Query 027294
Match_columns 225
No_of_seqs 142 out of 344
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 07:47:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027294.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027294hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3218 RNA polymerase, 25-kDa 100.0 3.9E-64 8.5E-69 431.8 16.6 170 36-206 6-178 (208)
2 PLN03111 DNA-directed RNA poly 100.0 4.8E-63 1E-67 428.7 16.5 177 32-209 1-179 (206)
3 PTZ00061 DNA-directed RNA poly 100.0 2.2E-61 4.7E-66 418.0 16.7 172 37-209 3-178 (205)
4 PF03871 RNA_pol_Rpb5_N: RNA p 100.0 2.4E-32 5.3E-37 210.5 0.5 89 32-121 1-92 (93)
5 PRK09570 rpoH DNA-directed RNA 99.7 7.2E-18 1.6E-22 127.6 2.6 48 162-209 3-50 (79)
6 PF01191 RNA_pol_Rpb5_C: RNA p 99.7 2.6E-17 5.5E-22 123.2 2.6 47 163-209 1-47 (74)
7 COG2012 RPB5 DNA-directed RNA 99.6 8.8E-17 1.9E-21 121.3 2.1 52 158-209 2-53 (80)
8 PF04471 Mrr_cat: Restriction 96.4 0.01 2.3E-07 44.3 6.0 76 85-162 36-112 (115)
9 TIGR00640 acid_CoA_mut_C methy 68.8 26 0.00055 28.5 7.1 87 46-150 19-105 (132)
10 PF03345 DDOST_48kD: Oligosacc 60.9 31 0.00067 33.7 7.1 86 46-150 14-101 (423)
11 cd02072 Glm_B12_BD B12 binding 59.9 47 0.001 27.3 7.0 75 47-139 17-91 (128)
12 PF13156 Mrr_cat_2: Restrictio 57.3 15 0.00032 30.4 3.7 81 69-150 16-99 (129)
13 PF05920 Homeobox_KN: Homeobox 56.0 3.3 7.2E-05 27.4 -0.3 24 173-196 7-30 (40)
14 PRK08485 DNA polymerase III su 50.4 39 0.00084 30.2 5.4 47 101-148 30-76 (206)
15 cd02067 B12-binding B12 bindin 48.6 98 0.0021 23.6 6.9 75 48-140 18-93 (119)
16 TIGR01501 MthylAspMutase methy 48.2 58 0.0013 26.9 5.8 75 46-138 18-92 (134)
17 cd02071 MM_CoA_mut_B12_BD meth 47.6 79 0.0017 24.7 6.3 73 49-140 19-92 (122)
18 PF13607 Succ_CoA_lig: Succiny 46.5 35 0.00075 28.0 4.3 79 47-145 15-98 (138)
19 PRK02261 methylaspartate mutas 45.8 1E+02 0.0022 25.1 6.9 72 48-138 22-94 (137)
20 KOG0975 Branched chain aminotr 43.7 11 0.00024 36.4 1.1 29 45-75 288-317 (379)
21 COG1787 Predicted endonuclease 43.2 54 0.0012 29.6 5.2 97 53-168 119-215 (217)
22 PRK09539 tRNA-splicing endonuc 42.9 1.4E+02 0.003 24.7 7.2 66 51-135 42-107 (124)
23 PF01939 DUF91: Protein of unk 41.3 46 0.001 30.0 4.5 59 98-159 149-211 (228)
24 PRK09545 znuA high-affinity zi 40.2 1.9E+02 0.0041 26.5 8.5 44 105-150 232-275 (311)
25 PF01963 TraB: TraB family; I 38.5 13 0.00029 31.8 0.7 15 48-62 244-258 (259)
26 PRK08058 DNA polymerase III su 38.0 1.3E+02 0.0027 27.7 7.0 96 99-195 80-187 (329)
27 PRK03298 hypothetical protein; 35.3 66 0.0014 29.2 4.5 39 110-150 161-202 (224)
28 PF08479 POTRA_2: POTRA domain 33.9 34 0.00075 24.5 2.1 53 10-63 5-57 (76)
29 COG4889 Predicted helicase [Ge 33.5 76 0.0016 34.9 5.2 101 85-191 61-179 (1518)
30 PRK04280 arginine repressor; P 32.7 94 0.002 25.9 4.8 88 48-150 23-113 (148)
31 TIGR01120 rpiB ribose 5-phosph 31.7 1.1E+02 0.0024 25.6 5.1 20 43-62 11-30 (143)
32 PRK05571 ribose-5-phosphate is 31.4 1.1E+02 0.0024 25.7 5.1 20 43-62 12-31 (148)
33 COG1637 Predicted nuclease of 29.9 76 0.0017 29.2 4.1 57 99-157 175-238 (253)
34 cd02070 corrinoid_protein_B12- 29.1 2.5E+02 0.0054 23.8 7.0 75 48-141 101-178 (201)
35 PF01297 TroA: Periplasmic sol 29.0 3.2E+02 0.007 23.6 7.8 44 104-149 178-221 (256)
36 cd01017 AdcA Metal binding pro 28.2 4.3E+02 0.0092 23.5 9.4 44 105-150 200-243 (282)
37 PF11985 DUF3486: Protein of u 28.0 39 0.00085 28.5 1.8 27 45-76 14-40 (180)
38 KOG0460 Mitochondrial translat 27.1 1.3E+02 0.0029 29.5 5.4 83 112-202 129-216 (449)
39 PF11513 TA0956: Thermoplasma 26.9 2E+02 0.0044 23.1 5.5 57 69-128 45-105 (110)
40 PRK05564 DNA polymerase III su 26.7 1.4E+02 0.0031 26.8 5.4 43 105-147 69-114 (313)
41 PRK14042 pyruvate carboxylase 26.2 2.2E+02 0.0047 29.2 6.9 127 5-144 38-186 (596)
42 KOG1232 Proteins containing th 25.8 54 0.0012 32.5 2.5 62 11-73 332-404 (511)
43 PF01650 Peptidase_C13: Peptid 25.3 2.1E+02 0.0046 25.8 6.1 48 92-139 102-160 (256)
44 TIGR00678 holB DNA polymerase 25.2 2.7E+02 0.0059 22.8 6.3 91 102-193 69-171 (188)
45 cd01019 ZnuA Zinc binding prot 25.0 5E+02 0.011 23.2 9.1 40 104-146 207-246 (286)
46 PF13167 GTP-bdg_N: GTP-bindin 24.7 1.4E+02 0.0029 23.4 4.1 53 109-165 41-93 (95)
47 TIGR03798 ocin_TIGR03798 bacte 24.4 73 0.0016 22.5 2.4 21 46-66 27-47 (64)
48 TIGR02370 pyl_corrinoid methyl 24.2 3.3E+02 0.0072 23.2 6.9 76 47-141 102-180 (197)
49 PTZ00215 ribose 5-phosphate is 23.7 2.1E+02 0.0044 24.2 5.3 20 43-62 14-35 (151)
50 cd01900 YchF YchF subfamily. 23.3 46 0.00099 30.4 1.5 25 177-201 244-268 (274)
51 COG1110 Reverse gyrase [DNA re 23.0 2.6E+02 0.0056 31.1 7.0 72 108-190 107-178 (1187)
52 PRK08622 galactose-6-phosphate 22.7 1.9E+02 0.0041 25.1 5.0 20 43-62 12-31 (171)
53 cd01018 ZntC Metal binding pro 21.8 5.6E+02 0.012 22.6 9.0 44 105-150 197-240 (266)
54 cd02069 methionine_synthase_B1 21.5 3.4E+02 0.0074 23.6 6.5 77 47-142 106-183 (213)
55 COG3373 Uncharacterized protei 20.9 49 0.0011 26.5 1.0 38 16-57 58-101 (108)
No 1
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=100.00 E-value=3.9e-64 Score=431.77 Aligned_cols=170 Identities=40% Similarity=0.679 Sum_probs=167.2
Q ss_pred hhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC-CCCCceEEEeecCCCCCCcEEEEecCCCccchhhH
Q 027294 36 SRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVI 114 (225)
Q Consensus 36 ~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~-p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~I 114 (225)
+.|++||||+|||++||||||||.|+++|+++++++|+++||+. |+|++|+|+|.|++||+++|+|||+++++||+|+|
T Consensus 6 e~E~~rl~~ar~T~~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk~~ 85 (208)
T KOG3218|consen 6 EEEIYRLYLARKTAMQMLRDRGYTVTQEELDLTLEEFKARYGDKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVKTM 85 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCccccHHHhhhhHHHHHHHhccCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHHHH
Confidence 78999999999999999999999999999999999999999998 99999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc--cceeeeecceeeeecccccccCCcccCChHHHHHHHHHcCCC
Q 027294 115 RSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE 192 (225)
Q Consensus 115 r~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~--~~IEvF~E~ELl~nit~H~lVPkH~vl~~eEk~~lL~~y~i~ 192 (225)
|.++.+| .++|+++||||+|+++||+|++++..++ |.||+|+|+||+||||+|+|||||++||+|||++||++|+++
T Consensus 86 k~~~~~~-~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l~ 164 (208)
T KOG3218|consen 86 KTYVIQM-QSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKLK 164 (208)
T ss_pred HHHHHHH-HhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcCC
Confidence 9999999 8899999999999999999999999998 999999999999999999999999999999999999999999
Q ss_pred CCCccceecCCCcc
Q 027294 193 EKQQHNRHLCWTTT 206 (225)
Q Consensus 193 ~~QLP~I~~~d~~~ 206 (225)
++|||||+.+||-.
