+- +-..+.|..+ =.| -.+|+|.
T Consensus 38 va~Al~~~~rppVIWL~~~eCTGCSeSlLrs~~P~i~~lild~IsL~YHeTlmaa~G~~Ae~~l~~~~~~~~G~yiLVVE 117 (371)
T PRK10468 38 MAESVTNPQRPPVIWIGAQECTGCTESLLRATHPTVENLVLETISLEYHEVLSAAFGHQVEENKHNALEKYKGQYVLVVD 117 (371)
T ss_pred HHHHHHCCCCCCEEEEECCCCCCCHHHHHCCCCCCHHHHHHHHEEEEECCCCCHHCCHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf 99999628999879985776788189987637998999965313220023002322299999999999864798599982
Q ss_pred CCCCHHHH---------HHHHHHHHHCCCCCEEEEECCCCCCCCCCCCC--CCEECCCCCCC---CCEEECCCCCCCHHH
Q ss_conf 41345569---------99999998468666199853556688634788--72207722232---230674887689899
Q gi|254780853|r 100 GTLTNKMA---------SALRRVYDQMPEPRYVISMGSCANGGGYYHYS--YSVVRGCDRIV---PVDIYVPGCPPTAEA 165 (185)
Q Consensus 100 G~vT~km~---------~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~~s--Y~v~~g~d~~i---PVDvyVPGCPPrPea 165 (185)
|.|..++. +.+..+-+..+.-+.|||+|+||.-||+-.-. ..-..|+.+++ || +.||||||.|+.
T Consensus 118 GsIP~~~~G~yc~igGk~~~e~l~e~A~~A~AVIAvGtCAs~GGIpAA~PNPTgA~gv~~~l~~kPV-INiPGCP~~P~~ 196 (371)
T PRK10468 118 GSIPLKDNGIYCMVAGEPIVDHIRKAAEGAAAIIAIGSCSAWGGVAAAGVNPTGAVSLQEVLPGKTV-INIPGCPPNPHN 196 (371)
T ss_pred CCCCCCCCCEEEEECCEEHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCCCCHHHHCCCCCC-CCCCCCCCCHHH
T ss_conf 7654589962698779329999999872275688886041247844578998764308886489971-046999998016
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999999
Q gi|254780853|r 166 LIYGILLLQK 175 (185)
Q Consensus 166 il~gl~~L~~ 175 (185)
++..|+.+.-
T Consensus 197 ~~gtl~~~l~ 206 (371)
T PRK10468 197 FLATVAHIIT 206 (371)
T ss_pred HHHHHHHHHH
T ss_conf 9999999995
No 13
>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA); InterPro: IPR001821 Hydrogenases catalyse the reversible oxidation of molecular hydrogen and play a vital role in anaerobic metabolism. Metal-containing hydrogenases are subdivided into three classes: Fe ('iron only') hydrogenases; Ni-Fe hydrogenases; and Ni-Fe-Se hydrogenases . Hydrogen oxidation is coupled to the reduction of electron acceptors (such as oxygen, nitrate, sulphate, carbon dioxide and fumarate), whereas proton reduction (hydrogen evolution) is essential in pyruvate fermentation or in the disposal of excess electrons. The Ni-Fe hydrogenases, when isolated, are found to catalyse both hydrogen evolution and uptake, with low-potential multihaem cytochromes, such as cytochrome c3, acting as either electron donors or acceptors, depending on their oxidation state . Both periplasmic (soluble) and membrane-bound hydrogenases are known. The Ni-Fe hydrogenases are heterodimeric proteins consisting of small (S) and large (L) subunits. The small subunit contains three iron-sulphur clusters (two [4Fe-4S] and one [3Fe-4S]); the large subunit contains a nickel ion , . Small subunits of membrane-bound Ni-Fe hydrogenases contain a C-terminal domain of about 40 residues that is absent in periplasmic forms. The 3D structure of the Ni-Fe hydrogenase from Desulfovibrio gigas has been determined at 2.85A resolution . The small subunit consists of two domains, I(S) and II(S). The alpha/beta twisted open sheet structure of the N-terminal I(S) domain is similar to that of flavodoxin; the C-terminal II(S) domain contains two alpha-helices and has no beta-structure. The Fe-S clusters are distributed almost along a straight line, with the [3Fe-4S] cluster located half-way between the two [4Fe-4S] clusters. The two [4Fe-4S] clusters have been termed proximal (prox) and distal (dist), based on their distance to the Ni atom. Domain I(S) binds the [4Fe-4S]prox cluster, while domain II(S) binds the [4Fe-4S]dist and [3Fe-4S] clusters. The [4Fe-4S]prox cluster is coordinated by Cys-17, Cys-20, Cys-112 and Cys-148; [4Fe-4S]dist is coordinated by His-185, Cys-188, Cys-213 and Cys-219; and [3Fe-4S] is coordinated by Cys-228, Cys-246 and Cys-249. [4Fe-4S]dist is the first known example of a [4Fe-4S] cluster in protein structure ligated by a His side chain. A crown of acidic residues surrounds the partially-exposed His-185 and this might provide a recognition site for the redox partner (cytochrome c3) . A mechanism of electron transfer from the Ni active site through the Fe-S clusters to the cytochrome c3 has been suggested . The role of the [3Fe-4S] cluster is not clear: its high redox potential and its absence from some homologous hydrogenases put its involvement in electron transfer in doubt .; GO: 0008901 ferredoxin hydrogenase activity, 0051536 iron-sulfur cluster binding, 0006118 electron transport, 0009375 ferredoxin hydrogenase complex.
Probab=95.94 E-value=0.012 Score=36.49 Aligned_cols=133 Identities=18% Similarity=0.334 Sum_probs=79.6
Q ss_pred EEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCH------------------------------HHCC----E
Q ss_conf 88559999845612883477523546521356633666786------------------------------7648----4
Q gi|254780853|r 39 LVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDL------------------------------ERFG----F 84 (185)
Q Consensus 39 i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~------------------------------eRfG----~ 84 (185)
.......+-|--|-.-+|....-..||.-.+.....|..+- +++- +
T Consensus 38 ~~~~~~~~~~~~~~p~~w~~~~~c~~c~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~ 117 (370)
T TIGR00391 38 APLLAWAVENPPRLPVIWLHGLECTGCTESLLRSAHPTVEDLILDLISLEYHETLLAAAGFQAEENLHDALEKYKGKYIL 117 (370)
T ss_pred HHHHHHHHHCCCCCCEEEEECHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCEEE
T ss_conf 46777764124557466730101100135665320303567777665200123444330202456677777752585689
Q ss_pred EE-CCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCC--CCCEECCCCCCCCC--EEECCCC
Q ss_conf 87-0682206079971413455699999999846866619985355668863478--87220772223223--0674887
Q gi|254780853|r 85 AP-RASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY--SYSVVRGCDRIVPV--DIYVPGC 159 (185)
Q Consensus 85 ~~-~~sPRqADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~~--sY~v~~g~d~~iPV--DvyVPGC 159 (185)
.. -.-|...+-++..++-.. +.+..+-.....-..+++.|+|+.-||+-.. +..-..++++++|- -+.+|||
T Consensus 118 ~~~g~~p~~~~~~~~~~p~~~---~~~~~~~~~~~~~~~~~~~g~c~~~g~~~~~~~~p~~~~~~~~~~~~~~~~~~pgc 194 (370)
T TIGR00391 118 AVEGGPPLGDEGLLCLGPSGE---PGVEELRKAAEGAAAIIAWGTCSSWGGVQAAGPNPTGATPLDKVLPDKPVINVPGC 194 (370)
T ss_pred EECCCCCCCCCCEEEECCCCC---HHHHHHHHHHHHHHHEEEECCCCCCCCCCCCCCCCCCCCCHHHHCCCCCEEECCCC
T ss_conf 973877646550266336664---35788776542101001110100014310145674444312333167633434788
Q ss_pred CCCHHHHHHHHHHHH
Q ss_conf 689899999999999
Q gi|254780853|r 160 PPTAEALIYGILLLQ 174 (185)
Q Consensus 160 PPrPeail~gl~~L~ 174 (185)
||.|..++.-+..+.
