Query 030846
Match_columns 170
No_of_seqs 135 out of 340
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 05:27:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030846.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030846hhsearch_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 5.5E-66 1.2E-70 419.3 16.9 167 3-169 4-171 (208)
2 PLN03111 DNA-directed RNA poly 100.0 4.9E-65 1.1E-69 418.3 17.3 170 1-170 1-170 (206)
3 PTZ00061 DNA-directed RNA poly 100.0 1.6E-63 3.4E-68 408.9 17.1 166 5-170 2-169 (205)
4 PF03871 RNA_pol_Rpb5_N: RNA p 100.0 1.6E-34 3.6E-39 211.6 0.2 90 1-91 1-93 (93)
5 PRK09570 rpoH DNA-directed RNA 99.6 3.7E-16 8E-21 111.8 2.2 39 132-170 3-41 (79)
6 PF01191 RNA_pol_Rpb5_C: RNA p 99.6 9.6E-16 2.1E-20 108.5 2.1 38 133-170 1-38 (74)
7 COG2012 RPB5 DNA-directed RNA 99.6 1.4E-15 3E-20 108.1 2.3 42 128-169 2-43 (80)
8 PF04471 Mrr_cat: Restriction 96.9 0.0034 7.3E-08 44.9 5.9 64 66-132 48-112 (115)
9 TIGR00640 acid_CoA_mut_C methy 77.6 18 0.00039 27.7 7.8 86 15-117 19-104 (132)
10 cd02072 Glm_B12_BD B12 binding 71.1 29 0.00062 26.8 7.4 75 16-107 17-91 (128)
11 cd02067 B12-binding B12 bindin 63.9 53 0.0011 23.7 7.4 75 17-108 18-93 (119)
12 PF03345 DDOST_48kD: Oligosacc 63.5 37 0.0008 31.3 7.7 85 15-117 14-100 (423)
13 PF13607 Succ_CoA_lig: Succiny 63.0 15 0.00033 28.4 4.5 80 16-114 15-99 (138)
14 TIGR01501 MthylAspMutase methy 62.9 29 0.00063 27.0 6.0 75 15-106 18-92 (134)
15 PF13156 Mrr_cat_2: Restrictio 61.2 15 0.00033 28.5 4.2 81 38-118 16-99 (129)
16 cd02071 MM_CoA_mut_B12_BD meth 59.9 59 0.0013 24.0 7.1 74 18-108 19-92 (122)
17 PRK09539 tRNA-splicing endonuc 59.6 59 0.0013 25.2 7.2 65 21-103 43-107 (124)
18 PRK02261 methylaspartate mutas 58.1 70 0.0015 24.6 7.4 74 16-106 21-94 (137)
19 PRK08485 DNA polymerase III su 56.8 29 0.00063 29.1 5.4 45 70-115 30-75 (206)
20 KOG0975 Branched chain aminotr 50.4 6.9 0.00015 35.6 0.8 29 14-44 288-317 (379)
21 COG1787 Predicted endonuclease 49.9 42 0.0009 28.4 5.2 59 76-138 157-215 (217)
22 PRK08058 DNA polymerase III su 49.7 83 0.0018 27.4 7.4 96 68-163 80-185 (329)
23 cd02070 corrinoid_protein_B12- 48.8 1.1E+02 0.0023 24.7 7.4 76 17-109 101-178 (201)
24 PF13167 GTP-bdg_N: GTP-bindin 47.3 41 0.0009 24.7 4.4 53 78-135 41-93 (95)
25 TIGR02370 pyl_corrinoid methyl 47.0 1.1E+02 0.0024 24.6 7.3 77 16-109 102-180 (197)
26 COG4889 Predicted helicase [Ge 46.9 41 0.00088 34.8 5.4 82 54-136 61-155 (1518)
27 PF01939 DUF91: Protein of unk 46.3 35 0.00076 29.0 4.3 59 66-129 148-211 (228)
28 TIGR00689 rpiB_lacA_lacB sugar 42.8 60 0.0013 25.6 4.9 58 12-106 10-67 (144)
29 cd02069 methionine_synthase_B1 42.7 1E+02 0.0022 25.5 6.5 78 16-110 106-183 (213)
30 PF05920 Homeobox_KN: Homeobox 42.2 9.3 0.0002 23.6 0.2 24 143-166 7-30 (40)
31 PRK07132 DNA polymerase III su 39.3 1.8E+02 0.0039 25.4 7.8 88 75-163 66-165 (299)
32 PRK03298 hypothetical protein; 39.2 60 0.0013 27.6 4.7 50 67-117 148-201 (224)