T Consensus 165 e~qLPRIq~~Dpva 178 (208)
T KOG3218|consen 165 ETQLPRIQKKDPVA 178 (208)
T ss_pred cccCCeeeccChHH
Confidence 99999999999853
No 2
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=100.00 E-value=4.8e-63 Score=428.74 Aligned_cols=177 Identities=47% Similarity=0.741 Sum_probs=172.0
Q ss_pred CCCChhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccch
Q 027294 32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKV 111 (225)
Q Consensus 32 md~~~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgv 111 (225)
|+.++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+.|+|++|+|+|.+.+||+++|+|||+++++||+
T Consensus 1 ~~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~r~~l~~~~~~~~d~~~~i~V~F~~~~kvgv 80 (206)
T PLN03111 1 MDTGSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPKRSDPSKKILVFFPEEEKVGV 80 (206)
T ss_pred CCcchHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHHcCCcCHHHcEeeeecCCCCCCcEEEEeCCCCccCH
Confidence 46678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc--cceeeeecceeeeecccccccCCcccCChHHHHHHHHHc
Q 027294 112 NVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKY 189 (225)
Q Consensus 112 K~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~--~~IEvF~E~ELl~nit~H~lVPkH~vl~~eEk~~lL~~y 189 (225)
|+||.|+++| +++|++|||||+|+++||+|++++.+++ ++||+|+|+||+||||+|+|||+|++||+|||++||++|
T Consensus 81 k~ir~~~~~~-~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y 159 (206)
T PLN03111 81 KTIKTYAERM-KDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRY 159 (206)
T ss_pred HHHHHHHHHH-hhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHc
Confidence 9999999999 9999999999999999999999999996 999999999999999999999999999999999999999
Q ss_pred CCCCCCccceecCCCccccC
Q 027294 190 SIEEKQQHNRHLCWTTTKQS 209 (225)
Q Consensus 190 ~i~~~QLP~I~~~d~~~~~~ 209 (225)
+++++|||||+.+||..+-+
T Consensus 160 ~i~~~qLPrI~~~DPvary~ 179 (206)
T PLN03111 160 TVKETQLPRIQVSDPIARYY 179 (206)
T ss_pred CCCHHHCCcccccChhhHhc
Confidence 99999999999999987653
No 3
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=2.2e-61 Score=417.96 Aligned_cols=172 Identities=33% Similarity=0.472 Sum_probs=165.8
Q ss_pred hhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC-CCCCceEEEeecCCCCCCcEEEEecC-CCccchhhH
Q 027294 37 RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKRILVVFCG-PGIVKVNVI 114 (225)
Q Consensus 37 ~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~-p~r~~L~i~~~~~~dp~~kI~VfF~~-e~kVgvK~I 114 (225)
+++.||||+|||++|||+||||.|+++|+++|+++|+++||+. +.|++|+|+|++.+||+++|+|||++ +++||+|+|
T Consensus 3 ~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~i 82 (205)
T PTZ00061 3 DSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKPI 82 (205)
T ss_pred HHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHHH
Confidence 6789999999999999999999999999999999999999987 47899999999999999999999998 579999999
Q ss_pred HHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc--cceeeeecceeeeecccccccCCcccCChHHHHHHHHHcCCC
Q 027294 115 RSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE 192 (225)
Q Consensus 115 r~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~--~~IEvF~E~ELl~nit~H~lVPkH~vl~~eEk~~lL~~y~i~ 192 (225)
|.|+++| +++|++|||||+|+++||+|++++.+++ ++||+|+|+||+||||+|+|||+|++||+|||++||++|+++
T Consensus 83 r~~~~~~-~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i~ 161 (205)
T PTZ00061 83 RELTEKM-EEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVK 161 (205)
T ss_pred HHHHHHH-hhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCCC
Confidence 9999999 9999999999999999999999999996 899999999999999999999999999999999999999999
Q ss_pred CCCccceecCCCccccC
Q 027294 193 EKQQHNRHLCWTTTKQS 209 (225)
Q Consensus 193 ~~QLP~I~~~d~~~~~~ 209 (225)
++|||||+.+||..+-+
T Consensus 162 ~~qLPrI~~~DPvary~ 178 (205)
T PTZ00061 162 ESQLPRIQSADPVARYF 178 (205)
T ss_pred HHHCCcccccChhhHhc
Confidence 99999999999987643
No 4
>PF03871 RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal domain; InterPro: IPR005571 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region, plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) (IPR000783 from INTERPRO) [, , , ]. This entry represents the N-terminal domain of eukaryotic RPB5, which has a core structure consisting of 3 layers alpha/beta/alpha []. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure []. This module is important for positioning the downstream DNA.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3H0G_Q 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E 1I50_E ....
Probab=99.97 E-value=2.4e-32 Score=210.45 Aligned_cols=89 Identities=42% Similarity=0.722 Sum_probs=74.7
Q ss_pred CCCChhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCC---CCCCCceEEEeecCCCCCCcEEEEecCCCc
Q 027294 32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ---DPDVDRLRISISHQSDPSKRILVVFCGPGI 108 (225)
Q Consensus 32 md~~~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~---~p~r~~L~i~~~~~~dp~~kI~VfF~~e~k 108 (225)
|| ++.|++|||||||||+|||+||||.|+++|+++|+++|+++||+ .|+|++|+|++.+.+||+++|+|||+++++
T Consensus 1 m~-~~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~k 79 (93)
T PF03871_consen 1 MD-DDEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDKIFVFFPEEPK 79 (93)
T ss_dssp ---TTHHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--EEEEEE-SSSC
T ss_pred Cc-cHHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCeEEEEeCCCCC
Confidence 45 44899999999999999999999999999999999999999998 799999999999999999999999999999
Q ss_pred cchhhHHHHHHHH
Q 027294 109 VKVNVIRSIISQI 121 (225)
Q Consensus 109 VgvK~Ir~~~e~m 121 (225)
||+|+||.|+++|
T Consensus 80 vgvk~Ir~~~~~m 92 (93)
T PF03871_consen 80 VGVKTIRKYCERM 92 (93)
T ss_dssp ESCCCCHHHCHHH
T ss_pred cCHHHHHHHHHhc
Confidence 9999999999998
No 5
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=99.69 E-value=7.2e-18 Score=127.59 Aligned_cols=48 Identities=29% Similarity=0.463 Sum_probs=45.8
Q ss_pred eeecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCccccC
Q 027294 162 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQS 209 (225)
Q Consensus 162 l~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~~ 209 (225)
.||||+|+|||+|++||+||+++||++|+++++|||||+.+||..+..
T Consensus 3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~ 50 (79)
T PRK09570 3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAI 50 (79)
T ss_pred ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhc
Confidence 589999999999999999999999999999999999999999987754
No 6
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=99.66 E-value=2.6e-17 Score=123.20 Aligned_cols=47 Identities=40% Similarity=0.558 Sum_probs=39.7
Q ss_pred eecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCccccC
Q 027294 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQS 209 (225)
Q Consensus 163 ~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~~ 209 (225)
||||+|+|||+|++||+||+++||++|+++++|||||+.+||..+.+
T Consensus 1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~ 47 (74)
T PF01191_consen 1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSSDPVARYL 47 (74)
T ss_dssp S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETTSHHHHHT
T ss_pred CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCcccccChhhhhc
Confidence 79999999999999999999999999999999999999999987644
No 7
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=99.63 E-value=8.8e-17 Score=121.26 Aligned_cols=52 Identities=29% Similarity=0.379 Sum_probs=48.5
Q ss_pred cceeeeecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCccccC
Q 027294 158 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQS 209 (225)
Q Consensus 158 E~ELl~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~~ 209 (225)
++.+.||+++|+|||+|++||+||++++|++|+|+++|||||+.+||..+.+
T Consensus 2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~DPva~~l 53 (80)
T COG2012 2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKASDPVAKAL 53 (80)
T ss_pred ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCcccccChhHHHc
Confidence 5778999999999999999999999999999999999999999999966543
No 8
>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.
Probab=96.39 E-value=0.01 Score=44.30 Aligned_cols=76 Identities=21% Similarity=0.270 Sum_probs=41.6
Q ss_pred eEEEeecCCCCCCcEEEEecC-CCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhccceeeeecceee
Q 027294 85 LRISISHQSDPSKRILVVFCG-PGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLL 162 (225)
Q Consensus 85 L~i~~~~~~dp~~kI~VfF~~-e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~~~IEvF~E~ELl 162 (225)
.-+.+.+......+++|-+-. ..+++.+.|+.++..+ ...+..++|||+.+++|+.|++.+.... .|+++.-++|.