T Consensus 195 pp~~~~~~~~~~~~~ 209 (370)
T TIGR00391 195 PPNPDNLLATVLYLL 209 (370)
T ss_pred CCCHHHHHHHHHHHH
T ss_conf 875025666666555
No 14
>pfam00919 UPF0004 Uncharacterized protein family UPF0004. This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain.
Probab=79.82 E-value=3.9 Score=21.85 Aligned_cols=71 Identities=23% Similarity=0.373 Sum_probs=41.1
Q ss_pred CEEEEECCCC--CCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEEC-CCC----HHHHHHHHHHHHHCCCCCEEEEEC
Q ss_conf 3477523546--521356633666786764848706822060799714-134----556999999998468666199853
Q gi|254780853|r 55 LMWMTFGLAC--CAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAG-TLT----NKMASALRRVYDQMPEPRYVISMG 127 (185)
Q Consensus 55 lwp~~fg~aC--C~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG-~vT----~km~~~l~~~yeqmpePK~ViA~G 127 (185)
+|..+||..= -+-|.+ ..-+.+.|...+.+|-.||++||.- +|| +|+...++++..+ ..|...|.+.
T Consensus 2 v~i~T~GC~~N~~Dse~i-----~~~l~~~G~~~~~~~~~AD~iiiNTC~V~~~A~~k~~~~i~~~~~~-~~p~~~iiv~ 75 (98)
T pfam00919 2 VYIETLGCQMNQADSEIM-----AGLLKKAGYELVDDPEEADVVVVNTCAVREKAEQKSRQTIRRLKRL-KNPDAKIVVT 75 (98)
T ss_pred EEEEECCCCCCHHHHHHH-----HHHHHHCCCEECCCHHCCCEEEEEEEECCHHHHHHHHHHHHHHHHH-CCCCCEEEEE
T ss_conf 899967998769999999-----9999987898858710099899996131128999999999999984-2999889999
Q ss_pred CCCC
Q ss_conf 5566
Q gi|254780853|r 128 SCAN 131 (185)
Q Consensus 128 ~Ca~ 131 (185)
-|..
T Consensus 76 GC~a 79 (98)
T pfam00919 76 GCMA 79 (98)
T ss_pred EECC
T ss_conf 8503
No 15
>cd01980 Chlide_reductase_Y Chlide_reductase_Y : Y subunit of chlorophyllide (chlide) reductase (BchY). Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase catalyzes the reduction of the B-ring of the tetrapyrolle. Chlide reductase is a three subunit enzyme (subunits are designated BchX, BchY and BchZ). The similarity between these three subunits and the subunits for nitrogenase suggests that BchX serves as an electron donor for the BchY-BchY catalytic subunits.
Probab=68.82 E-value=6.1 Score=20.74 Aligned_cols=114 Identities=18% Similarity=0.262 Sum_probs=70.5
Q ss_pred CCEEEEECCCCCCHHHHHHCCCCCCHHHCCE-EECCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCC-
Q ss_conf 8347752354652135663366678676484-87068220607997141345569999999984686661998535566-
Q gi|254780853|r 54 SLMWMTFGLACCAVEMMQASMPRYDLERFGF-APRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCAN- 131 (185)
Q Consensus 54 Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~-~~~~sPRqADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~- 131 (185)
--+++--|+.||.-=+-. .+ .=+|. ...+.|+-+..-+++|.+......+++. ..+-++|+.++-+|+|..
T Consensus 32 dsfflvvGs~tC~y~Ltf--~s----hf~~ar~~~~~~~~~~a~l~~g~l~e~lr~~~~~-ia~~~~~~~I~vigtC~~E 104 (416)
T cd01980 32 GAATVLVGDAGCLYGLTF--VS----HFYAARRSIVAVPLSSETLSTGKLFEDIREAIRK-LADPPAYTFIPVISLCVAE 104 (416)
T ss_pred CCEEEEECCCCHHHHHHH--HH----HHHHCCCCCCCCCCCHHHHHCCCHHHHHHHHHHH-HHCCCCCCEEEEECCCCHH
T ss_conf 735999647712618999--88----8763130003466212444137467999999998-6076888889996566176
Q ss_pred -CCCCCCCCCCEECCCCCCCCCEEECCCCC--CCHHHHHHHHHHHHHHH
Q ss_conf -88634788722077222322306748876--89899999999999999
Q gi|254780853|r 132 -GGGYYHYSYSVVRGCDRIVPVDIYVPGCP--PTAEALIYGILLLQKKI 177 (185)
Q Consensus 132 -sGG~f~~sY~v~~g~d~~iPVDvyVPGCP--PrPeail~gl~~L~~ki 177 (185)
+|=.-.....-..|+ +| +++--+|-| -.+++..-+++.+-.+.
T Consensus 105 ~ig~~lell~~~~~gv-~I--i~~~~~G~~t~a~~~~~da~~~~~~~r~ 150 (416)
T cd01980 105 TAGVAEELLPKQIDGV-RV--ILVRGPAFPIHSHPEAKDVGAMLLLARF 150 (416)
T ss_pred HHCCCHHHCHHHCCCC-EE--EEEECCCCCCEECCHHHHHHHHHHCCCC
T ss_conf 5376743375551896-59--9963588500312015899999863555
No 16
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein; InterPro: IPR013366 Salmonella typhimurium is capable of growth on ethanolamine as a sole source of carbon nitrogen and energy . During growth on this compound the cells form a multimolecular structure known as a metabolosome, which is similar to the carboxysome used by some photosynthetic bacteria to fix CO2, and is thought to contain the enzymes needed to metabolise this compound to acetyl-CoA. The metabolosome is not directly involved in the biochemistry of ethanolamine utilization - instead its role is thought to be to concentrate the enzymes involved in this process, while also protecting the cell from the build-up of toxic intermediates . The genes involved in growth on ethanolamine are encoded in a 17-gene operon known as the ethanolamine utilization (eut) operon. EutJ shows similarity to chaperonins and may play a role in assembly of the metabolosme , though it is not necessary for growth on this compound..
Probab=60.24 E-value=13 Score=18.87 Aligned_cols=48 Identities=21% Similarity=0.340 Sum_probs=43.0
Q ss_pred CCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCC
Q ss_conf 068220607997141345569999999984686661998535566886
Q gi|254780853|r 87 RASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGG 134 (185)
Q Consensus 87 ~~sPRqADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG 134 (185)
+++-.++.+.-+.=||-.|||..+++-.+.-+--+.=++=|+|+-++=
T Consensus 163 ~~~k~e~E~F~~v~PV~qKmA~Iv~~hi~~~~v~~~yLVGGac~~~~f 210 (240)
T TIGR02529 163 RDKKKEEEVFSVVKPVVQKMASIVKKHIEGQKVKDLYLVGGACSFSGF 210 (240)
T ss_pred HCCCCCEEEEEEECCHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHH
T ss_conf 305884378876041377789999998511883368982440052246
No 17
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type; InterPro: IPR004634 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signalling function. During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . These enzymes have a molecular mass around 67 kDa and a duplication such that the N-terminal half shares extensive homology with the C-terminal half and was shown in E. coli to form homotetramers. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both. ; GO: 0009003 signal peptidase activity, 0006465 signal peptide processing, 0016021 integral to membrane.