33 PRK12399 tagatose 1,6-diphosph 36.7 70 0.0015 28.7 4.9 101 67-170 123-245 (324)
34 PF02310 B12-binding: B12 bind 36.7 1.5E+02 0.0033 20.9 6.9 97 16-131 18-115 (121)
35 PRK05571 ribose-5-phosphate is 36.7 88 0.0019 24.7 5.0 20 12-31 12-31 (148)
36 PRK05564 DNA polymerase III su 35.0 98 0.0021 26.4 5.5 86 74-159 69-164 (313)
37 COG1715 Mrr Restriction endonu 34.9 1.2E+02 0.0027 26.9 6.1 53 66-118 214-267 (308)
38 TIGR01120 rpiB ribose 5-phosph 34.8 98 0.0021 24.3 5.0 20 12-31 11-30 (143)
39 TIGR03798 ocin_TIGR03798 bacte 34.2 44 0.00096 22.2 2.6 20 16-35 28-47 (64)
40 COG1637 Predicted nuclease of 34.0 67 0.0014 27.8 4.2 49 68-117 175-227 (253)
41 PRK12615 galactose-6-phosphate 33.6 1.1E+02 0.0023 25.0 5.1 20 12-31 12-31 (171)
42 TIGR01232 lacD tagatose 1,6-di 33.3 72 0.0016 28.6 4.4 97 67-170 124-246 (325)
43 PRK04280 arginine repressor; P 31.7 1.7E+02 0.0037 22.9 5.9 25 16-40 22-46 (148)
44 PRK07993 DNA polymerase III su 31.0 1.2E+02 0.0025 26.8 5.4 95 68-163 76-184 (334)
45 TIGR02133 RPI_actino ribose 5- 29.3 73 0.0016 25.1 3.5 20 12-31 12-31 (148)
46 PTZ00215 ribose 5-phosphate is 29.2 1.6E+02 0.0034 23.4 5.4 20 12-31 14-35 (151)
47 TIGR00678 holB DNA polymerase 28.9 2.7E+02 0.0059 21.5 7.7 96 70-165 68-173 (188)
48 PRK05917 DNA polymerase III su 28.6 1.6E+02 0.0035 25.7 5.8 48 68-115 63-116 (290)
49 TIGR02328 conserved hypothetic 27.8 60 0.0013 25.1 2.6 23 9-31 48-70 (120)
50 PRK08622 galactose-6-phosphate 27.6 1.5E+02 0.0033 24.1 5.1 20 12-31 12-31 (171)
51 PF08011 DUF1703: Protein of u 27.5 1.5E+02 0.0033 21.3 4.7 44 17-73 9-53 (105)
52 cd02643 R3H_NF-X1 R3H domain o 27.4 1.3E+02 0.0029 20.7 4.2 48 81-129 16-63 (74)
53 PRK04161 tagatose 1,6-diphosph 27.2 1.2E+02 0.0027 27.2 4.8 102 67-170 125-247 (329)
54 PF07862 Nif11: Nitrogen fixat 27.0 37 0.00079 21.3 1.1 19 16-34 30-48 (49)
55 PRK06871 DNA polymerase III su 26.6 1.8E+02 0.0039 25.7 5.8 90 68-158 76-177 (325)
56 PLN02559 chalcone--flavonone i 26.3 49 0.0011 28.3 2.1 74 35-116 128-206 (230)
57 PF01650 Peptidase_C13: Peptid 25.8 2E+02 0.0044 24.4 5.8 49 61-109 102-162 (256)
58 KOG0373 Serine/threonine speci 25.4 32 0.00068 29.9 0.8 81 23-111 83-171 (306)
59 PF11985 DUF3486: Protein of u 24.9 35 0.00076 27.2 0.9 17 14-30 14-30 (180)
60 PRK03094 hypothetical protein; 24.6 31 0.00067 24.8 0.5 15 17-31 12-26 (80)
61 TIGR01119 lacB galactose-6-pho 24.3 1.9E+02 0.0041 23.5 5.1 20 12-31 12-31 (171)
62 cd01900 YchF YchF subfamily. 24.0 28 0.00062 30.0 0.3 23 147-169 244-266 (274)
63 KOG2130 Phosphatidylserine-spe 23.8 85 0.0018 28.6 3.2 62 77-144 117-180 (407)
64 COG1137 YhbG ABC-type (unclass 23.3 1.6E+02 0.0035 25.3 4.6 40 72-117 167-206 (243)
65 PRK09545 znuA high-affinity zi 23.2 4.9E+02 0.011 22.5 8.8 81 11-113 190-270 (311)
66 PRK07276 DNA polymerase III su 23.0 2.8E+02 0.006 24.2 6.2 94 68-163 74-178 (290)