T Consensus 36 iDi~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~-~~~~~~~~iivt~~~~t~~a~~~~~~~~-~I~l~d~~~L~ 112 (115)
T PF04471_consen 36 IDIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKA-KKYGADKGIIVTSSGFTPEAKEFAEKFK-NIELIDGEDLQ 112 (115)
T ss_dssp EEEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHH-GGGT-SEEEEE-SSEE-HHHHHHHH---------------
T ss_pred EEEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhh-hccCCCEEEEEECCcCCHHHHHHHHhhc-ccccccccccc
Confidence 344444433232456666633 3589999999999999 8889999999999999999999887743 57766666553
No 9
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=68.80 E-value=26 Score=28.50 Aligned_cols=87 Identities=8% Similarity=0.140 Sum_probs=55.9
Q ss_pred HHHHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcC
Q 027294 46 RRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125 (225)
Q Consensus 46 rrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~e 125 (225)
.+-+.-||++-||.|.+.-...|.++|.+..-+. +-+ ...+ |.-..-.+..++.+++.+ .++
T Consensus 19 ~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e~-~ad-ii~i---------------Ssl~~~~~~~~~~~~~~L-~~~ 80 (132)
T TIGR00640 19 AKVIATAYADLGFDVDVGPLFQTPEEIARQAVEA-DVH-VVGV---------------SSLAGGHLTLVPALRKEL-DKL 80 (132)
T ss_pred HHHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHc-CCC-EEEE---------------cCchhhhHHHHHHHHHHH-Hhc
Confidence 3556789999999999988888999998875321 111 1111 222223456688888888 777
Q ss_pred CCcEEEEEEcCCCCHHHHHHHhhhc
Q 027294 126 TLTGLILILQNQITSQATKAVGLFQ 150 (225)
Q Consensus 126 nv~r~IlVvq~~lT~~Ark~i~~~~ 150 (225)
+.....+++.+.+.+.-...+.+++
T Consensus 81 g~~~i~vivGG~~~~~~~~~l~~~G 105 (132)
T TIGR00640 81 GRPDILVVVGGVIPPQDFDELKEMG 105 (132)
T ss_pred CCCCCEEEEeCCCChHhHHHHHHCC
Confidence 7765556666656554445555554
No 10
>PF03345 DDOST_48kD: Oligosaccharyltransferase 48 kDa subunit beta; InterPro: IPR005013 During N-linked glycosylation of proteins, oligosaccharide chains are assembled on the carrier molecule dolichyl pyrophosphate in the following order: 2 molecules of N-acetylglucosamine (GlcNAc), 9 molecules of mannose, and 3 molecules of glucose. These 14-residue oligosaccharide cores are then transferred to asparagine residues on nascent polypeptide chains in the endoplasmic reticulum (ER). As proteins progress through the Golgi apparatus, the oligosaccharide cores are modified by trimming and extension to generate a diverse array of glycosylated proteins [, ]. The oligosaccharyl transferase complex (OST complex) 2.4.1.119 from EC transfers 14-sugar branched oligosaccharides from dolichyl pyrophosphate to asparagine residues []. The complex contains nine protein subunits: Ost1p, Ost2p, Ost3p, Ost4p, Ost5p, Ost6p, Stt3p, Swp1p, and Wbp1p, all of which are integral membrane proteins of the ER. The OST complex interacts with the Sec61p pore complex [] involved in protein import into the ER. This entry represents subunits OST3 and OST6. OST3 is homologous to OST6 [], and several lines of evidence indicate that they are alternative members of the OST complex. Disruption of both OST3 and OST6 causes severe underglycosylation of soluble and membrane-bound glycoproteins and a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation []. This entry also includes the magnesium transporter protein 1, also known as OST3 homologue B, which might be involved in N-glycosylation through its association with the oligosaccharyl transferase (OST) complex. Wbp1p is the beta subunit of the OST complex, one of the original six subunits purified []. Wbp1 is essential [, ], but conditional mutants have decreased transferase activity [, ]. Wbp1p is homologous to mammalian OST48 [].; GO: 0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity, 0018279 protein N-linked glycosylation via asparagine, 0005789 endoplasmic reticulum membrane
Probab=60.90 E-value=31 Score=33.69 Aligned_cols=86 Identities=19% Similarity=0.289 Sum_probs=50.2
Q ss_pred HHHHHHHhcCCCCccChhhhc-cCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhc
Q 027294 46 RRTVLEMLKDRGYAVALSEIN-LSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNR 124 (225)
Q Consensus 46 rrTv~EMl~DRGY~V~~~El~-~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~ 124 (225)
..+.++.|++|||.+.=...+ -++.=| +||+ ...+-|.+.....+. |. +.++++.|-+|++.=
T Consensus 14 yS~Ff~~L~~rg~~l~~~~~~d~~l~L~--~~ge-~~YD~LIif~~~~k~--------~g--~~ls~~~ll~Fvd~G--- 77 (423)
T PF03345_consen 14 YSTFFNSLKERGYELTFKSADDESLSLF--KYGE-RLYDHLIIFPPSVKE--------FG--GSLSPKTLLDFVDNG--- 77 (423)
T ss_pred HHHHHHHHHhCCCEEEEecCCCCCcchh--hCCh-hhcceEEEeCCcccc--------cC--CCCCHHHHHHHHhCC---
Confidence 678899999999999542221 122323 3343 234455444332222 11 347788887775542
Q ss_pred CCCcEEEEEEcCC-CCHHHHHHHhhhc
Q 027294 125 DTLTGLILILQNQ-ITSQATKAVGLFQ 150 (225)
Q Consensus 125 env~r~IlVvq~~-lT~~Ark~i~~~~ 150 (225)
...+++..+. ++...|..+.+++
T Consensus 78 ---gNilv~~s~~~~~~~ir~~~~E~g 101 (423)
T PF03345_consen 78 ---GNILVAGSSDAIPDSIREFANELG 101 (423)
T ss_pred ---CcEEEEeCCCcCcHHHHHHHHHCC
Confidence 3355566666 7777788888876
No 11
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=59.86 E-value=47 Score=27.27 Aligned_cols=75 Identities=11% Similarity=0.118 Sum_probs=51.2
Q ss_pred HHHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCC
Q 027294 47 RTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDT 126 (225)
Q Consensus 47 rTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~en 126 (225)
+-+.-||++.||.|-+--+..+.++|.+..-+. +-+-+.+++ --.-.+..++.+++.+ .+.+
T Consensus 17 niv~~~L~~~GfeVidLG~~v~~e~~v~aa~~~-~adiVglS~----------------L~t~~~~~~~~~~~~l-~~~g 78 (128)
T cd02072 17 KILDHAFTEAGFNVVNLGVLSPQEEFIDAAIET-DADAILVSS----------------LYGHGEIDCKGLREKC-DEAG 78 (128)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEec----------------cccCCHHHHHHHHHHH-HHCC
Confidence 455569999999999988888999998876332 111222222 1123456788888888 8889
Q ss_pred CcEEEEEEcCCCC
Q 027294 127 LTGLILILQNQIT 139 (225)
Q Consensus 127 v~r~IlVvq~~lT 139 (225)
+....+++.+.+.
T Consensus 79 l~~v~vivGG~~~ 91 (128)
T cd02072 79 LKDILLYVGGNLV 91 (128)
T ss_pred CCCCeEEEECCCC
Confidence 8666667777753
No 12
>PF13156 Mrr_cat_2: Restriction endonuclease
Probab=57.26 E-value=15 Score=30.41 Aligned_cols=81 Identities=15% Similarity=0.155 Sum_probs=52.3
Q ss_pred HHHHHHHhCCCCCCCceEEEeecCCCCC-CcEEEEe-cCCCccchhhHHHHHHHHhhcCCCcEEEEEEc-CCCCHHHHHH
Q 027294 69 VQDFRAIYGQDPDVDRLRISISHQSDPS-KRILVVF-CGPGIVKVNVIRSIISQIVNRDTLTGLILILQ-NQITSQATKA 145 (225)
Q Consensus 69 ldeF~~~yg~~p~r~~L~i~~~~~~dp~-~kI~VfF-~~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq-~~lT~~Ark~ 145 (225)
..+|-.+++....---+-+++..+++.. -.|.+-| ..+.+|..+.|-.|+... ....+.+.|||.- .++++-|.++
T Consensus 16 w~dwp~~~~~~~~DtGIDLVA~~~~~g~~~AIQCKfY~~~~~I~k~didSF~s~s-gk~~f~~rliisTt~~~s~nAe~~ 94 (129)
T PF13156_consen 16 WSDWPERYGWGGKDTGIDLVARTRDGGEYWAIQCKFYDPDHTIQKSDIDSFFSAS-GKSRFSRRLIISTTDKWSKNAEKA 94 (129)
T ss_pred hhhhhHhhCCCCCCCCEeEEEEEcCCCcEEEEEEEeeCCCceEcHHHhhHHHHhc-CCccccCcEEEEcCcHhhHHHHHH
Confidence 4556655543211123455555444322 2355555 444799999999999998 7778888887744 4789999888
Q ss_pred Hhhhc
Q 027294 146 VGLFQ 150 (225)
Q Consensus 146 i~~~~ 150 (225)
+..-.
T Consensus 95 l~~q~ 99 (129)
T PF13156_consen 95 LENQS 99 (129)
T ss_pred HHcCC
Confidence 87654
No 13
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=55.97 E-value=3.3 Score=27.41 Aligned_cols=24 Identities=29% Similarity=0.375 Sum_probs=18.6
Q ss_pred CcccCChHHHHHHHHHcCCCCCCc
Q 027294 173 KHQVLTDQEKEKLLKKYSIEEKQQ 196 (225)
Q Consensus 173 kH~vl~~eEk~~lL~~y~i~~~QL 196 (225)
.|+..|++||++|.+..++...|+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi 30 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQI 30 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHH
Confidence 688999999999999999887765
No 14
>PRK08485 DNA polymerase III subunit delta'; Validated
Probab=50.36 E-value=39 Score=30.19 Aligned_cols=47 Identities=15% Similarity=0.147 Sum_probs=31.7
Q ss_pred EEecCCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhh
Q 027294 101 VVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGL 148 (225)
Q Consensus 101 VfF~~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~ 148 (225)
.||..+ .+||..||.+++.+....+-.+.||.--..+|..|..++-.
T Consensus 30 ~~f~~~-~i~Vd~iReii~~~~~~~~~~k~iI~~a~~l~~~A~NaLLK 76 (206)
T PRK08485 30 RFFIKE-EFKIEDAKEVIAEAYIAESEEKIIVIAAPSYGIEAQNALLK 76 (206)
T ss_pred EEECCC-CCCHHHHHHHHHHHhhCCCCcEEEEEchHhhCHHHHHHHHH
Confidence 344333 69999999999997333344555655556789888776643
No 15
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=48.58 E-value=98 Score=23.61 Aligned_cols=75 Identities=15% Similarity=0.263 Sum_probs=44.8
Q ss_pred HHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCC
Q 027294 48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTL 127 (225)
Q Consensus 48 Tv~EMl~DRGY~V~~~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~env 127 (225)
-+..+|+..||.|..-..+++.++|.+.... .+|. +++ ++....-....++.+++.+ .+.+-
T Consensus 18 ~~~~~l~~~G~~V~~lg~~~~~~~l~~~~~~--------------~~pd--vV~-iS~~~~~~~~~~~~~i~~l-~~~~~ 79 (119)
T cd02067 18 IVARALRDAGFEVIDLGVDVPPEEIVEAAKE--------------EDAD--AIG-LSGLLTTHMTLMKEVIEEL-KEAGL 79 (119)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHH--------------cCCC--EEE-EeccccccHHHHHHHHHHH-HHcCC
Confidence 4567999999999876677888898776432 1111 111 1222223457788888888 66655
Q ss_pred -cEEEEEEcCCCCH
Q 027294 128 -TGLILILQNQITS 140 (225)
Q Consensus 128 -~r~IlVvq~~lT~ 140 (225)
+-.|+|-....+.
T Consensus 80 ~~~~i~vGG~~~~~ 93 (119)
T cd02067 80 DDIPVLVGGAIVTR 93 (119)
T ss_pred CCCeEEEECCCCCh
Confidence 3334444444444
No 16
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=48.22 E-value=58 Score=26.87 Aligned_cols=75 Identities=11% Similarity=0.127 Sum_probs=50.2
Q ss_pred HHHHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcC
Q 027294 46 RRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125 (225)
Q Consensus 46 rrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~e 125 (225)
.+-+.-||++.||.|-.-=...+.++|.+..-+. +.+-+-++.- -.-.+..++.+++.+ .++
T Consensus 18 k~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~~~-~adiVglS~l----------------~~~~~~~~~~~~~~l-~~~ 79 (134)
T TIGR01501 18 NKILDHAFTNAGFNVVNLGVLSPQEEFIKAAIET-KADAILVSSL----------------YGHGEIDCKGLRQKC-DEA 79 (134)
T ss_pred HHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEecc----------------cccCHHHHHHHHHHH-HHC
Confidence 3567789999999999877788999998875322 1222222221 113345688888888 888
Q ss_pred CCcEEEEEEcCCC
Q 027294 126 TLTGLILILQNQI 138 (225)
Q Consensus 126 nv~r~IlVvq~~l 138 (225)
++....+|+.+.+
T Consensus 80 gl~~~~vivGG~~ 92 (134)
T TIGR01501 80 GLEGILLYVGGNL 92 (134)
T ss_pred CCCCCEEEecCCc
Confidence 8866666676653
No 17
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=47.60 E-value=79 Score=24.73 Aligned_cols=73 Identities=12% Similarity=0.159 Sum_probs=46.2
Q ss_pred HHHHhcCCCCccChhhhccCHHHHHHHhCCC-CCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCC
Q 027294 49 VLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTL 127 (225)
Q Consensus 49 v~EMl~DRGY~V~~~El~~sldeF~~~yg~~-p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~env 127 (225)
+.-|++..||.|..--.+.+.++|.+.-.+. ++ - |.+.+.. .-....++.+++++ .+.+.