Probab=59.10 E-value=7 Score=20.37 Aligned_cols=32 Identities=28% Similarity=0.640 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHCCCC--C-EEEEECCCCCCCCCC
Q ss_conf 5699999999846866--6-199853556688634
Q gi|254780853|r 105 KMASALRRVYDQMPEP--R-YVISMGSCANGGGYY 136 (185)
Q Consensus 105 km~~~l~~~yeqmpeP--K-~ViA~G~Ca~sGG~f 136 (185)
--.+.+++--+..-.- | .+|+||+-|-|||.|
T Consensus 375 ~Ase~IR~e~~~~~~~GkKPVivSMG~~AASGgYW 409 (614)
T TIGR00705 375 FASEIIRRELERLQARGKKPVIVSMGAMAASGGYW 409 (614)
T ss_pred EHHHHHHHHHHHHHHCCCCCEEEECCHHHHCCCCH
T ss_conf 28789999999998268997898435023205300
No 18
>PRK11148 cyclic 3',5'-adenosine monophosphate phosphodiesterase; Provisional
Probab=49.47 E-value=24 Score=17.26 Aligned_cols=37 Identities=14% Similarity=0.265 Sum_probs=20.4
Q ss_pred CCCCCCCEEEEECCCCH----HHHHHHHHHHHHCCCCCEEE
Q ss_conf 68220607997141345----56999999998468666199
Q gi|254780853|r 88 ASPRQSDVMIVAGTLTN----KMASALRRVYDQMPEPRYVI 124 (185)
Q Consensus 88 ~sPRqADvliVtG~vT~----km~~~l~~~yeqmpePK~Vi 124 (185)
.....+|++|+||-+|. .-...+++..+..+-|-+++
T Consensus 51 ~~~~~~D~viiTGDLs~dgs~esY~~l~~~L~~l~~P~~~l 91 (275)
T PRK11148 51 AEQHEFDLIVATGDLAQDHSAEAYQHFAEGIAPLRKPCVWL 91 (275)
T ss_pred HCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf 45999889997640258999999999999997269998995
No 19
>TIGR02841 spore_YyaC putative sporulation protein YyaC; InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown..
Probab=49.16 E-value=19 Score=17.85 Aligned_cols=62 Identities=21% Similarity=0.426 Sum_probs=38.6
Q ss_pred EEEECCCC-----HHHHHHHHHHHHHCCCCCEEEEECCC----CCCCCCCCCCCCEECC--CCCCCCC--EEECCC
Q ss_conf 99714134-----55699999999846866619985355----6688634788722077--2223223--067488
Q gi|254780853|r 96 MIVAGTLT-----NKMASALRRVYDQMPEPRYVISMGSC----ANGGGYYHYSYSVVRG--CDRIVPV--DIYVPG 158 (185)
Q Consensus 96 liVtG~vT-----~km~~~l~~~yeqmpePK~ViA~G~C----a~sGG~f~~sY~v~~g--~d~~iPV--DvyVPG 158 (185)
+.|=||+. .||.+.|+.++..-+.| |+||+-|| .+=|-++=+.-..-.| +.+-+|- |+||-|
T Consensus 34 ~~V~GTL~~PVHA~NL~e~l~~I~k~h~~P-FiIAiDACLG~~~~VG~i~~~~~PlkPGaAvnK~LP~VGDl~itG 108 (140)
T TIGR02841 34 FHVYGTLEEPVHAVNLEEKLKIIKKKHKNP-FIIAIDACLGKLKSVGHITIGKGPLKPGAAVNKDLPAVGDLSITG 108 (140)
T ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHCCCC-CEEEEECCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEE
T ss_conf 488733787701253898999998626898-189986246870132068876704488857779988725768753
No 20
>COG4820 EutJ Ethanolamine utilization protein, possible chaperonin [Amino acid transport and metabolism]
Probab=49.11 E-value=15 Score=18.54 Aligned_cols=64 Identities=19% Similarity=0.179 Sum_probs=46.5
Q ss_pred HHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCC
Q ss_conf 6336667867648487068220607997141345569999999984686661998535566886
Q gi|254780853|r 71 QASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGG 134 (185)
Q Consensus 71 a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG 134 (185)
-+.+-+-++|.---.-|+.-....+..+.-||-.|||+.+++-.|.-+---.-++-|+|+-+|-
T Consensus 179 lAG~ygi~~EeAE~~Kr~~k~~~Eif~~v~PV~eKMAeIv~~hie~~~i~dl~lvGGac~~~g~ 242 (277)
T COG4820 179 LAGNYGISLEEAEQYKRGHKKGEEIFPVVKPVYEKMAEIVARHIEGQGITDLWLVGGACMQPGV 242 (277)
T ss_pred EECCCCCCHHHHHHHHHCCCCCHHCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCH
T ss_conf 7135686776788764214452011200207999999999998445887605886363267027
No 21
>KOG3586 consensus
Probab=48.40 E-value=24 Score=17.24 Aligned_cols=101 Identities=23% Similarity=0.380 Sum_probs=72.4
Q ss_pred CCCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCHHHHHHHHHHHHHC-CCCCEEEEECCCCCCCCCCCCCCC-
Q ss_conf 652135663366678676484870682206079971413455699999999846-866619985355668863478872-
Q gi|254780853|r 64 CCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQM-PEPRYVISMGSCANGGGYYHYSYS- 141 (185)
Q Consensus 64 CC~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~km~~~l~~~yeqm-pePK~ViA~G~Ca~sGG~f~~sY~- 141 (185)
-|.+|.-++..-.+|+.- -||||-. .+.|-|.++-..-.+ |.-+|+|.|.--.++---|++.|+
T Consensus 81 ~~~Le~keLWdrFh~lGT-------------EMIITKs-GRRMFPTvrV~~~GldP~a~Y~vlmDvVPvD~KRYRYayH~ 146 (437)
T KOG3586 81 QVQLETKELWDRFHDLGT-------------EMIITKS-GRRMFPTVRVKFSGLDPMADYYVLMDVVPVDSKRYRYAYHS 146 (437)
T ss_pred EEEEEHHHHHHHHHHCCC-------------EEEEECC-CCCCCCEEEEEEECCCCCCCEEEEEEEEECCCCEEEEEECC
T ss_conf 798505899999975473-------------5898305-64346437999735780221589987776256402233312
Q ss_pred ----EECCCCCCCCCEEEC-CCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf ----207722232230674-88768989999999999999964
Q gi|254780853|r 142 ----VVRGCDRIVPVDIYV-PGCPPTAEALIYGILLLQKKIRR 179 (185)
Q Consensus 142 ----v~~g~d~~iPVDvyV-PGCPPrPeail~gl~~L~~ki~~ 179 (185)
|.+..|-.+|--+|| |-||-+.|+++.-++-. +|+|-
T Consensus 147 S~WlvAGkADp~~p~R~yvHPDSP~sGe~wmkqiVSF-dK~KL 188 (437)
T KOG3586 147 SSWLVAGKADPAPPPRVYVHPDSPASGEQWMKQIVSF-DKLKL 188 (437)
T ss_pred CCEEEECCCCCCCCCCEEECCCCCCCHHHHHHHHHCH-HEEEC
T ss_conf 3025514778999872466799988889998755122-10220
No 22
>KOG1111 consensus
Probab=47.73 E-value=21 Score=17.63 Aligned_cols=38 Identities=21% Similarity=0.326 Sum_probs=31.6
Q ss_pred CEECCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 220772223223067488768989999999999999964
Q gi|254780853|r 141 SVVRGCDRIVPVDIYVPGCPPTAEALIYGILLLQKKIRR 179 (185)
Q Consensus 141 ~v~~g~d~~iPVDvyVPGCPPrPeail~gl~~L~~ki~~ 179 (185)
.-++|+-+++|-| .+-=+.|.|+++.+++.+...|+++
T Consensus 301 TrVGGIpeVLP~d-~i~~~~~~~~dl~~~v~~ai~~~~~ 338 (426)
T KOG1111 301 TRVGGIPEVLPED-MITLGEPGPDDLVGAVEKAITKLRT 338 (426)
T ss_pred EECCCCCCCCCCC-CEECCCCCHHHHHHHHHHHHHHHCC
T ss_conf 5148866548701-0223689857778899999987415
No 23
>pfam09565 RE_NgoFVII NgoFVII restriction endonuclease. This family includes the NgoFVII (recognizes GCSGC but cleavage site unknown) restriction endonuclease.