67 PF11513 TA0956: Thermoplasma 22.8 2.1E+02 0.0046 21.4 4.6 58 38-97 45-106 (110)
68 PRK09426 methylmalonyl-CoA mut 22.7 3.3E+02 0.0071 26.9 7.2 88 13-117 596-684 (714)
69 PF13864 Enkurin: Calmodulin-b 21.7 56 0.0012 23.6 1.4 23 140-162 30-52 (98)
70 PF04355 SmpA_OmlA: SmpA / Oml 21.3 2.4E+02 0.0051 18.6 4.4 53 26-78 1-67 (71)
71 PLN00062 TATA-box-binding prot 21.2 4.5E+02 0.0097 21.3 6.9 89 8-119 66-169 (179)
72 KOG1232 Proteins containing th 21.0 79 0.0017 29.5 2.5 40 2-42 365-404 (511)
73 PF12641 Flavodoxin_3: Flavodo 20.9 2.6E+02 0.0057 22.0 5.2 52 66-117 68-123 (160)
74 PF02938 GAD: GAD domain; Int 20.7 59 0.0013 23.2 1.3 19 147-165 61-79 (95)
75 TIGR03147 cyt_nit_nrfF cytochr 20.5 1.2E+02 0.0025 23.6 3.0 31 13-49 61-91 (126)
76 COG4624 Iron only hydrogenase 20.4 70 0.0015 29.5 2.0 26 144-169 220-245 (411)
77 PRK05818 DNA polymerase III su 20.1 2.1E+02 0.0045 24.8 4.7 47 68-114 57-108 (261)
No 1
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=100.00 E-value=5.5e-66 Score=419.27 Aligned_cols=167 Identities=58% Similarity=0.890 Sum_probs=164.4
Q ss_pred CcHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCC-CCCcceEEEeecCCCCCCcEEEEeCCCCccchh
Q 030846 3 LSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGEN-MKREDLVINKALRNDSSDQIYVFFPDEQKVGVK 81 (170)
Q Consensus 3 ~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk 81 (170)
+++.|++||||+|||++||||||||.|+++|+++++++|+++||+. ++|++|+|++.|++||+++||||||++++||+|
T Consensus 4 ~~e~E~~rl~~ar~T~~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk 83 (208)
T KOG3218|consen 4 SKEEEIYRLYLARKTAMQMLRDRGYTVTQEELDLTLEEFKARYGDKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVK 83 (208)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhcCccccHHHhhhhHHHHHHHhccCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHH
Confidence 4578999999999999999999999999999999999999999998 889999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccccccccccccccccCHHHHHHHHhhcCC
Q 030846 82 TMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTV 161 (170)
Q Consensus 82 ~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni~~H~lVP~h~~l~~eE~~~ll~~y~~ 161 (170)
+||.|+.+|.++|+++||+|+|++|||+|++++..++|.|+||+|+|+||+||||+|+|||+|++||+|||++||++|++
T Consensus 84 ~~k~~~~~~~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l 163 (208)
T KOG3218|consen 84 TMKTYVIQMQSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKL 163 (208)
T ss_pred HHHHHHHHHHhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCC
Q 030846 162 KETQVSDK 169 (170)
Q Consensus 162 ~~~qlP~~ 169 (170)
+++|||+|
T Consensus 164 ~e~qLPRI 171 (208)
T KOG3218|consen 164 KETQLPRI 171 (208)
T ss_pred CcccCCee
Confidence 99999998
No 2
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=100.00 E-value=4.9e-65 Score=418.35 Aligned_cols=170 Identities=62% Similarity=0.940 Sum_probs=166.7
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccch
Q 030846 1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGV 80 (170)
Q Consensus 1 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgv 80 (170)
|++++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||++++|++|+|++++.+||+++|||||+++++||+
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 56788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccccccccccccccccCHHHHHHHHhhcC
Q 030846 81 KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYT 160 (170)
Q Consensus 81 k~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni~~H~lVP~h~~l~~eE~~~ll~~y~ 160 (170)
|+||.|+++|+++|+++||||+|+++||+|++++.++++.++||+|+|+||+||||+|+|||+|++||+|||++||++|+
T Consensus 81 k~ir~~~~~~~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y~ 160 (206)
T PLN03111 81 KTIKTYAERMKDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYT 160 (206)
T ss_pred HHHHHHHHHHhhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHcC
Confidence 99999999999999999999999999999999999998889999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCC
Q 030846 161 VKETQVSDKF 170 (170)
Q Consensus 161 ~~~~qlP~~~ 170 (170)
++++|||+|.
T Consensus 161 i~~~qLPrI~ 170 (206)
T PLN03111 161 VKETQLPRIQ 170 (206)
T ss_pred CCHHHCCccc
Confidence 9999999984
No 3
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=1.6e-63 Score=408.89 Aligned_cols=166 Identities=42% Similarity=0.659 Sum_probs=160.6
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCC-CCcceEEEeecCCCCCCcEEEEeCC-CCccchhH
Q 030846 5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-KREDLVINKALRNDSSDQIYVFFPD-EQKVGVKT 82 (170)
Q Consensus 5 ~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~-~r~~L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~ 82 (170)
++++.||||+|||++|||+||||.|+++|+++|+++|+++||+++ .|++|+|++++.+||+++|||||++ +++||+|+
T Consensus 2 ~~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~ 81 (205)
T PTZ00061 2 DDSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKP 81 (205)
T ss_pred cHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHH
Confidence 367899999999999999999999999999999999999999985 5899999999999999999999999 46999999
Q ss_pred HHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccccccccccccccccCHHHHHHHHhhcCCC
Q 030846 83 MKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVK 162 (170)
Q Consensus 83 Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~ 162 (170)
||.|+++|+++|++|||||+|+++||+|++++.++++.|+||+|+|+||+||||+|+|||+|++||+|||++||++|+++
T Consensus 82 ir~~~~~~~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i~ 161 (205)
T PTZ00061 82 IRELTEKMEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVK 161 (205)
T ss_pred HHHHHHHHhhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCCC
Confidence 99999999999999999999999999999999999988999999999999999999999999999999999999999999
Q ss_pred CCCCCCCC
Q 030846 163 ETQVSDKF 170 (170)
Q Consensus 163 ~~qlP~~~ 170 (170)
++|||+|.