T Consensus 19 ~~~~l~~~G~~vi~lG~~vp~e~~~~~a~~~~~d--~--------------V~iS~~~--~~~~~~~~~~~~~L-~~~~~ 79 (122)
T cd02071 19 IARALRDAGFEVIYTGLRQTPEEIVEAAIQEDVD--V--------------IGLSSLS--GGHMTLFPEVIELL-RELGA 79 (122)
T ss_pred HHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCC--E--------------EEEcccc--hhhHHHHHHHHHHH-HhcCC
Confidence 3458999999998876777888987764321 22 1 2222222 24456688888998 77777
Q ss_pred cEEEEEEcCCCCH
Q 027294 128 TGLILILQNQITS 140 (225)
Q Consensus 128 ~r~IlVvq~~lT~ 140 (225)
....+++.+...+
T Consensus 80 ~~i~i~~GG~~~~ 92 (122)
T cd02071 80 GDILVVGGGIIPP 92 (122)
T ss_pred CCCEEEEECCCCH
Confidence 5555566555443
No 18
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=46.54 E-value=35 Score=28.02 Aligned_cols=79 Identities=19% Similarity=0.390 Sum_probs=38.5
Q ss_pred HHHHHHhcCCCCccCh-----hhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHH
Q 027294 47 RTVLEMLKDRGYAVAL-----SEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQI 121 (225)
Q Consensus 47 rTv~EMl~DRGY~V~~-----~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m 121 (225)
-++++++++||.-++. .+..++..|+.+.|.+.| .-++++.|-+. ++.=+.|++.+
T Consensus 15 ~~~~~~~~~~g~g~s~~vs~Gn~~dv~~~d~l~~~~~D~---------------~t~~I~ly~E~----~~d~~~f~~~~ 75 (138)
T PF13607_consen 15 TAILDWAQDRGIGFSYVVSVGNEADVDFADLLEYLAEDP---------------DTRVIVLYLEG----IGDGRRFLEAA 75 (138)
T ss_dssp HHHHHHHHHTT-EESEEEE-TT-SSS-HHHHHHHHCT-S---------------S--EEEEEES------S-HHHHHHHH
T ss_pred HHHHHHHHHcCCCeeEEEEeCccccCCHHHHHHHHhcCC---------------CCCEEEEEccC----CCCHHHHHHHH
Confidence 4678899999988765 556778899988876544 44455556542 22235666665
Q ss_pred hhcCCCcEEEEEEcCCCCHHHHHH
Q 027294 122 VNRDTLTGLILILQNQITSQATKA 145 (225)
Q Consensus 122 ~~~env~r~IlVvq~~lT~~Ark~ 145 (225)
..-...+=|++++.+-|+..+++
T Consensus 76 -~~a~~~KPVv~lk~Grt~~g~~a 98 (138)
T PF13607_consen 76 -RRAARRKPVVVLKAGRTEAGARA 98 (138)
T ss_dssp -HHHCCCS-EEEEE----------
T ss_pred -HHHhcCCCEEEEeCCCchhhhhh
Confidence 33333356777777766655443
No 19
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=45.80 E-value=1e+02 Score=25.11 Aligned_cols=72 Identities=15% Similarity=0.113 Sum_probs=46.9
Q ss_pred HHHHHhcCCCCccChhhhccCHHHHHHHhCC-CCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCC
Q 027294 48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQ-DPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDT 126 (225)
Q Consensus 48 Tv~EMl~DRGY~V~~~El~~sldeF~~~yg~-~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~en 126 (225)
-+.-||++.||.|..-=...+.++|.+.-.+ .++ -+.++ +.. .-....++.+++.+ .+.+
T Consensus 22 iv~~~lr~~G~eVi~LG~~vp~e~i~~~a~~~~~d--~V~lS--------------~~~--~~~~~~~~~~~~~L-~~~~ 82 (137)
T PRK02261 22 ILDRALTEAGFEVINLGVMTSQEEFIDAAIETDAD--AILVS--------------SLY--GHGEIDCRGLREKC-IEAG 82 (137)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCC--EEEEc--------------Ccc--ccCHHHHHHHHHHH-HhcC
Confidence 4446999999999886667789999876422 122 22222 211 23566788888888 7777
Q ss_pred CcEEEEEEcCCC
Q 027294 127 LTGLILILQNQI 138 (225)
Q Consensus 127 v~r~IlVvq~~l 138 (225)
.....+++.+.+
T Consensus 83 ~~~~~i~vGG~~ 94 (137)
T PRK02261 83 LGDILLYVGGNL 94 (137)
T ss_pred CCCCeEEEECCC
Confidence 765556666766
No 20
>KOG0975 consensus Branched chain aminotransferase BCAT1, pyridoxal phosphate enzymes type IV superfamily [Amino acid transport and metabolism]
Probab=43.71 E-value=11 Score=36.38 Aligned_cols=29 Identities=24% Similarity=0.651 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCC-CccChhhhccCHHHHHHH
Q 027294 45 SRRTVLEMLKDRG-YAVALSEINLSVQDFRAI 75 (225)
Q Consensus 45 vrrTv~EMl~DRG-Y~V~~~El~~sldeF~~~ 75 (225)
.|++++|+++|+| |.|.+. +.|.+||.+.
T Consensus 288 TR~sileLa~~~g~~~V~Er--~vtv~e~~~A 317 (379)
T KOG0975|consen 288 TRKSILELARDLGEFKVEER--DVTVDELKTA 317 (379)
T ss_pred cHHHHHHHHHHhCceEEEEE--EEeHHHhhhh
Confidence 4899999999999 999885 4567788654
No 21
>COG1787 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]
Probab=43.18 E-value=54 Score=29.56 Aligned_cols=97 Identities=15% Similarity=0.154 Sum_probs=64.2
Q ss_pred hcCCCCccChhhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCCcEEEE
Q 027294 53 LKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLIL 132 (225)
Q Consensus 53 l~DRGY~V~~~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~env~r~Il 132 (225)
+..-||.++. +..-.+|-+.--..++.....+.+.+. ...|+.+.|+++.... -.-+...+++
T Consensus 119 ~t~~g~~~t~---Tqks~D~GADlia~~~g~~v~vQaKR~-------------~~aV~~kaiqEivask-~~Y~~eka~v 181 (217)
T COG1787 119 FTEKGFRITS---TQKSSDFGADLIAAKDGKKVAVQAKRY-------------ISAVSKKAIQEIVASK-AYYGCEKAKV 181 (217)
T ss_pred HHhcCeEEEe---eeccccchhHHHhccCCcEEeehhhHH-------------HHhhhHHHHHHHHHhh-hccCcceEEE
Confidence 3444777762 333456654443334444444443221 1369999999998887 7788999999
Q ss_pred EEcCCCCHHHHHHHhhhccceeeeecceeeeecccc
Q 027294 133 ILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKH 168 (225)
Q Consensus 133 Vvq~~lT~~Ark~i~~~~~~IEvF~E~ELl~nit~H 168 (225)
|+.+..|-.|++. ... ..+|+..-.++..+|..-
T Consensus 182 vTn~~yt~~aqkl-a~~-nsv~l~~r~~~~~f~~~~ 215 (217)
T COG1787 182 VTNGSYTYAAQKL-AQA-NSVELIDRDELSEFIREG 215 (217)
T ss_pred ecCCccchhHHHH-HHh-hcceEEecchHHhhhccc
Confidence 9999999877765 222 478888888888877643
No 22
>PRK09539 tRNA-splicing endonuclease subunit beta; Reviewed
Probab=42.90 E-value=1.4e+02 Score=24.70 Aligned_cols=66 Identities=18% Similarity=0.115 Sum_probs=36.3
Q ss_pred HHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCCcEE
Q 027294 51 EMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGL 130 (225)
Q Consensus 51 EMl~DRGY~V~~~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~env~r~ 130 (225)
.=||+|||.|... . .| |. + +... ..+...-++....+...+....|-.+.... ..-+-+-.
T Consensus 42 kDLR~RGyvVk~G-~-----kf----g~------~-~~~~-~~~~s~ylV~Vl~E~~~is~~eL~~~vr~a-~svrK~lV 102 (124)
T PRK09539 42 VDLKQRGRKTIDG-I-----DE----IS------L-IIKD-KENKYTAMVLIVDENEKVSFKKILDKLHFS-KSMNLELY 102 (124)
T ss_pred hhHHhCCCeeccC-C-----ce----eE------E-EEec-CCCCceEEEEEecCCCccCHHHHHHHHHHH-hhccceeE
Confidence 3489999999773 1 22 21 1 1111 223333344445666899999998877666 43333333
Q ss_pred EEEEc
Q 027294 131 ILILQ 135 (225)
Q Consensus 131 IlVvq 135 (225)
+=||.
T Consensus 103 LAVVD 107 (124)
T PRK09539 103 LAIVD 107 (124)
T ss_pred EEEEc
Confidence 33443
No 23
>PF01939 DUF91: Protein of unknown function DUF91; InterPro: IPR002793 The function of these prokaryotic proteins is unknown. Computational analysis suggests that they may form a restriction endonuclease-like fold, similar to that found in a variety of endonucleases and DNA repair enzymes [].; PDB: 2VLD_A.