Probab=44.89 E-value=28 Score=16.83 Aligned_cols=40 Identities=15% Similarity=0.315 Sum_probs=32.8
Q ss_pred CEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCC
Q ss_conf 0799714134556999999998468666199853556688
Q gi|254780853|r 94 DVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGG 133 (185)
Q Consensus 94 DvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sG 133 (185)
+++|++|.++..-...|+++-|.++.-|.-+-+|=+...|
T Consensus 10 el~I~sGY~s~~~~~~l~~i~e~~~~~~I~LivGM~~~eG 49 (296)
T pfam09565 10 ELLIASGYASNMALEELDKLVENHHILKITLIVGMYPSEG 49 (296)
T ss_pred EEEEEECCCCHHHHHHHHHHHHHCCCCEEEEEEECCCCCC
T ss_conf 7999960167799999999997579843799970351578
No 24
>TIGR01279 DPOR_bchN light-independent protochlorophyllide reductase, N subunit; InterPro: IPR005970 Synonym: dark protochlorophyllide reductase Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite. This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme . ; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction.
Probab=41.91 E-value=32 Score=16.56 Aligned_cols=67 Identities=18% Similarity=0.451 Sum_probs=50.4
Q ss_pred EEEEECCCCCCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCH------HHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf 4775235465213566336667867648487068220607997141345------5699999999846866619985355
Q gi|254780853|r 56 MWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTN------KMASALRRVYDQMPEPRYVISMGSC 129 (185)
Q Consensus 56 wp~~fg~aCC~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~------km~~~l~~~yeqmpePK~ViA~G~C 129 (185)
+.+-.||--|+ +|=..-+|+..-|.||-|=.+|=.+-++. .+...+.++.+.-|+||.+.-+|+|
T Consensus 26 FFLi~GT~TCA---------hfLQ~AlGVMiFA~PRFa~A~lee~DLs~~~~~~eeL~~v~~~i~~~~P~p~vifllssC 96 (458)
T TIGR01279 26 FFLIVGTHTCA---------HFLQNALGVMIFAEPRFAVALLEESDLSSAAPAYEELKRVVEQIKRERPNPSVIFLLSSC 96 (458)
T ss_pred EEEEEHHHHHH---------HHHHHHHCCEEEECCCCCEEEEECHHHHHCCCCHHHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf 01322235778---------998755076155236521466520023211630789999999998508996499996168
Q ss_pred CC
Q ss_conf 66
Q gi|254780853|r 130 AN 131 (185)
Q Consensus 130 a~ 131 (185)
+.
T Consensus 97 t~ 98 (458)
T TIGR01279 97 TP 98 (458)
T ss_pred CC
T ss_conf 86
No 25
>COG4981 Enoyl reductase domain of yeast-type FAS1 [Lipid metabolism]
Probab=40.67 E-value=20 Score=17.76 Aligned_cols=33 Identities=27% Similarity=0.357 Sum_probs=24.5
Q ss_pred HCCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHH
Q ss_conf 08768855999984561288347752354652135663366678676
Q gi|254780853|r 35 HKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLER 81 (185)
Q Consensus 35 ~~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eR 81 (185)
.-+|+..-=+++-.|-|+-|||.-+ ..|||.+|
T Consensus 452 PVpfVPvID~d~~rwwr~DSLWQS~--------------~~ryda~~ 484 (717)
T COG4981 452 PVPFVPVIDKDVRRWWRSDSLWQSH--------------DVRYDADR 484 (717)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHH--------------HCCCCCCC
T ss_conf 8784202106899986055155432--------------01357770
No 26
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=39.39 E-value=22 Score=17.50 Aligned_cols=45 Identities=31% Similarity=0.476 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCC---------CCCCCEECCCCCC
Q ss_conf 34556999999998468666199853556688634---------7887220772223
Q gi|254780853|r 102 LTNKMASALRRVYDQMPEPRYVISMGSCANGGGYY---------HYSYSVVRGCDRI 149 (185)
Q Consensus 102 vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f---------~~sY~v~~g~d~~ 149 (185)
-+..++..|+++.++- +.++.||.=|.|||.| -+..++++.++-+
T Consensus 114 as~~i~~~l~~l~~~~---PV~v~v~~~AASGGY~IA~aAd~I~a~p~si~GSIGVi 167 (317)
T COG0616 114 ASELIARALKRLRAKK---PVVVSVGGYAASGGYYIALAADKIVADPSSITGSIGVI 167 (317)
T ss_pred HHHHHHHHHHHHHHCC---CEEEEECCCCCCHHHHHHHCCCEEEECCCCCCCCCCEE
T ss_conf 9999999999875329---89999887320289999840787987798602135017
No 27
>cd07125 ALDH_PutA-P5CDH Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA. The proline catabolic enzymes of the aldehyde dehydrogenase (ALDH) protein superfamily, proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH, (EC=1.5.1.12 )), catalyze the two-step oxidation of proline to glutamate; P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two enzymes are fused into the bifunctional flavoenzyme, proline utilization A (PutA) These enzymes play important roles in cellular redox control, superoxide generation, and apoptosis. In certain prokaryotes such as Escherichia coli, PutA is also a transcriptional repressor of the proline utilization genes.
Probab=36.60 E-value=39 Score=16.06 Aligned_cols=100 Identities=15% Similarity=0.208 Sum_probs=65.7
Q ss_pred EHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCC------HHHCCEEECCCCCCCCEEEEECCC-CHHHHHHHHHHH
Q ss_conf 5999984561288347752354652135663366678------676484870682206079971413-455699999999
Q gi|254780853|r 42 SVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYD------LERFGFAPRASPRQSDVMIVAGTL-TNKMASALRRVY 114 (185)
Q Consensus 42 ~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD------~eRfG~~~~~sPRqADvliVtG~v-T~km~~~l~~~y 114 (185)
-+|+..+.+-.... .+-|..|++.+-.-.-.+.|| .++..-.-++.|.+.|.. .||+ +.+-...++...