T Consensus 162 ~~qLPrI~ 169 (205)
T PTZ00061 162 ESQLPRIQ 169 (205)
T ss_pred HHHCCccc
Confidence 99999984
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=99.98 E-value=1.6e-34 Score=211.63 Aligned_cols=90 Identities=62% Similarity=1.022 Sum_probs=74.6
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcC---CCCCcceEEEeecCCCCCCcEEEEeCCCCc
Q 030846 1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGE---NMKREDLVINKALRNDSSDQIYVFFPDEQK 77 (170)
Q Consensus 1 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~---~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~ 77 (170)
|+ +++|++||||||||++|||+||||.|+++|+++|+++|+++||+ .++|++|+|++.+.+||+++|+|||+++++
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 55 45999999999999999999999999999999999999999999 677999999999999999999999999999
Q ss_pred cchhHHHHHHHHHh
Q 030846 78 VGVKTMKTYTNRMK 91 (170)
Q Consensus 78 vgvk~Ir~~~~~~~ 91 (170)
||+|+||.|+++|+
T Consensus 80 vgvk~Ir~~~~~m~ 93 (93)
T PF03871_consen 80 VGVKTIRKYCERMK 93 (93)
T ss_dssp ESCCCCHHHCHHH-
T ss_pred cCHHHHHHHHHhcC
Confidence 99999999999984
No 5
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=99.59 E-value=3.7e-16 Score=111.77 Aligned_cols=39 Identities=41% Similarity=0.666 Sum_probs=37.6
Q ss_pred ccccccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846 132 LVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF 170 (170)
Q Consensus 132 l~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~ 170 (170)
.||||+|+|||+|++||+||+++||++|+++++|||||.
T Consensus 3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~ 41 (79)
T PRK09570 3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIK 41 (79)
T ss_pred ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCcee
Confidence 589999999999999999999999999999999999984
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=99.56 E-value=9.6e-16 Score=108.45 Aligned_cols=38 Identities=47% Similarity=0.819 Sum_probs=31.8
Q ss_pred cccccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846 133 VNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF 170 (170)
Q Consensus 133 ~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~ 170 (170)
||||+|+|||+|++||+||++++|++|+++++|||+|.
T Consensus 1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~ 38 (74)
T PF01191_consen 1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKIL 38 (74)
T ss_dssp S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEE
T ss_pred CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCccc
Confidence 79999999999999999999999999999999999973
No 7
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=99.55 E-value=1.4e-15 Score=108.09 Aligned_cols=42 Identities=40% Similarity=0.616 Sum_probs=40.5
Q ss_pred ccccccccccccccccccccCHHHHHHHHhhcCCCCCCCCCC
Q 030846 128 EAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDK 169 (170)
Q Consensus 128 e~ELl~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~ 169 (170)
++.+.||+++|+|||+|++||+||++++|++|+|+++|||||
T Consensus 2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI 43 (80)
T COG2012 2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKI 43 (80)
T ss_pred ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCcc
Confidence 567899999999999999999999999999999999999998
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=96.86 E-value=0.0034 Score=44.91 Aligned_cols=64 Identities=22% Similarity=0.376 Sum_probs=38.3
Q ss_pred CcEEEEeCC-CCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccc
Q 030846 66 DQIYVFFPD-EQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELL 132 (170)
Q Consensus 66 ~~i~VfF~~-~~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl 132 (170)
..++|.+-. ..+++.+.|+.++..+...+...++||+.+++|+.|++.+.... .|+++.-++|.