Probab=41.33 E-value=46 Score=29.97 Aligned_cols=59 Identities=14% Similarity=0.105 Sum_probs=34.0
Q ss_pred cEEEEecCC--CccchhhHHHHHHHHhhcCC--CcEEEEEEcCCCCHHHHHHHhhhccceeeeecc
Q 027294 98 RILVVFCGP--GIVKVNVIRSIISQIVNRDT--LTGLILILQNQITSQATKAVGLFQFKVEMFQIT 159 (225)
Q Consensus 98 kI~VfF~~e--~kVgvK~Ir~~~e~m~~~en--v~r~IlVvq~~lT~~Ark~i~~~~~~IEvF~E~ 159 (225)
-++|..--. ..=.+.++..|++.+..+.+ -=|+|||.++ +|+.|+..+.+.+ ||+...+
T Consensus 149 ~VVIElKR~~a~~~aV~QL~rY~~~l~~~~~~~~VRGilvA~~-i~~~a~~ll~~~g--lef~~ld 211 (228)
T PF01939_consen 149 LVVIELKRRRADRDAVEQLLRYVELLKRDPGLEPVRGILVAPS-ITPQARELLEDRG--LEFVELD 211 (228)
T ss_dssp EEEEEE-SS-B-HHHHHHHHHHHHHHHHHH--S-EEEEEEES--B-HHHHHHHHHHT---EEEE--
T ss_pred EEEEEEEeccCCHHHHHHHHHHHHHHhhccCCCceeEEEECCC-CCHHHHHHHHHcC--CEEEEec
Confidence 356666433 22336777778888833332 2379999876 9999999988765 6555443
No 24
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=40.25 E-value=1.9e+02 Score=26.50 Aligned_cols=44 Identities=7% Similarity=-0.094 Sum_probs=28.2
Q ss_pred CCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc
Q 027294 105 GPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ 150 (225)
Q Consensus 105 ~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~ 150 (225)
.+...+.+.|.++++.+ ++.++. +|++=.+.-+..++...++.+
T Consensus 232 ~~~eps~~~l~~l~~~i-k~~~v~-~If~e~~~~~~~~~~la~e~g 275 (311)
T PRK09545 232 PEIQPGAQRLHEIRTQL-VEQKAT-CVFAEPQFRPAVIESVAKGTS 275 (311)
T ss_pred CCCCCCHHHHHHHHHHH-HHcCCC-EEEecCCCChHHHHHHHHhcC
Confidence 44567899999999999 999988 555543333333333334333
No 25
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=38.55 E-value=13 Score=31.80 Aligned_cols=15 Identities=40% Similarity=0.840 Sum_probs=12.7
Q ss_pred HHHHHhcCCCCccCh
Q 027294 48 TVLEMLKDRGYAVAL 62 (225)
Q Consensus 48 Tv~EMl~DRGY~V~~ 62 (225)
-|+++|++|||.|+.
T Consensus 244 gvl~lLr~~Gy~V~~ 258 (259)
T PF01963_consen 244 GVLDLLRKKGYTVEP 258 (259)
T ss_pred hHHHHHHhCCceeec
Confidence 488999999999864
No 26
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=37.97 E-value=1.3e+02 Score=27.74 Aligned_cols=96 Identities=16% Similarity=0.171 Sum_probs=54.6
Q ss_pred EEEEecCCCccchhhHHHHHHHHhh---cCCCcEEEEEEc-CCCCHHHHHHHhhh----ccceeeeecc----eeeeecc
Q 027294 99 ILVVFCGPGIVKVNVIRSIISQIVN---RDTLTGLILILQ-NQITSQATKAVGLF----QFKVEMFQIT----DLLVNIT 166 (225)
Q Consensus 99 I~VfF~~e~kVgvK~Ir~~~e~m~~---~env~r~IlVvq-~~lT~~Ark~i~~~----~~~IEvF~E~----ELl~nit 166 (225)
+.+++++...+++..||.+++.+ . -++-.+.|||-. ..+|..|..++... +-.+-++..+ .|+==|.
T Consensus 80 ~~~i~~~~~~i~id~ir~l~~~~-~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIr 158 (329)
T PRK08058 80 VHLVAPDGQSIKKDQIRYLKEEF-SKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTIL 158 (329)
T ss_pred EEEeccccccCCHHHHHHHHHHH-hhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHH
Confidence 33444556789999999999987 4 445567777765 56788775554332 2111122211 1111122
Q ss_pred cccccCCcccCChHHHHHHHHHcCCCCCC
Q 027294 167 KHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195 (225)
Q Consensus 167 ~H~lVPkH~vl~~eEk~~lL~~y~i~~~Q 195 (225)
+--.+=.-..+++++....|++.++.+.+
T Consensus 159 SRc~~i~~~~~~~~~~~~~L~~~gi~~~~ 187 (329)
T PRK08058 159 SRCQVVEFRPLPPESLIQRLQEEGISESL 187 (329)
T ss_pred hhceeeeCCCCCHHHHHHHHHHcCCChHH
Confidence 22222234557888888888887766543
No 27
>PRK03298 hypothetical protein; Provisional
Probab=35.29 E-value=66 Score=29.16 Aligned_cols=39 Identities=21% Similarity=0.171 Sum_probs=31.3
Q ss_pred chhhHHHHHHHHhhcC---CCcEEEEEEcCCCCHHHHHHHhhhc
Q 027294 110 KVNVIRSIISQIVNRD---TLTGLILILQNQITSQATKAVGLFQ 150 (225)
Q Consensus 110 gvK~Ir~~~e~m~~~e---nv~r~IlVvq~~lT~~Ark~i~~~~ 150 (225)
+|.++..|++.+ ..+ .-=|||||.|+ +|++|+..+.+-+
T Consensus 161 aV~QL~RYve~l-~rd~~~~~VRGIlvAp~-It~~Ar~Ll~drG 202 (224)
T PRK03298 161 GVEQLTRYLELL-NRDPLLAPVRGVFAAQE-IKPQARTLAEDRG 202 (224)
T ss_pred HHHHHHHHHHHH-hhCcCcCCceEEEECCc-CCHHHHHHHHHcC
Confidence 688999999999 433 23579999755 9999999988766
No 28
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=33.93 E-value=34 Score=24.52 Aligned_cols=53 Identities=11% Similarity=0.213 Sum_probs=31.9
Q ss_pred ccccccCCCCCCCCccccccccCCCChhhHHHHHHHHHHHHHHhcCCCCccChh
Q 027294 10 SMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALS 63 (225)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~md~~~~e~~rL~rvrrTv~EMl~DRGY~V~~~ 63 (225)
++..+|..-+.-..+..-...+.. .......|..+.+.+-+.++++||..+..
T Consensus 5 ~i~~~G~~~~~~~~l~~~~~~~~g-~~l~~~~l~~~~~~l~~~y~~~GY~~s~v 57 (76)
T PF08479_consen 5 GIRFEGNTLLPEEELQAILAPYIG-RCLTLADLQQLADALTNYYREKGYITSRV 57 (76)
T ss_dssp EEEEES-TSSSCCHHHHHHGGGTT-SBB-HHHHHHHHHHHHHHHHHTT-TT-EE
T ss_pred EEEEECCCcCCHHHHHHHHHHhcC-CCcCHHHHHHHHHHHHHHHHHcCceEEEE
Confidence 344556555555444444444333 22345778899999999999999998763
No 29
>COG4889 Predicted helicase [General function prediction only]
Probab=33.54 E-value=76 Score=34.89 Aligned_cols=101 Identities=16% Similarity=0.222 Sum_probs=71.6
Q ss_pred eEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc--------------
Q 027294 85 LRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ-------------- 150 (225)
Q Consensus 85 L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~-------------- 150 (225)
+.+++...++.--.|.+-|-. .+++...|..|+..+ ..-+++++|||.-...++-|.+++++..
T Consensus 61 idlva~~d~g~ytaiQcKFy~-nslak~di~sF~t~l-gkt~f~~gliiSTtdw~sNA~~aieq~~~~~~~Iglsei~es 138 (1518)
T COG4889 61 IDLVAREDNGNYTAIQCKFYQ-NSLAKGDIDSFFTAL-GKTGFKNGLIISTTDWTSNAEKAIEQQRSPGMRIGLSEIAES 138 (1518)
T ss_pred eeEEEEccCCCeEEEEeeeec-cccccccccHHHHHh-ccccccCceEEEecccchhHHHHHHhhhCccceecHHHHhcC
Confidence 444554433333457777755 689999999999999 8889999999977779999999987653
Q ss_pred -cceeeeecceeeeecc---cccccCCcccCChHHHHHHHHHcCC
Q 027294 151 -FKVEMFQITDLLVNIT---KHVLKPKHQVLTDQEKEKLLKKYSI 191 (225)
Q Consensus 151 -~~IEvF~E~ELl~nit---~H~lVPkH~vl~~eEk~~lL~~y~i 191 (225)
...++|.-.||..|++ .|.+-|.. .+-++..++-+..
T Consensus 139 ~IDW~~f~p~e~~~nl~l~~~kk~R~hQ----q~Aid~a~~~F~~ 179 (1518)
T COG4889 139 PIDWDIFDPTELQDNLPLKKPKKPRPHQ----QTAIDAAKEGFSD 179 (1518)
T ss_pred CCChhhcCccccccccccCCCCCCChhH----HHHHHHHHhhccc
Confidence 2447788899999987 33333321 3445566666665
No 30
>PRK04280 arginine repressor; Provisional
Probab=32.69 E-value=94 Score=25.93 Aligned_cols=88 Identities=7% Similarity=0.171 Sum_probs=43.4
Q ss_pred HHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCC-cEEEEecCCCccchhhHHHHHHHHh-hcC
Q 027294 48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSK-RILVVFCGPGIVKVNVIRSIISQIV-NRD 125 (225)
Q Consensus 48 Tv~EMl~DRGY~V~~~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~-kI~VfF~~e~kVgvK~Ir~~~e~m~-~~e 125 (225)
-+.+.|+++|+.|+|.-+...+.+. .+.. ..+.+. ..|+.+.+...-....++..+.... +-+
T Consensus 23 eL~~~L~~~Gi~vTQATiSRDikeL-------------~lvK--v~~~~G~~~Y~lp~~~~~~~~~~l~~~~~~~v~sv~ 87 (148)
T PRK04280 23 ELVDRLREEGFNVTQATVSRDIKEL-------------HLVK--VPLPDGRYKYSLPADQRFNPLQKLKRALMDSFVKID 87 (148)
T ss_pred HHHHHHHHcCCCeehHHHHHHHHHc-------------CCEE--eecCCCcEEEeeccccccchHHHHHHHHHHHEEEEe
Confidence 4678899999999998664333333 2221 222222 2455443321111233443333321 223
Q ss_pred CCcEEEEE-EcCCCCHHHHHHHhhhc
Q 027294 126 TLTGLILI-LQNQITSQATKAVGLFQ 150 (225)
Q Consensus 126 nv~r~IlV-vq~~lT~~Ark~i~~~~ 150 (225)
.....|+| +..+..+....+++.+.
T Consensus 88 ~~~~~vvikT~pG~A~~va~~iD~~~ 113 (148)
T PRK04280 88 GAGNLLVLKTLPGNANSIGALIDNLD 113 (148)
T ss_pred eeCCEEEEEcCCChHHHHHHHHHhCC
Confidence 44445554 54555555566666654
No 31
>TIGR01120 rpiB ribose 5-phosphate isomerase B. Involved in the non-oxidative branch of the pentose phospate pathway.