T Consensus 293 Dld~Aa~~~~~~~f--~naGQ~C~a~~Rv~V~~~i~d~f~~~l~~~~~~l~vGdp~d~~t~--~GPlis~~~~~~v~~~i 368 (518)
T cd07125 293 LPEQAVKDVVQSAF--GSAGQRCSALRLLYLQEEIAERFIEMLKGAMASLKVGDPWDLSTD--VGPLIDKPAGKLLRAHT 368 (518)
T ss_pred CHHHHHHHHHHHHH--CCCCCCCCCCCEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCC--CCCCCCHHHHHHHHHHH
T ss_conf 89999985343153--030898666960455030799999999987634866795667798--88686999999999999
Q ss_pred HHCCCCCEEEEECCCCCCCCCCCCCCCEECCC
Q ss_conf 84686661998535566886347887220772
Q gi|254780853|r 115 DQMPEPRYVISMGSCANGGGYYHYSYSVVRGC 146 (185)
Q Consensus 115 eqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~ 146 (185)
+....-..++.-|.+....|.|. ...++.++
T Consensus 369 ~~~~~~g~~v~~g~~~~~~G~f~-~PTvl~~v 399 (518)
T cd07125 369 ELMRGEAWLIAPAPLDDGNGYFV-APGIIEIV 399 (518)
T ss_pred HHHHHCCCEECCCCCCCCCCCEE-CCEEEECC
T ss_conf 99986597246778788998675-57898369
No 28
>TIGR00396 leuS_bact leucyl-tRNA synthetase; InterPro: IPR002302 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Leucyl tRNA synthetase (6.1.1.4 from EC) is an alpha monomer that belongs to class Ia. There are two different families of leucyl-tRNA synthetases. This family includes the eubacterial and mitochondrial synthetases. The crystal structure of leucyl-tRNA synthetase from the hyperthermophile Thermus thermophilus has an overall architecture that is similar to that of isoleucyl-tRNA synthetase, except that the putative editing domain is inserted at a different position in the primary structure. This feature is unique to prokaryote-like leucyl-tRNA synthetases, as is the presence of a novel additional flexibly inserted domain . ; GO: 0000166 nucleotide binding, 0004823 leucine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006429 leucyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=35.64 E-value=12 Score=18.99 Aligned_cols=13 Identities=38% Similarity=0.917 Sum_probs=7.5
Q ss_pred CCCCCCCEEECCC
Q ss_conf 2223223067488
Q gi|254780853|r 146 CDRIVPVDIYVPG 158 (185)
Q Consensus 146 ~d~~iPVDvyVPG 158 (185)
+++.+|||+||-|
T Consensus 558 ~~~wlPVD~YiGG 570 (916)
T TIGR00396 558 AEYWLPVDLYIGG 570 (916)
T ss_pred HHHCCCCCEEECC
T ss_conf 9755884410262
No 29
>PRK10949 protease 4; Provisional
Probab=35.64 E-value=31 Score=16.60 Aligned_cols=18 Identities=44% Similarity=0.776 Sum_probs=15.0
Q ss_pred CCEEEEECCCCCCCCCCC
Q ss_conf 661998535566886347
Q gi|254780853|r 120 PRYVISMGSCANGGGYYH 137 (185)
Q Consensus 120 PK~ViA~G~Ca~sGG~f~ 137 (185)
-..|++||+-|.|||.|-
T Consensus 397 KPVVvSMG~vAASGGYwI 414 (618)
T PRK10949 397 KPVVVSMGGMAASGGYWI 414 (618)
T ss_pred CCEEEEECCCCCCCCEEE
T ss_conf 979999701015662588
No 30
>TIGR01284 alt_nitrog_alph nitrogenase alpha chain; InterPro: IPR005974 The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene. Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I. This model represents the alpha chains of various forms of the nitrogen-fixing enzyme nitrogenase: vanadium-iron, iron-iron, and molybdenum-iron. Most examples of NifD, the molybdenum-iron type nitrogenase alpha chain, are excluded from this model and described instead by equivalog model IPR005972 from INTERPRO.; GO: 0016163 nitrogenase activity, 0051536 iron-sulfur cluster binding, 0009399 nitrogen fixation.
Probab=33.71 E-value=33 Score=16.48 Aligned_cols=138 Identities=15% Similarity=0.333 Sum_probs=92.1
Q ss_pred HCCCCCCCCCCCCHHH-HHHHHHHHHCC--------EEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHH---------
Q ss_conf 0477767633364257-77667541087--------68855999984561288347752354652135663---------
Q gi|254780853|r 11 ISGQSSCSLEKVDADF-SRISSEITHKG--------FLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQA--------- 72 (185)
Q Consensus 11 ~~~~~~~~~~~i~~~~-~~~~~~~~~~~--------~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~--------- 72 (185)
++.+.....+.+|.-. ..++..++++| +|.+.+.|.+ ...|--+.|-+-...++
T Consensus 18 ~K~~ge~~~d~lP~~n~~TIPG~~sERGCAfcGAK~VIgg~~KD~i--------h~iHgPvGCtaYdtw~TKRYptsqem 89 (468)
T TIGR01284 18 VKKKGEDEADALPAANLATIPGSLSERGCAFCGAKLVIGGALKDAI--------HVIHGPVGCTAYDTWQTKRYPTSQEM 89 (468)
T ss_pred ECCCCCCHHHHCCCCHHCCCCCCCCCHHHHHHCCCCCCCCCCCCEE--------EEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf 8178896244313102137886534001556067633252100145--------55306833365578852334455647
Q ss_pred -CCCCCCHHHCCEEE--CCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCEECCCCCC
Q ss_conf -36667867648487--068220607997141345569999999984686661998535566886347887220772223
Q gi|254780853|r 73 -SMPRYDLERFGFAP--RASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRI 149 (185)
Q Consensus 73 -~~p~yD~eRfG~~~--~~sPRqADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~d~~ 149 (185)
-++-|-++.|-+.+ -..-+.+||.. |- -.++...+..+.++||+=|.++.--+|++. =+=.|=-|+-+-|-+=
T Consensus 90 PDnsmfPi~~FnlKY~~~TD~kEshvVF--Gg-~k~Lk~~i~EAf~efP~ikr~~~Y~TC~Ta-LIGDDI~Aia~eV~ee 165 (468)
T TIGR01284 90 PDNSMFPIEKFNLKYVYATDLKESHVVF--GG-EKKLKRSILEAFKEFPEIKRMIVYATCATA-LIGDDIDAIAKEVMEE 165 (468)
T ss_pred CCCCCCCCCCCCEEEEEEECCEECCEEE--CH-HHHHHHHHHHHHHHCCCCCEEEEECCCCCC-CCCCCHHHHHHHHHHH
T ss_conf 8874165545000168850230032265--72-677777799998605433237784167874-3244478999998752
Q ss_pred CC-CEEECCCCC
Q ss_conf 22-306748876
Q gi|254780853|r 150 VP-VDIYVPGCP 160 (185)
Q Consensus 150 iP-VDvyVPGCP 160 (185)
+| |||++=-||
T Consensus 166 ~p~vDvf~~n~P 177 (468)
T TIGR01284 166 IPDVDVFAVNAP 177 (468)
T ss_pred CCCCCEEEEECC
T ss_conf 799428998177
No 31
>TIGR00075 hypD hydrogenase expression/formation protein HypD; InterPro: IPR002780 HypD is involved in the hyp operon which is needed for the activity of the three hydrogenase isoenzymes in Escherichia coli. HypD is one of the genes needed for formation of these enzymes . This protein has been found in Gram-negative and Gram-positive bacteria and Archaea. HypD contains many possible metal binding residues, which may bind to nickel. Transposon Tn5 insertions into HypD resulted in Rhizobium leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas .; GO: 0046872 metal ion binding.
Probab=30.46 E-value=33 Score=16.49 Aligned_cols=30 Identities=30% Similarity=0.579 Sum_probs=16.0
Q ss_pred CCCCCCCCEEEC---CCCCC--CHHHHHHHHHHHH
Q ss_conf 722232230674---88768--9899999999999
Q gi|254780853|r 145 GCDRIVPVDIYV---PGCPP--TAEALIYGILLLQ 174 (185)
Q Consensus 145 g~d~~iPVDvyV---PGCPP--rPeail~gl~~L~ 174 (185)
|+++++|-.+-+ ||||- .|..-||--+.|-
T Consensus 59 Gl~~LLPeN~~~v~GPGCPVCv~P~~~ID~a~~LA 93 (384)
T TIGR00075 59 GLRDLLPENVELVHGPGCPVCVTPMEEIDEAIELA 93 (384)
T ss_pred CHHHHCCCCEEEECCCCCCEEECCHHHHHHHHHHH
T ss_conf 63562876437734844881355737899999986
No 32
>pfam07796 DUF1638 Protein of unknown function (DUF1638). This family contains sequences covering an approximately 270 amino acid stretch of a group of hypothetical proteins. These proteins are expressed by archaeal species of the Methanosarcina genus.