T Consensus 48 ~~~~vqcK~~~~~v~~~~v~~~~~~~~~~~~~~~iivt~~~~t~~a~~~~~~~~---~I~l~d~~~L~ 112 (115)
T PF04471_consen 48 ERILVQCKRYKKKVDVKAVRQLIGKAKKYGADKGIIVTSSGFTPEAKEFAEKFK---NIELIDGEDLQ 112 (115)
T ss_dssp EEEEEEE---S-EE-HHHHHHHHHHHGGGT-SEEEEE-SSEE-HHHHHHHH-----------------
T ss_pred eEEEEEEEEeccccchHHHHHHhhhhhccCCCEEEEEECCcCCHHHHHHHHhhc---ccccccccccc
Confidence 466666633 35899999999999999999999999999999999999887653 47777766663
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=77.64 E-value=18 Score=27.72 Aligned_cols=86 Identities=10% Similarity=0.070 Sum_probs=56.3
Q ss_pred HHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcC
Q 030846 15 RRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSEN 94 (170)
Q Consensus 15 rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~ 94 (170)
.+-+.-||++-||.|-+.-...|.++|.+..-+. +-+-+.+ |.-..-.+..++.+++.+.+++
T Consensus 19 ~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e~-~adii~i----------------Ssl~~~~~~~~~~~~~~L~~~g 81 (132)
T TIGR00640 19 AKVIATAYADLGFDVDVGPLFQTPEEIARQAVEA-DVHVVGV----------------SSLAGGHLTLVPALRKELDKLG 81 (132)
T ss_pred HHHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHc-CCCEEEE----------------cCchhhhHHHHHHHHHHHHhcC
Confidence 3556789999999999988889999998875332 1111222 2222335667888999998888
Q ss_pred CCeEEEEEcCCCCHHHHHHHHhc
Q 030846 95 VFRAILVVQQNLTPFARTCIQEI 117 (170)
Q Consensus 95 ~~~~IiV~q~~lt~~Ar~~~~~~ 117 (170)
.....+++.+.+.+.-...+.++
T Consensus 82 ~~~i~vivGG~~~~~~~~~l~~~ 104 (132)
T TIGR00640 82 RPDILVVVGGVIPPQDFDELKEM 104 (132)
T ss_pred CCCCEEEEeCCCChHhHHHHHHC
Confidence 86655566655555434445444
No 10
>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=71.12 E-value=29 Score=26.82 Aligned_cols=75 Identities=16% Similarity=0.242 Sum_probs=53.1
Q ss_pred HHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCC
Q 030846 16 RTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV 95 (170)
Q Consensus 16 rTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~ 95 (170)
+-+.-||++.||.|-+--++.|.++|.+..-+. +-+-+.+++ --.-++..++..++.+.+.++
T Consensus 17 niv~~~L~~~GfeVidLG~~v~~e~~v~aa~~~-~adiVglS~----------------L~t~~~~~~~~~~~~l~~~gl 79 (128)
T cd02072 17 KILDHAFTEAGFNVVNLGVLSPQEEFIDAAIET-DADAILVSS----------------LYGHGEIDCKGLREKCDEAGL 79 (128)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEec----------------cccCCHHHHHHHHHHHHHCCC
Confidence 455669999999999988899999999976433 122233332 112456778899999999999
Q ss_pred CeEEEEEcCCCC
Q 030846 96 FRAILVVQQNLT 107 (170)
Q Consensus 96 ~~~IiV~q~~lt 107 (170)
....+++.+.+.
T Consensus 80 ~~v~vivGG~~~ 91 (128)
T cd02072 80 KDILLYVGGNLV 91 (128)
T ss_pred CCCeEEEECCCC
Confidence 666667777653
No 11
>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=63.95 E-value=53 Score=23.75 Aligned_cols=75 Identities=21% Similarity=0.267 Sum_probs=47.4
Q ss_pred HHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCC-
Q 030846 17 TVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV- 95 (170)
Q Consensus 17 Tv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~- 95 (170)
-+..+++..||.|..-..+++.++|.+..... +|. +|.++....-....++.+++.+++.+.