Probab=31.68 E-value=1.1e+02 Score=25.59 Aligned_cols=20 Identities=20% Similarity=0.414 Sum_probs=17.0
Q ss_pred HHHHHHHHHHhcCCCCccCh
Q 027294 43 YLSRRTVLEMLKDRGYAVAL 62 (225)
Q Consensus 43 ~rvrrTv~EMl~DRGY~V~~ 62 (225)
|..+..+.+.|+++||.|.+
T Consensus 11 ~~lK~~l~~~L~~~g~eV~D 30 (143)
T TIGR01120 11 FILKEEIKAFLVERGVKVID 30 (143)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 55678899999999999965
No 32
>PRK05571 ribose-5-phosphate isomerase B; Provisional
Probab=31.40 E-value=1.1e+02 Score=25.69 Aligned_cols=20 Identities=20% Similarity=0.336 Sum_probs=16.9
Q ss_pred HHHHHHHHHHhcCCCCccCh
Q 027294 43 YLSRRTVLEMLKDRGYAVAL 62 (225)
Q Consensus 43 ~rvrrTv~EMl~DRGY~V~~ 62 (225)
|..+..+.++|++.||.|.+
T Consensus 12 ~~lK~~l~~~L~~~g~eV~D 31 (148)
T PRK05571 12 FELKEEIIEHLEELGHEVID 31 (148)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 55678899999999999966
No 33
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=29.91 E-value=76 Score=29.23 Aligned_cols=57 Identities=21% Similarity=0.248 Sum_probs=41.0
Q ss_pred EEEEecCC--CccchhhHHHHHHHHhhcCCCc--EEEEEEcCCCCHHHHHHHhhhc---cceeeee
Q 027294 99 ILVVFCGP--GIVKVNVIRSIISQIVNRDTLT--GLILILQNQITSQATKAVGLFQ---FKVEMFQ 157 (225)
Q Consensus 99 I~VfF~~e--~kVgvK~Ir~~~e~m~~~env~--r~IlVvq~~lT~~Ark~i~~~~---~~IEvF~ 157 (225)
+.|...-. .-..+..++.|++.+ .++... |||||.++ +|+.|++.+.+-+ .++|-+.
T Consensus 175 viiElKR~ka~~~Av~QL~RYv~~l-~~~~~~~VRGiLvAp~-it~~a~~ll~~~GLef~kle~~~ 238 (253)
T COG1637 175 VIIELKRRKAGLSAVSQLKRYVELL-REDTGDKVRGILVAPS-ITEQARRLLEDEGLEFVKLEPPK 238 (253)
T ss_pred EEEEEecccCCchHHHHHHHHHHHc-ccccCceEEEEEEccc-ccHHHHHHHHHcCceEEEcCCch
Confidence 44454322 345688889999999 777777 99999855 9999999998765 3555444
No 34
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=29.14 E-value=2.5e+02 Score=23.84 Aligned_cols=75 Identities=16% Similarity=0.258 Sum_probs=46.3
Q ss_pred HHHHHhcCCCCccChhhhccCHHHHHHHhCC-CCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCC
Q 027294 48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQ-DPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDT 126 (225)
Q Consensus 48 Tv~EMl~DRGY~V~~~El~~sldeF~~~yg~-~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~en 126 (225)
-+..+++..||.|..--.+.+.++|.+.-.. .|+ -+.++ +.. .-....++.+++.+ .+.+
T Consensus 101 ~v~~~l~~~G~~vi~lG~~~p~~~l~~~~~~~~~d--~v~lS--------------~~~--~~~~~~~~~~i~~l-r~~~ 161 (201)
T cd02070 101 LVATMLEANGFEVIDLGRDVPPEEFVEAVKEHKPD--ILGLS--------------ALM--TTTMGGMKEVIEAL-KEAG 161 (201)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCC--EEEEe--------------ccc--cccHHHHHHHHHHH-HHCC
Confidence 3456899999999765567788999876532 222 22222 211 23467789999998 6666
Q ss_pred C--cEEEEEEcCCCCHH
Q 027294 127 L--TGLILILQNQITSQ 141 (225)
Q Consensus 127 v--~r~IlVvq~~lT~~ 141 (225)
. +--|+|-...+++.
T Consensus 162 ~~~~~~i~vGG~~~~~~ 178 (201)
T cd02070 162 LRDKVKVMVGGAPVNQE 178 (201)
T ss_pred CCcCCeEEEECCcCCHH
Confidence 5 33455555556654
No 35
>PF01297 TroA: Periplasmic solute binding protein family; InterPro: IPR006127 This is a family of ABC transporter metal-binding lipoproteins. An example is the periplasmic zinc-binding protein TroA P96116 from SWISSPROT that interacts with an ATP-binding cassette transport system in Treponema pallidum and plays a role in the transport of zinc across the cytoplasmic membrane. Related proteins are found in both Gram-positive and Gram-negative bacteria. ; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2PS9_A 2PS0_A 2OSV_A 2OGW_A 2PS3_A 2PRS_B 3MFQ_C 3GI1_B 2OV3_A 1PQ4_A ....
Probab=29.00 E-value=3.2e+02 Score=23.60 Aligned_cols=44 Identities=9% Similarity=-0.022 Sum_probs=27.2
Q ss_pred cCCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhh
Q 027294 104 CGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF 149 (225)
Q Consensus 104 ~~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~ 149 (225)
..+...+.+.+.++.+.+ ++.++. +|++-.+.-+..++....+.
T Consensus 178 ~~~~~ps~~~l~~l~~~i-k~~~v~-~i~~e~~~~~~~~~~la~~~ 221 (256)
T PF01297_consen 178 SPGEEPSPKDLAELIKLI-KENKVK-CIFTEPQFSSKLAEALAKET 221 (256)
T ss_dssp SSSSSS-HHHHHHHHHHH-HHTT-S-EEEEETTS-THHHHHHHHCC
T ss_pred ccccCCCHHHHHHHHHHh-hhcCCc-EEEecCCCChHHHHHHHHHc
Confidence 456679999999999999 889987 45554444444343333333
No 36
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=28.23 E-value=4.3e+02 Score=23.47 Aligned_cols=44 Identities=7% Similarity=0.034 Sum_probs=29.2
Q ss_pred CCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc
Q 027294 105 GPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ 150 (225)
Q Consensus 105 ~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~ 150 (225)
.+...+.+.|.++++.+ +++++. +|++=.+--+..++...++.+
T Consensus 200 ~~~eps~~~l~~l~~~i-k~~~v~-~if~e~~~~~~~~~~la~~~g 243 (282)
T cd01017 200 PEVEPSPKQLAELVEFV-KKSDVK-YIFFEENASSKIAETLAKETG 243 (282)
T ss_pred CCCCCCHHHHHHHHHHH-HHcCCC-EEEEeCCCChHHHHHHHHHcC
Confidence 45568899999999999 999988 555544433344444334433
No 37
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=28.02 E-value=39 Score=28.50 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=19.5
Q ss_pred HHHHHHHHhcCCCCccChhhhccCHHHHHHHh
Q 027294 45 SRRTVLEMLKDRGYAVALSEINLSVQDFRAIY 76 (225)
Q Consensus 45 vrrTv~EMl~DRGY~V~~~El~~sldeF~~~y 76 (225)
+|..+.+||+|+||.-.+ + +++|.+..
T Consensus 14 ir~~l~~~L~~~~~t~~e--i---~~~~~~~~ 40 (180)
T PF11985_consen 14 IREWLDQMLRDGGFTQYE--I---LAEWLEEL 40 (180)
T ss_pred HHHHHHHHHHhCCCChHH--H---HHHHHHhh
Confidence 788899999999976544 2 45666655
No 38
>KOG0460 consensus Mitochondrial translation elongation factor Tu [Translation, ribosomal structure and biogenesis]
Probab=27.07 E-value=1.3e+02 Score=29.50 Aligned_cols=83 Identities=19% Similarity=0.277 Sum_probs=58.3
Q ss_pred hhHHHHHHHHhhcCCCcEEEEEEcC--CCCHHHHHHHhhhc-cceeeeecceeeeecccccccCCcccCC--hHHHHHHH
Q 027294 112 NVIRSIISQIVNRDTLTGLILILQN--QITSQATKAVGLFQ-FKVEMFQITDLLVNITKHVLKPKHQVLT--DQEKEKLL 186 (225)
Q Consensus 112 K~Ir~~~e~m~~~env~r~IlVvq~--~lT~~Ark~i~~~~-~~IEvF~E~ELl~nit~H~lVPkH~vl~--~eEk~~lL 186 (225)
..||+.|.-. ...+.||||+.. +.=|+.|..+-... ..| +.+.|=|.+-.+|++-+.|. +-|.++||
T Consensus 129 DYIKNMItGa---aqMDGaILVVaatDG~MPQTrEHlLLArQVGV-----~~ivvfiNKvD~V~d~e~leLVEmE~RElL 200 (449)
T KOG0460|consen 129 DYIKNMITGA---AQMDGAILVVAATDGPMPQTREHLLLARQVGV-----KHIVVFINKVDLVDDPEMLELVEMEIRELL 200 (449)
T ss_pred HHHHHhhcCc---cccCceEEEEEcCCCCCcchHHHHHHHHHcCC-----ceEEEEEecccccCCHHHHHHHHHHHHHHH
Confidence 4566666544 455779999643 34477777665433 222 55666677888887766654 78999999
Q ss_pred HHcCCCCCCccceecC
Q 027294 187 KKYSIEEKQQHNRHLC 202 (225)
Q Consensus 187 ~~y~i~~~QLP~I~~~ 202 (225)
..|+..-...|-|.-|
T Consensus 201 se~gf~Gd~~PvI~GS 216 (449)
T KOG0460|consen 201 SEFGFDGDNTPVIRGS 216 (449)
T ss_pred HHcCCCCCCCCeeecc
Confidence 9999999999999755
No 39
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=26.91 E-value=2e+02 Score=23.12 Aligned_cols=57 Identities=18% Similarity=0.292 Sum_probs=34.0
Q ss_pred HHHHHHHhCC--C--CCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCCc
Q 027294 69 VQDFRAIYGQ--D--PDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLT 128 (225)
Q Consensus 69 ldeF~~~yg~--~--p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~env~ 128 (225)
+.+|.++|.- . |.-...-|++-+. ..+-+-|-|++-..=-.+.|+.+++.. ...|.+
T Consensus 45 lmdFIsryARTDEImPEDKTvGFvviN~--dKK~mSvsFsdideNmK~~i~ei~kky-kd~Gyk 105 (110)
T PF11513_consen 45 LMDFISRYARTDEIMPEDKTVGFVVINK--DKKMMSVSFSDIDENMKNSIEEIVKKY-KDSGYK 105 (110)
T ss_dssp HHHHHHHH---S---TTSEEEEEEEEET--TTTEEEEEE-S--CCHHHHHHHHHHHH-HCCS-E
T ss_pred HHHHHHHhhcccccCCCCceeEEEEEec--CCeEEEEEecchhHHHHHHHHHHHHHh-hcCCce
Confidence 7899999963 2 5445555555433 334578899865322277889998888 666654
No 40
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=26.74 E-value=1.4e+02 Score=26.78 Aligned_cols=43 Identities=26% Similarity=0.318 Sum_probs=31.4
Q ss_pred CCCccchhhHHHHHHHHh--hcCCCcEEEEEEc-CCCCHHHHHHHh
Q 027294 105 GPGIVKVNVIRSIISQIV--NRDTLTGLILILQ-NQITSQATKAVG 147 (225)
Q Consensus 105 ~e~kVgvK~Ir~~~e~m~--~~env~r~IlVvq-~~lT~~Ark~i~ 147 (225)
+...+++..||.+++.+. --++=.+.|||.. ..+|..|..++-
T Consensus 69 ~~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~~a~naLL 114 (313)
T PRK05564 69 NKKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTEQAQNAFL 114 (313)
T ss_pred cCCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcCHHHHHHHH
Confidence 456799999999999762 2345577888877 778887766554
No 41
>PRK14042 pyruvate carboxylase subunit B; Provisional
Probab=26.16 E-value=2.2e+02 Score=29.18 Aligned_cols=127 Identities=17% Similarity=0.232 Sum_probs=75.3
Q ss_pred CCCCCccccccCCCCCCCCccccccccCCCChhhHHHHHH--HHHHHHHHhc----CCCCccChhhhccCHHHHHHHhCC
Q 027294 5 NGYDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYL--SRRTVLEMLK----DRGYAVALSEINLSVQDFRAIYGQ 78 (225)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~md~~~~e~~rL~r--vrrTv~EMl~----DRGY~V~~~El~~sldeF~~~yg~ 78 (225)
-||. |+|+-||.+|.+ |+--.-+ +.-|--|.+| +.+|-+|||- ==||.--.+++ .+.|.+....