Probab=29.71 E-value=50 Score=15.39 Aligned_cols=33 Identities=30% Similarity=0.467 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHCCCC--CEEEEECCCCCC-CCCC
Q ss_conf 55699999999846866--619985355668-8634
Q gi|254780853|r 104 NKMASALRRVYDQMPEP--RYVISMGSCANG-GGYY 136 (185)
Q Consensus 104 ~km~~~l~~~yeqmpeP--K~ViA~G~Ca~s-GG~f 136 (185)
.+..+.|....++|.+- +.+++.|.|.++ |++-
T Consensus 12 ~~L~~~v~~~i~~~~~~~d~Ill~YG~CG~g~g~l~ 47 (166)
T pfam07796 12 EKLKSAVYEAIDEMREFSDGILLFYGDCGTGLGLLE 47 (166)
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHH
T ss_conf 999999999999705026828999724888712699
No 33
>TIGR02306 RNA_lig_DRB0094 RNA ligase, DRB0094 family; InterPro: IPR012646 RNA repair, though not as well characterised as DNA repair, is an important component of many biological systems. These include the kinteoplastid RNA-editing process and the defence of bacteriophage T4 against tRNA damage caused by host nucleases. RNA ligase is an essential enzyme in the process of RNA repair . It is part of the broader nucleotidyl transferase superfamily which includes DNA ligase and RNA capping enzymes, and has the same basic mechanism as other memebers of this family. The RNA ligase family is divided into two distinct branches: the Rnl-1 like proteins, found only in viruses and fungi so far, and the Rnl2-like proteins which have been found in all three kingdoms of life. This entry represents a small group of known and predicted RNA ligases found in some bacterial and phage species. The best characterised memeber is found in Deinococcus radiodurans, a bacterium capable of withstanding a variety of adverse environmental conditions including extreme amounts of radiation. Ligase activity is apparently specific to nicks within either duplex RNA or an RNA:DNA hybrid and is dependenton divalent cations such as manganese . These proteins have a distinctive domain structure, lacking the C-terminal domain observed in other Rnl2-like ligases, and possesing a distinctive N-terminal domain not found in other ligases but which is important for catalytic activity..
Probab=29.53 E-value=27 Score=16.99 Aligned_cols=55 Identities=16% Similarity=0.135 Sum_probs=41.7
Q ss_pred EEHHHHHHHHHCCCCEEEEECCCCCCHHHHH--HCCCCCCHHHCCEEE-CCCCCCCCEEEE
Q ss_conf 5599998456128834775235465213566--336667867648487-068220607997
Q gi|254780853|r 41 TSVDQLVTWARTGSLMWMTFGLACCAVEMMQ--ASMPRYDLERFGFAP-RASPRQSDVMIV 98 (185)
Q Consensus 41 t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a--~~~p~yD~eRfG~~~-~~sPRqADvliV 98 (185)
+.+++++.-.. +-|-.=+|.|-.+|-.. -+-++.|+||++..+ +..++.||.-++
T Consensus 111 ~d~ae~LgI~k---wePP~p~tm~ge~e~~PPa~~~~~~D~E~~q~y~~~f~~kyag~~v~ 168 (374)
T TIGR02306 111 KDLAELLGITK---WEPPVPGTMAGEVETVPPADFLKKTDVERIQRYVDRFKEKYAGEKVV 168 (374)
T ss_pred CCHHHHCCCEE---ECCCCCCCCCCCCCCCCCHHHCCCCCHHHHCCCHHHCCHHHCCCCEE
T ss_conf 31886559358---72774688888888888067535567345142011003000786278
No 34
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg); InterPro: IPR004577 All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. The enzyme incises DNA at 8-oxoG residues, and excises 7,8-dihydro-8-oxoguanine from damaged DNA. It has beta-lyase activity that nicks DNA 3' to the lesion.; GO: 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006281 DNA repair, 0005634 nucleus.
Probab=28.32 E-value=14 Score=18.68 Aligned_cols=11 Identities=45% Similarity=0.625 Sum_probs=8.3
Q ss_pred CCCCCCCEEEC
Q ss_conf 22232230674
Q gi|254780853|r 146 CDRIVPVDIYV 156 (185)
Q Consensus 146 ~d~~iPVDvyV 156 (185)
-++++||||||
T Consensus 297 k~~avPVDVh~ 307 (379)
T TIGR00588 297 KPQAVPVDVHV 307 (379)
T ss_pred CCCCEEEHHHH
T ss_conf 89710111568
No 35
>TIGR01860 VNFD nitrogenase vanadium-iron protein, alpha chain; InterPro: IPR010142 This entry represents the alpha chain of the vanadium-containing component of the vanadium-iron nitrogenase compound I. The complex also includes a second alpha chain, two beta chains and two delta chains. Component I interacts with compound II also known as the iron-protein which transfers electrons to compound I where the catalysis occurs.; GO: 0016163 nitrogenase activity, 0051212 vanadium ion binding, 0051536 iron-sulfur cluster binding, 0009399 nitrogen fixation.
Probab=28.23 E-value=53 Score=15.23 Aligned_cols=100 Identities=21% Similarity=0.349 Sum_probs=77.6
Q ss_pred ECCCCCCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCC
Q ss_conf 23546521356633666786764848706822060799714134556999999998468666199853556688634788
Q gi|254780853|r 60 FGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHYS 139 (185)
Q Consensus 60 fg~aCC~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~~s 139 (185)
.|---|+..-.++---.-|-+.|-+.++-|--.-+--+|-|. -+++...++.+++++|+=|-.+..-+|+..= +=.+.
T Consensus 69 hGP~GCaydtWhtkryP~dn~~f~lky~Ws~d~ke~h~vfG~-ek~l~k~~~eaf~e~P~ikrm~vyttC~tal-iGd~~ 146 (461)
T TIGR01860 69 HGPVGCAYDTWHTKRYPSDNGNFQLKYVWSSDMKESHVVFGG-EKQLEKSIREAFKEFPDIKRMIVYTTCATAL-IGDDI 146 (461)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCEEEECC-HHHHHHHHHHHHHHCCHHEEEEEEECCCHHH-HCCCH
T ss_conf 056432212310244778777434799861367552267543-2557889999986220130043431133011-04656
Q ss_pred CCEECCC-CCCCCCEEECCCCCC
Q ss_conf 7220772-223223067488768
Q gi|254780853|r 140 YSVVRGC-DRIVPVDIYVPGCPP 161 (185)
Q Consensus 140 Y~v~~g~-d~~iPVDvyVPGCPP 161 (185)
-+|++.+ .+.-.||+++--||-
T Consensus 147 kav~~~~~~~~~dvd~f~veCPG 169 (461)
T TIGR01860 147 KAVVKKVQKELEDVDIFVVECPG 169 (461)
T ss_pred HHHHHHHHHCCCCCEEEEEECCC
T ss_conf 89999997403663089984687
No 36
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=26.66 E-value=57 Score=15.07 Aligned_cols=76 Identities=12% Similarity=0.033 Sum_probs=43.5
Q ss_pred HCCEEEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCEEECCCCCCCCEEEEECCCCHHHHHHHHHHH
Q ss_conf 08768855999984561288347752354652135663366678676484870682206079971413455699999999
Q gi|254780853|r 35 HKGFLVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFAPRASPRQSDVMIVAGTLTNKMASALRRVY 114 (185)
Q Consensus 35 ~~~~i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~~~~~sPRqADvliVtG~vT~km~~~l~~~y 114 (185)
+..+.-+.-.-+..|.++.-.=+...+..-= |.+.+--.....-+++|++|++|-...--...+.++.
T Consensus 13 ~G~i~dsn~~~l~~~l~~~G~~v~~~~iv~D------------d~~~i~~~l~~~~~~~DlIIttGG~s~g~~D~t~~~l 80 (133)
T cd00758 13 QGQIEDTNGPALEALLEDLGCEVIYAGVVPD------------DADSIRAALIEASREADLVLTTGGTGVGRRDVTPEAL 80 (133)
T ss_pred CCCEEEHHHHHHHHHHHHCCCEEEEEEEECC------------CHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCHHHHH
T ss_conf 7829973799999999988997989889897------------9999999999986149999993886679885189999
Q ss_pred HHCCCCCE
Q ss_conf 84686661
Q gi|254780853|r 115 DQMPEPRY 122 (185)
Q Consensus 115 eqmpePK~ 122 (185)
+++-+..+
T Consensus 81 ~~~g~~~~ 88 (133)
T cd00758 81 AELGEREA 88 (133)
T ss_pred HHHCCCEE
T ss_conf 98539288
No 37
>PRK10712 fructose-specific PTS system IIBC component; Provisional
Probab=25.64 E-value=60 Score=14.95 Aligned_cols=30 Identities=13% Similarity=0.161 Sum_probs=22.1
Q ss_pred CCHHHCCEEECCCCCCCCEEEEECCCCHHH
Q ss_conf 786764848706822060799714134556
Q gi|254780853|r 77 YDLERFGFAPRASPRQSDVMIVAGTLTNKM 106 (185)
Q Consensus 77 yD~eRfG~~~~~sPRqADvliVtG~vT~km 106 (185)
--.+|.|..++..|-+||+.++.|......