T Consensus 18 ~~~~~l~~~G~~V~~lg~~~~~~~l~~~~~~~--------------~pd---vV~iS~~~~~~~~~~~~~i~~l~~~~~~ 80 (119)
T cd02067 18 IVARALRDAGFEVIDLGVDVPPEEIVEAAKEE--------------DAD---AIGLSGLLTTHMTLMKEVIEELKEAGLD 80 (119)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc--------------CCC---EEEEeccccccHHHHHHHHHHHHHcCCC
Confidence 45678999999997766778898998754221 111 222222223356788889999988766
Q ss_pred CeEEEEEcCCCCH
Q 030846 96 FRAILVVQQNLTP 108 (170)
Q Consensus 96 ~~~IiV~q~~lt~ 108 (170)
.-.|+|.....+.
T Consensus 81 ~~~i~vGG~~~~~ 93 (119)
T cd02067 81 DIPVLVGGAIVTR 93 (119)
T ss_pred CCeEEEECCCCCh
Confidence 4445555544454
No 12
>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=63.47 E-value=37 Score=31.34 Aligned_cols=85 Identities=20% Similarity=0.318 Sum_probs=48.8
Q ss_pred HHHHHHHhcCCCCCCChhhhc-cCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhc
Q 030846 15 RRTVMQMLRDRGYFVGDFEIN-MSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSE 93 (170)
Q Consensus 15 rrTv~eMl~DRGY~v~~~e~~-~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e 93 (170)
..+.++.|++|||.++=...+ -+++-| +||+.. .+.|.+...+.+. |. +.++++.|-+|++.
T Consensus 14 yS~Ff~~L~~rg~~l~~~~~~d~~l~L~--~~ge~~-YD~LIif~~~~k~--------~g--~~ls~~~ll~Fvd~---- 76 (423)
T PF03345_consen 14 YSTFFNSLKERGYELTFKSADDESLSLF--KYGERL-YDHLIIFPPSVKE--------FG--GSLSPKTLLDFVDN---- 76 (423)
T ss_pred HHHHHHHHHhCCCEEEEecCCCCCcchh--hCChhh-cceEEEeCCcccc--------cC--CCCCHHHHHHHHhC----
Confidence 678899999999999522221 122233 244332 4556554433221 22 35788888887662
Q ss_pred CCCeEEEEEcCC-CCHHHHHHHHhc
Q 030846 94 NVFRAILVVQQN-LTPFARTCIQEI 117 (170)
Q Consensus 94 ~~~~~IiV~q~~-lt~~Ar~~~~~~ 117 (170)
| ...++++.+. ++...|..+.++
T Consensus 77 G-gNilv~~s~~~~~~~ir~~~~E~ 100 (423)
T PF03345_consen 77 G-GNILVAGSSDAIPDSIREFANEL 100 (423)
T ss_pred C-CcEEEEeCCCcCcHHHHHHHHHC
Confidence 3 3355555555 667777776665
No 13
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=62.98 E-value=15 Score=28.39 Aligned_cols=80 Identities=11% Similarity=0.253 Sum_probs=41.5
Q ss_pred HHHHHHhcCCCCCCC-----hhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHH
Q 030846 16 RTVMQMLRDRGYFVG-----DFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRM 90 (170)
Q Consensus 16 rTv~eMl~DRGY~v~-----~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~ 90 (170)
-+++.++.+||.-++ -.+..++..++.+.+.+ ||.-++.+.|.+. ++.=+.|++.+
T Consensus 15 ~~~~~~~~~~g~g~s~~vs~Gn~~dv~~~d~l~~~~~---------------D~~t~~I~ly~E~----~~d~~~f~~~~ 75 (138)
T PF13607_consen 15 TAILDWAQDRGIGFSYVVSVGNEADVDFADLLEYLAE---------------DPDTRVIVLYLEG----IGDGRRFLEAA 75 (138)
T ss_dssp HHHHHHHHHTT-EESEEEE-TT-SSS-HHHHHHHHCT----------------SS--EEEEEES------S-HHHHHHHH
T ss_pred HHHHHHHHHcCCCeeEEEEeCccccCCHHHHHHHHhc---------------CCCCCEEEEEccC----CCCHHHHHHHH
Confidence 357888999988775 34567788899887644 4445555555542 22237888888
Q ss_pred hhcCCCeEEEEEcCCCCHHHHHHH
Q 030846 91 KSENVFRAILVVQQNLTPFARTCI 114 (170)
Q Consensus 91 ~~e~~~~~IiV~q~~lt~~Ar~~~ 114 (170)
..-...+=|++++.+-|+..+++.