T Consensus 38 ~g~~-siE~~gGatfd~-----~~rfl~e-dpwerl~~~r~~~pnt~lqmL~Rg~N~vGy~~~~d~v---v~~~v~~a~~ 107 (596)
T PRK14042 38 VGFW-AMEVWGGATFDA-----CLRFLKE-DPWSRLRQLRQALPNTQLSMLLRGQNLLGYRNYADDV---VRAFVKLAVN 107 (596)
T ss_pred cCCC-EEEeeCCcccce-----eecccCC-CHHHHHHHHHHhCCCCceEEEeccccccccccCChHH---HHHHHHHHHH
Confidence 3554 699999999987 7665433 3333333333 3468899997 55666655555 4566665322
Q ss_pred C-CCCCceEEEeec--------------CCCCCCcEEEEecCCCccchhhHHHHHHHHhhcCCCcEEEEE-EcCCCCHHH
Q 027294 79 D-PDVDRLRISISH--------------QSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILI-LQNQITSQA 142 (225)
Q Consensus 79 ~-p~r~~L~i~~~~--------------~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~env~r~IlV-vq~~lT~~A 142 (225)
+ .+ -.++.-.- +..-.-...+.|...+..+.+.+-++++++ .+-++++.-|. +-+-++|.+
T Consensus 108 ~Gid--v~Rifd~lnd~~n~~~~i~~~k~~G~~~~~~i~yt~sp~~t~e~~~~~ak~l-~~~Gad~I~IkDtaG~l~P~~ 184 (596)
T PRK14042 108 NGVD--VFRVFDALNDARNLKVAIDAIKSHKKHAQGAICYTTSPVHTLDNFLELGKKL-AEMGCDSIAIKDMAGLLTPTV 184 (596)
T ss_pred cCCC--EEEEcccCcchHHHHHHHHHHHHcCCEEEEEEEecCCCCCCHHHHHHHHHHH-HHcCCCEEEeCCcccCCCHHH
Confidence 1 11 12222111 111111244558888888888888999998 88888865544 555678866
Q ss_pred HH
Q 027294 143 TK 144 (225)
Q Consensus 143 rk 144 (225)
-.
T Consensus 185 v~ 186 (596)
T PRK14042 185 TV 186 (596)
T ss_pred HH
Confidence 43
No 42
>KOG1232 consensus Proteins containing the FAD binding domain [Energy production and conversion]
Probab=25.85 E-value=54 Score=32.50 Aligned_cols=62 Identities=23% Similarity=0.384 Sum_probs=44.3
Q ss_pred cccccCCCCCCCC-----cccccccc------CCCChhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHH
Q 027294 11 MEMEGGNGYNGEP-----TESCLSGF------VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFR 73 (225)
Q Consensus 11 ~~~~~~~~~~~~~-----~~~~~~~~------md~~~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~ 73 (225)
+|-.|.|+-+.++ +..|+.+. |.+++.+..++|+.|..+=+-|..-|| |-..++.+.+++|-
T Consensus 332 iETsGSn~dhD~eKl~afl~d~lek~lIsDGv~a~d~~~~~~lW~~Re~ip~a~~~~g~-vyKyDvSLpL~d~Y 404 (511)
T KOG1232|consen 332 IETSGSNKDHDEEKLTAFLEDCLEKGLISDGVLAQDEAEAQKLWKIRESIPEALQKAGG-VYKYDVSLPLEDLY 404 (511)
T ss_pred EEecCCCccccHHHHHHHHHHhhhhcccccceecCCHHHHHHHHHHHhccHHHHHhcCC-EEEeeccccHHHHH
Confidence 4555666554433 34565543 677889999999999999999999995 55556777777663
No 43
>PF01650 Peptidase_C13: Peptidase C13 family; InterPro: IPR001096 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean). The blood fluke parasite Schistosoma mansoni has two cysteine proteases in its digestive tract, one a cathepsin B-like protease, the other termed hemoglobinase [, ]. The latter has been hard to purify, free of cathepsin B, and expressed forms in Escherichia coli prove to be inactive, suggesting that hemoglobinase may act in association with cathepsin B [, ]. Plant vacuolar processing enzyme and legumain from legumes [] have been shown to have sequence and functional similarity to hemoglobinase. The catalytic residues of the family are currently unknown, but sequence alignments reveal one totally conserved cysteine and two totally conserved histidines.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=25.32 E-value=2.1e+02 Score=25.79 Aligned_cols=48 Identities=6% Similarity=0.265 Sum_probs=34.6
Q ss_pred CCCCCCcEEEEec-----------CCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCC
Q 027294 92 QSDPSKRILVVFC-----------GPGIVKVNVIRSIISQIVNRDTLTGLILILQNQIT 139 (225)
Q Consensus 92 ~~dp~~kI~VfF~-----------~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT 139 (225)
.+++++.+||||. +.+.|..+.++..++.|..+....+++||+...-+
T Consensus 102 ~s~~~D~vfiy~~~HG~~~~l~~~~~~~l~~~~L~~~L~~m~~~~~y~~lv~~veaC~S 160 (256)
T PF01650_consen 102 NSTENDNVFIYFTGHGGPGFLKFPDGEELTADDLADALDKMHEKKRYKKLVFVVEACYS 160 (256)
T ss_pred cCCCCCeEEEEEeccCCCCcccCCCcccccHHHHHHHHHHHHhhCCcceEEEEEecccc
Confidence 3566677888773 45677888999999999556666778888766543
No 44
>TIGR00678 holB DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
Probab=25.22 E-value=2.7e+02 Score=22.75 Aligned_cols=91 Identities=15% Similarity=0.185 Sum_probs=45.5
Q ss_pred EecCCCccchhhHHHHHHHHhhc---CCCcEEEEEEc-CCCCHHHHHHHhhh----c-cceeeeecce---eeeeccccc
Q 027294 102 VFCGPGIVKVNVIRSIISQIVNR---DTLTGLILILQ-NQITSQATKAVGLF----Q-FKVEMFQITD---LLVNITKHV 169 (225)
Q Consensus 102 fF~~e~kVgvK~Ir~~~e~m~~~---env~r~IlVvq-~~lT~~Ark~i~~~----~-~~IEvF~E~E---Ll~nit~H~ 169 (225)
+......+++..|+.+++.+ .. .+-.+.|||-. ..++..|..++... + ..+=+|.-.. |+=-|.+.-
T Consensus 69 ~~~~~~~~~~~~i~~i~~~~-~~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~ 147 (188)
T TIGR00678 69 LEPEGQSIKVDQVRELVEFL-SRTPQESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRC 147 (188)
T ss_pred eccccCcCCHHHHHHHHHHH-ccCcccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhc
Confidence 33444568899999888887 43 34344444422 45666554433222 1 1111121111 111122222
Q ss_pred ccCCcccCChHHHHHHHHHcCCCC
Q 027294 170 LKPKHQVLTDQEKEKLLKKYSIEE 193 (225)
Q Consensus 170 lVPkH~vl~~eEk~~lL~~y~i~~ 193 (225)
.+=.-..++.+|....|++.++.+
T Consensus 148 ~~~~~~~~~~~~~~~~l~~~gi~~ 171 (188)
T TIGR00678 148 QVLPFPPLSEEALLQWLIRQGISE 171 (188)
T ss_pred EEeeCCCCCHHHHHHHHHHcCCCH
Confidence 222344578888888888875443
No 45
>cd01019 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=24.98 E-value=5e+02 Score=23.24 Aligned_cols=40 Identities=10% Similarity=0.055 Sum_probs=27.0
Q ss_pred cCCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHH
Q 027294 104 CGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV 146 (225)
Q Consensus 104 ~~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i 146 (225)
..+...+.+.|+.++..+ ++.++. +||+ ....++.+.+.+
T Consensus 207 ~~~~eps~~~l~~l~~~i-k~~~v~-~If~-e~~~~~~~~~~i 246 (286)
T cd01019 207 DPEIDPGAKRLAKIRKEI-KEKGAT-CVFA-EPQFHPKIAETL 246 (286)
T ss_pred CCCCCCCHHHHHHHHHHH-HHcCCc-EEEe-cCCCChHHHHHH
Confidence 344678899999999999 999988 4444 333444443434
No 46
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=24.65 E-value=1.4e+02 Score=23.39 Aligned_cols=53 Identities=13% Similarity=0.276 Sum_probs=35.2
Q ss_pred cchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhccceeeeecceeeeec
Q 027294 109 VKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNI 165 (225)
Q Consensus 109 VgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~~~IEvF~E~ELl~ni 165 (225)
+|.--+..+.+.+ ...+++ ++|+...+||...+.++... .++++.-..|+..|
T Consensus 41 iG~GK~eei~~~~-~~~~~d--~vvfd~~Lsp~Q~rNLe~~~-~~~V~DRt~LIL~I 93 (95)
T PF13167_consen 41 IGSGKVEEIKELI-EELDAD--LVVFDNELSPSQQRNLEKAL-GVKVIDRTQLILEI 93 (95)
T ss_pred echhHHHHHHHHH-hhcCCC--EEEECCCCCHHHHHHHHHHH-CCeeeccccHHHHH
Confidence 3444455555555 555664 45667789999888887663 67778777777665
No 47
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=24.42 E-value=73 Score=22.55 Aligned_cols=21 Identities=10% Similarity=0.325 Sum_probs=17.5
Q ss_pred HHHHHHHhcCCCCccChhhhc
Q 027294 46 RRTVLEMLKDRGYAVALSEIN 66 (225)
Q Consensus 46 rrTv~EMl~DRGY~V~~~El~ 66 (225)
-.-+++..+..||.++..|+.