T Consensus 25 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 54 (563)
T PRK10712 25 AAARKAKLEIIDNPNDAELAIVLGDSIPND 54 (563)
T ss_pred HHHHHCCCCEECCCCCCCEEEEECCCCCCH
T ss_conf 999976972444720177899945766755
No 38
>COG3449 DNA gyrase inhibitor [DNA replication, recombination, and repair]
Probab=25.39 E-value=24 Score=17.23 Aligned_cols=42 Identities=29% Similarity=0.415 Sum_probs=33.8
Q ss_pred EEEEHHHHHHHHHCCCCEE---EEECCCCCCHHHHHHCCCCCCHH
Q ss_conf 8855999984561288347---75235465213566336667867
Q gi|254780853|r 39 LVTSVDQLVTWARTGSLMW---MTFGLACCAVEMMQASMPRYDLE 80 (185)
Q Consensus 39 i~t~~d~l~nW~R~~Slwp---~~fg~aCC~iE~~a~~~p~yD~e 80 (185)
+..++++|+.|+|.+-|-| ..||.+|=+-|....-.-|||+-
T Consensus 25 ~~~~~~~l~~W~~~~~l~p~~S~~~gI~~ddP~~tp~e~~R~D~c 69 (154)
T COG3449 25 LKQTFEQLIAWRRENGLLPEQSETLGIYQDDPDTTPAEKCRYDAC 69 (154)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCHHHCEEEEE
T ss_conf 889999999999972999987527887668978898788516589
No 39
>pfam09897 DUF2124 Uncharacterized protein conserved in archaea (DUF2124). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=23.38 E-value=66 Score=14.70 Aligned_cols=100 Identities=14% Similarity=0.338 Sum_probs=59.4
Q ss_pred EEHHHHHHHHHCCCC---EEEEECCCCCCHHHHHHCCCCCCHHHCCEEE--CCCCCCCCEEEEECCCCHH----HHHHHH
Q ss_conf 559999845612883---4775235465213566336667867648487--0682206079971413455----699999
Q gi|254780853|r 41 TSVDQLVTWARTGSL---MWMTFGLACCAVEMMQASMPRYDLERFGFAP--RASPRQSDVMIVAGTLTNK----MASALR 111 (185)
Q Consensus 41 t~~d~l~nW~R~~Sl---wp~~fg~aCC~iE~~a~~~p~yD~eRfG~~~--~~sPRqADvliVtG~vT~k----m~~~l~ 111 (185)
+....|+.++-|+-. +..+.+ ++| . +..+-+..+|+.+ -.++-++|++++.|-++.. ..+.++
T Consensus 32 ~PFaeL~~yaIR~~~~e~~FiP~~----~~e--~--a~~i~~~~~G~q~~~~~~~~~~D~lVlmGGLAMP~~~vt~e~v~ 103 (147)
T pfam09897 32 TPFAELFGYAIRDTVLEQYFIPDT----DEE--K--ARKIEVTDVGMQVLGENTDLNPDVLVLLGGLAMPKSGVTPEDVK 103 (147)
T ss_pred CCHHHHHEEEEECCCCCEEECCCC----CHH--H--CEEEEECCCCEEECCCCCCCCCCEEEEECCCCCCCCCCCHHHHH
T ss_conf 266965211320466654876788----966--8--22887358733771776789998999967655799998999999
Q ss_pred HHHHHCCCCCEEEEECCCCCCCCCCCCCCCEECCCCCCCCCEEECCC
Q ss_conf 99984686661998535566886347887220772223223067488
Q gi|254780853|r 112 RVYDQMPEPRYVISMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPG 158 (185)
Q Consensus 112 ~~yeqmpePK~ViA~G~Ca~sGG~f~~sY~v~~g~d~~iPVDvyVPG 158 (185)
.+-+..++.| .+|.|=.| +|.. .|.|+.|+-|.-|-|
T Consensus 104 ~li~k~~~~k---viGvCFms--~F~k-----agW~~~IdFD~iID~ 140 (147)
T pfam09897 104 ELIEKLNPKK---VIGVCFMS--MFEK-----AGWDDKIDFDLIIDA 140 (147)
T ss_pred HHHHHCCCCC---EEEEEHHH--HHHH-----CCCCCCCCCCEEEEC
T ss_conf 9999649987---89997499--8987-----699876675588764
No 40
>TIGR01862 N2-ase-Ialpha nitrogenase component I, alpha chain; InterPro: IPR010143 This entry represents all three varieties (Fe-Fe, Mo-Fe and V-Fe) of the component I alpha chain of nitrogenase. Nitrogenase (1.18.6.1 from EC) is the enzyme system responsible for biological nitrogen fixation. Nitrogenase is an oligomeric complex which consists of two components: component 2 is an homodimer of an iron-sulphur protein, while component 1 which contains the active site for the reduction of nitrogen to ammonia exists in three different forms: the molybdenum-iron containing protein (MoFe) is a hetero-tetramer consisting of two pairs of alpha (nifD) and beta (nifK) subunits; the vanadium-iron containing protein (VFe) is a hexamer of two pairs each of alpha (vnfD), beta (vnfK), and delta (vnfG) subunits; the third form seems to only contain iron and is a hexamer composed of alpha (anfD), beta (anfK), and delta (anfG) subunits. The alpha and beta chains of the three types of component 1 are evolutionary related and they are also related to proteins nifE and nifN, which are most probably involved in the iron-molybdenum cofactor biosynthesis .; GO: 0016163 nitrogenase activity, 0051536 iron-sulfur cluster binding, 0009399 nitrogen fixation.
Probab=21.40 E-value=64 Score=14.77 Aligned_cols=109 Identities=17% Similarity=0.381 Sum_probs=80.0
Q ss_pred CCEEEEEHHHHHH------------HHHCCCCEEEEECCCCCCHHHHHHCCCCCCHHHCCEE--ECCCCCCCCEEEEECC
Q ss_conf 8768855999984------------5612883477523546521356633666786764848--7068220607997141
Q gi|254780853|r 36 KGFLVTSVDQLVT------------WARTGSLMWMTFGLACCAVEMMQASMPRYDLERFGFA--PRASPRQSDVMIVAGT 101 (185)
Q Consensus 36 ~~~i~t~~d~l~n------------W~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~eRfG~~--~~~sPRqADvliVtG~ 101 (185)
+++|.+.+.|.+- |+.+....--..|+ ++.|-+|+|-.. |...-..+||..=
T Consensus 42 KgVi~GpiKD~iHi~HGPvGC~~ytw~tkRy~~~~~~g~-----------g~~fPiekF~~~Y~~~TD~~EsdiVFG--- 107 (510)
T TIGR01862 42 KGVIGGPIKDMIHISHGPVGCTYYTWGTKRYPSDNENGV-----------GANFPIEKFFLKYVFSTDMQESDIVFG--- 107 (510)
T ss_pred CCCCCCCCCCEEEEEECCCCCCCCCCCCEECCCCCCCCC-----------CCCCCHHHEEEEEEEEECCEECCEEEC---
T ss_conf 741232212678887467245766788301156888887-----------643553030113688513455014767---
Q ss_pred CCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCC-CCCCCEECCCCCCCC-CEEECCCCC
Q ss_conf 34556999999998468666199853556688634-788722077222322-306748876
Q gi|254780853|r 102 LTNKMASALRRVYDQMPEPRYVISMGSCANGGGYY-HYSYSVVRGCDRIVP-VDIYVPGCP 160 (185)
Q Consensus 102 vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f-~~sY~v~~g~d~~iP-VDvyVPGCP 160 (185)
--+|++..+..+++.+|+-|-+.---+|++ |+- .|=-||-+-+-+=+| |||+.=-||
T Consensus 108 G~kkLk~~I~EA~~~FP~~k~~~vY~TCp~--gLIGDDI~Ava~~v~~E~~~~dv~~~~cp 166 (510)
T TIGR01862 108 GEKKLKKAIHEAFEEFPEIKAISVYATCPT--GLIGDDIEAVAKEVSKEIGDVDVVAVNCP 166 (510)
T ss_pred HHHHHHHHHHHHHHHCCCCCCEEEEECCCC--EEECCCHHHHHHHHHHHCCCCCEEEEECC
T ss_conf 057888889999973742041478731672--00043478999997552689866988778
No 41
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type; InterPro: IPR004635 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. This group of sequences represent both long and short forms of the bacterial SppA and homologs found in the archaea and plants. Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signaling function. During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . ; GO: 0008233 peptidase activity, 0006508 proteolysis.
Probab=21.29 E-value=31 Score=16.65 Aligned_cols=37 Identities=32% Similarity=0.618 Sum_probs=21.0
Q ss_pred CCCC--HHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCC
Q ss_conf 4134--5569999999984686661998535566886347
Q gi|254780853|r 100 GTLT--NKMASALRRVYDQMPEPRYVISMGSCANGGGYYH 137 (185)
Q Consensus 100 G~vT--~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~ 137 (185)
|+|. ......|+++-.. ..=+.|+.||.-|.|||+|-
T Consensus 56 G~V~~S~Eiy~~l~~~~k~-~kkPVv~~~g~~aaSGGYYi 94 (224)
T TIGR00706 56 GTVVASEEIYEKLKKLKKE-AKKPVVASMGGVAASGGYYI 94 (224)
T ss_pred CCCHHHHHHHHHHHHHHHH-CCCEEEEEECCCCHHHHHHH
T ss_conf 9752268999999863453-08858998368322679999
No 42
>TIGR02539 SepCysS Sep-tRNA:Cys-tRNA synthase; InterPro: IPR013375 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Many archaeal species lack cysteinyl-tRNA synthetase, an essential enzyme that provides Cys-tRNA(Cys) in other organisms. Instead, in a two step pathway, tRNA-Cys is acylated with O-phosphoserine (Sep) to form Sep-tRNA(Cys), which is subsequently converted to Cys-tRNA(Cys) . This pathway is also thought to function as the sole route of cysteine biosynthesis in these organisms. Several other archaeal species use both this pathway and direct tRNA(Cys) aminoacylation to synthesize Cys-tRNA(Cys), but this pathway appears to be the only route for cysteine biosynthesis. Proteins in this entry catalyse the second step in this pathway using pyridoxal phosphate and a sulphur donor to synthesize Cys from Sep while attached to the tRNA..
Probab=20.78 E-value=45 Score=15.67 Aligned_cols=15 Identities=13% Similarity=-0.011 Sum_probs=5.1
Q ss_pred HHHHHHCCCCCCHHH
Q ss_conf 135663366678676
Q gi|254780853|r 67 VEMMQASMPRYDLER 81 (185)
Q Consensus 67 iE~~a~~~p~yD~eR 81 (185)
.|+..++|--|-+-|
T Consensus 177 ~gvPlLLNCAY~vGR 191 (381)
T TIGR02539 177 KGVPLLLNCAYTVGR 191 (381)
T ss_pred CCCCEEECCCCEEEE
T ss_conf 078622124505210
No 43
>TIGR00089 TIGR00089 RNA modification enzyme, MiaB family; InterPro: IPR005839 This entry represents a family defined on the basis of sequence similarity. Most of these proteins are not yet characterised, but those that are include CDK5 regulatory subunit-associated protein 1, which specifically inhibits CDK5 activation by CDK5R1 . MiaB, a tRNA modification enzyme . The size of proteins in this entry ranges from 47 to 61 kDa and they contain six conserved cysteines, three of which are clustered. .
Probab=20.75 E-value=75 Score=14.38 Aligned_cols=105 Identities=22% Similarity=0.260 Sum_probs=61.4
Q ss_pred EEEEECCCC--CCHHHHHHCCCCCCHHH-CCEEECCCCCCCCEEEEEC-----CCCHHHHHHHHHHHHHCCC-CC-EEEE
Q ss_conf 477523546--52135663366678676-4848706822060799714-----1345569999999984686-66-1998
Q gi|254780853|r 56 MWMTFGLAC--CAVEMMQASMPRYDLER-FGFAPRASPRQSDVMIVAG-----TLTNKMASALRRVYDQMPE-PR-YVIS 125 (185)
Q Consensus 56 wp~~fg~aC--C~iE~~a~~~p~yD~eR-fG~~~~~sPRqADvliVtG-----~vT~km~~~l~~~yeqmpe-PK-~ViA 125 (185)
+.-+||.+= -+-|.|+ -.+.- .|...+.+|-.|||+||.= .--.|+...|.++-++=++ |. ..|.
T Consensus 3 ~i~T~GC~~N~~Dse~m~-----~~L~~~~G~~~~~~~~~ADv~i~NTC~vr~~ae~k~~~~l~~~~~~k~~~~~d~~i~ 77 (455)
T TIGR00089 3 YIETYGCQMNEADSEIMA-----GLLKEAAGYEVTDDPEEADVIIINTCAVREKAEQKVRSELGELAKLKKKNPDDAKIV 77 (455)
T ss_pred EEEEECCCCCHHHHHHHH-----HHHHHHCCEEECCCCCCCCEEEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCEEE
T ss_conf 899706665578899999-----988874471433886644579985345651578999999999998277788885899
Q ss_pred ECCCCCCCCCCCCCCCEECC-CCCCCCCEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf 53556688634788722077-222322306748876898999999999999
Q gi|254780853|r 126 MGSCANGGGYYHYSYSVVRG-CDRIVPVDIYVPGCPPTAEALIYGILLLQK 175 (185)
Q Consensus 126 ~G~Ca~sGG~f~~sY~v~~g-~d~~iPVDvyVPGCPPrPeail~gl~~L~~ 175 (185)
+.-|-..=- . .- +.+..+||+++- |=..+-|.+.|-++.+
T Consensus 78 V~GC~aq~~-----~---~~l~~~~p~~d~~~G--~~~~~~~~~~i~~~~~ 118 (455)
T TIGR00089 78 VAGCLAQRE-----G---EELLKRIPEVDIVLG--TQDVERIPELINSAEE 118 (455)
T ss_pred EECCCCCCC-----H---HHHHHHCCCEEEEEC--CHHHHHHHHHHHHHHC
T ss_conf 846443238-----7---899964585699984--3137889999999863
No 44
>cd00069 GHB Glycoprotein hormone beta chain homologues. Gonadotropins; reproductive hormones consisting of two glycosylated chains (alpha and beta) of similar topology with Cysteine-knot motifs.
Probab=20.35 E-value=45 Score=15.64 Aligned_cols=15 Identities=33% Similarity=0.890 Sum_probs=10.7
Q ss_pred CCCCCEEECCCCCCC
Q ss_conf 232230674887689
Q gi|254780853|r 148 RIVPVDIYVPGCPPT 162 (185)
Q Consensus 148 ~~iPVDvyVPGCPPr 162 (185)
++.=.-+.+|||||.
T Consensus 53 ~~~y~t~~lpgCp~g 67 (102)
T cd00069 53 ELSYETVRLPGCPPG 67 (102)
T ss_pred EEEEEEEECCCCCCC
T ss_conf 159999988898799
Done!