T Consensus 27 ~e~~~~lA~~~Gf~ft~~el~ 47 (64)
T TIGR03798 27 PEDRVAIAKEAGFEFTGEDLK 47 (64)
T ss_pred HHHHHHHHHHcCCCCCHHHHH
Confidence 355788899999999999883
No 48
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=24.19 E-value=3.3e+02 Score=23.18 Aligned_cols=76 Identities=13% Similarity=0.151 Sum_probs=48.5
Q ss_pred HHHHHHhcCCCCccChhhhccCHHHHHHHhCC-CCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcC
Q 027294 47 RTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ-DPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125 (225)
Q Consensus 47 rTv~EMl~DRGY~V~~~El~~sldeF~~~yg~-~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~e 125 (225)
+-+..|++..||.|..--.+.+.++|.+..-. .|+ -+.+++. . .-.+..++.+++.+ .+.
T Consensus 102 ~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~~~~~pd--~v~lS~~--------------~--~~~~~~~~~~i~~l-~~~ 162 (197)
T TIGR02370 102 NIVVTMLRANGFDVIDLGRDVPIDTVVEKVKKEKPL--MLTGSAL--------------M--TTTMYGQKDINDKL-KEE 162 (197)
T ss_pred HHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHcCCC--EEEEccc--------------c--ccCHHHHHHHHHHH-HHc
Confidence 45567999999999986678889999877532 233 2222321 1 22355688888998 777
Q ss_pred CCc-E-EEEEEcCCCCHH
Q 027294 126 TLT-G-LILILQNQITSQ 141 (225)
Q Consensus 126 nv~-r-~IlVvq~~lT~~ 141 (225)
+.. + -|+|-...+++.
T Consensus 163 ~~~~~v~i~vGG~~~~~~ 180 (197)
T TIGR02370 163 GYRDSVKFMVGGAPVTQD 180 (197)
T ss_pred CCCCCCEEEEEChhcCHH
Confidence 654 2 355655556654
No 49
>PTZ00215 ribose 5-phosphate isomerase; Provisional
Probab=23.72 E-value=2.1e+02 Score=24.23 Aligned_cols=20 Identities=10% Similarity=0.449 Sum_probs=16.9
Q ss_pred HHHHHHHHHHhcC--CCCccCh
Q 027294 43 YLSRRTVLEMLKD--RGYAVAL 62 (225)
Q Consensus 43 ~rvrrTv~EMl~D--RGY~V~~ 62 (225)
|..+..+.+.|++ +||.|.+
T Consensus 14 ~~lK~~l~~~L~~~~~g~eV~D 35 (151)
T PTZ00215 14 FDLKNEIIDYIKNKGKEYKIED 35 (151)
T ss_pred HHHHHHHHHHHHhccCCCEEEE
Confidence 5567888999999 9999976
No 50
>cd01900 YchF YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor.
Probab=23.33 E-value=46 Score=30.40 Aligned_cols=25 Identities=20% Similarity=0.311 Sum_probs=22.3
Q ss_pred CChHHHHHHHHHcCCCCCCccceec
Q 027294 177 LTDQEKEKLLKKYSIEEKQQHNRHL 201 (225)
Q Consensus 177 l~~eEk~~lL~~y~i~~~QLP~I~~ 201 (225)
|+++|+++.|+.|+++++.|+||-.
T Consensus 244 l~~ee~~~fl~~~gi~es~l~riI~ 268 (274)
T cd01900 244 LDEEEAAEFLEELGLEESGLDRLIR 268 (274)
T ss_pred CCHHHHHHHHHHcCCccccHHHHHH
Confidence 5789999999999999999999853
No 51
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=22.96 E-value=2.6e+02 Score=31.05 Aligned_cols=72 Identities=14% Similarity=0.210 Sum_probs=48.5
Q ss_pred ccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhccceeeeecceeeeecccccccCCcccCChHHHHHHHH
Q 027294 108 IVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLK 187 (225)
Q Consensus 108 kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~~~IEvF~E~ELl~nit~H~lVPkH~vl~~eEk~~lL~ 187 (225)
-+|..+.-.+..-.....| .|..+|++.. .-++|+.. +|+-|.+..=-++ --+| =|-.|+.+||++.|+
T Consensus 107 GvGKTTfg~~~sl~~a~kg-kr~yii~PT~--~Lv~Q~~~----kl~~~~e~~~~~~---~~~~-yh~~l~~~ekee~le 175 (1187)
T COG1110 107 GVGKTTFGLLMSLYLAKKG-KRVYIIVPTT--TLVRQVYE----RLKKFAEDAGSLD---VLVV-YHSALPTKEKEEALE 175 (1187)
T ss_pred CCchhHHHHHHHHHHHhcC-CeEEEEecCH--HHHHHHHH----HHHHHHhhcCCcc---eeee-eccccchHHHHHHHH
Confidence 5888888888887655666 7888887653 55666665 3444554433222 2344 788889999999999
Q ss_pred HcC
Q 027294 188 KYS 190 (225)
Q Consensus 188 ~y~ 190 (225)
+..
T Consensus 176 ~i~ 178 (1187)
T COG1110 176 RIE 178 (1187)
T ss_pred HHh
Confidence 765
No 52
>PRK08622 galactose-6-phosphate isomerase subunit LacB; Reviewed
Probab=22.69 E-value=1.9e+02 Score=25.05 Aligned_cols=20 Identities=25% Similarity=0.220 Sum_probs=16.9
Q ss_pred HHHHHHHHHHhcCCCCccCh
Q 027294 43 YLSRRTVLEMLKDRGYAVAL 62 (225)
Q Consensus 43 ~rvrrTv~EMl~DRGY~V~~ 62 (225)
|-.+..+.+.|++.||.|.+
T Consensus 12 ~~lK~~l~~~L~~~G~eV~D 31 (171)
T PRK08622 12 TDEKMAVSDYLKSKGHEVID 31 (171)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 55678899999999999966
No 53
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=21.75 E-value=5.6e+02 Score=22.56 Aligned_cols=44 Identities=7% Similarity=0.034 Sum_probs=29.7
Q ss_pred CCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc
Q 027294 105 GPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ 150 (225)
Q Consensus 105 ~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~ 150 (225)
.+...+.+.|+++++.+ ++.++. +|++-.+.-+..++...++.+
T Consensus 197 ~~~eps~~~l~~l~~~i-k~~~v~-~if~e~~~~~~~~~~la~~~g 240 (266)
T cd01018 197 EGKEPSPADLKRLIDLA-KEKGVR-VVFVQPQFSTKSAEAIAREIG 240 (266)
T ss_pred CCCCCCHHHHHHHHHHH-HHcCCC-EEEEcCCCCcHHHHHHHHHcC
Confidence 44568999999999999 999998 555544444444444434444
No 54
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=21.49 E-value=3.4e+02 Score=23.65 Aligned_cols=77 Identities=14% Similarity=0.172 Sum_probs=49.8
Q ss_pred HHHHHHhcCCCCccChhhhccCHHHHHHHhCC-CCCCCceEEEeecCCCCCCcEEEEecCCCccchhhHHHHHHHHhhcC
Q 027294 47 RTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ-DPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125 (225)
Q Consensus 47 rTv~EMl~DRGY~V~~~El~~sldeF~~~yg~-~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~Ir~~~e~m~~~e 125 (225)
+-+.-||+.+||.|..-=.+.+.++|.+...+ +|+ -+.+++ --.-.+..++++++++ .+.
T Consensus 106 ~iv~~~l~~~G~~Vi~LG~~vp~e~~v~~~~~~~~~--~V~lS~----------------~~~~~~~~~~~~i~~L-~~~ 166 (213)
T cd02069 106 NLVGVILSNNGYEVIDLGVMVPIEKILEAAKEHKAD--IIGLSG----------------LLVPSLDEMVEVAEEM-NRR 166 (213)
T ss_pred HHHHHHHHhCCCEEEECCCCCCHHHHHHHHHHcCCC--EEEEcc----------------chhccHHHHHHHHHHH-Hhc
Confidence 44567999999999886667889999877532 222 222222 1124577889999999 777
Q ss_pred CCcEEEEEEcCCCCHHH
Q 027294 126 TLTGLILILQNQITSQA 142 (225)
Q Consensus 126 nv~r~IlVvq~~lT~~A 142 (225)
+.+--|+|-....|...
T Consensus 167 ~~~~~i~vGG~~~~~~~ 183 (213)
T cd02069 167 GIKIPLLIGGAATSRKH 183 (213)
T ss_pred CCCCeEEEEChhcCHHH
Confidence 77545555554555543
No 55
>COG3373 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.88 E-value=49 Score=26.49 Aligned_cols=38 Identities=24% Similarity=0.321 Sum_probs=25.9
Q ss_pred CCCCCCCC------ccccccccCCCChhhHHHHHHHHHHHHHHhcCCC
Q 027294 16 GNGYNGEP------TESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRG 57 (225)
Q Consensus 16 ~~~~~~~~------~~~~~~~~md~~~~e~~rL~rvrrTv~EMl~DRG 57 (225)
|+-||||. +.+|.-+ .-....||=---|.+.||++|..
T Consensus 58 g~RYnGe~SLi~LGLVe~~~~----nGfKyykltdygkk~veml~D~~ 101 (108)
T COG3373 58 GVRYNGEESLIGLGLVEVEQK----NGFKYYKLTEYGKKMVEMLRDKK 101 (108)
T ss_pred CCcccCchhhhhcceeEeeec----CCEEEEehhHHHHHHHHHHhccc
Confidence 67799986 4555543 33455666666788999998853
Done!