T Consensus 76 ~~a~~~KPVv~lk~Grt~~g~~aa 99 (138)
T PF13607_consen 76 RRAARRKPVVVLKAGRTEAGARAA 99 (138)
T ss_dssp HHHCCCS-EEEEE-----------
T ss_pred HHHhcCCCEEEEeCCCchhhhhhh
Confidence 765555778888888877666553
No 14
>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=62.92 E-value=29 Score=26.95 Aligned_cols=75 Identities=17% Similarity=0.253 Sum_probs=52.0
Q ss_pred HHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcC
Q 030846 15 RRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSEN 94 (170)
Q Consensus 15 rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~ 94 (170)
.+-+.-||++.||.|-+-=...|.++|.+..-+. +-+-+.+|.. -.-.+..++.+.+.+.+++
T Consensus 18 k~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~~~-~adiVglS~l----------------~~~~~~~~~~~~~~l~~~g 80 (134)
T TIGR01501 18 NKILDHAFTNAGFNVVNLGVLSPQEEFIKAAIET-KADAILVSSL----------------YGHGEIDCKGLRQKCDEAG 80 (134)
T ss_pred HHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEecc----------------cccCHHHHHHHHHHHHHCC
Confidence 3567789999999999888889999999875333 1222333321 1234556888999999999
Q ss_pred CCeEEEEEcCCC
Q 030846 95 VFRAILVVQQNL 106 (170)
Q Consensus 95 ~~~~IiV~q~~l 106 (170)
+....+|+.+.+
T Consensus 81 l~~~~vivGG~~ 92 (134)
T TIGR01501 81 LEGILLYVGGNL 92 (134)
T ss_pred CCCCEEEecCCc
Confidence 876666666653
No 15
>PF13156 Mrr_cat_2: Restriction endonuclease
Probab=61.25 E-value=15 Score=28.52 Aligned_cols=81 Identities=10% Similarity=0.158 Sum_probs=51.3
Q ss_pred HHHHHHHhcCCCCCcceEEEeecCCCC-CCcEEEEe-CCCCccchhHHHHHHHHHhhcCCCeEEEEEcC-CCCHHHHHHH
Q 030846 38 KEQFIAKFGENMKREDLVINKALRNDS-SDQIYVFF-PDEQKVGVKTMKTYTNRMKSENVFRAILVVQQ-NLTPFARTCI 114 (170)
Q Consensus 38 ~~~F~~~~~~~~~r~~L~~~~~~~~dp-~~~i~VfF-~~~~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~-~lt~~Ar~~~ 114 (170)
..+|..+++.+..-.-.-+.+...++. -=-|-+-| ..+.+|..+.|-.|+.......+.+.|||.-. ++++.|.+++
T Consensus 16 w~dwp~~~~~~~~DtGIDLVA~~~~~g~~~AIQCKfY~~~~~I~k~didSF~s~sgk~~f~~rliisTt~~~s~nAe~~l 95 (129)
T PF13156_consen 16 WSDWPERYGWGGKDTGIDLVARTRDGGEYWAIQCKFYDPDHTIQKSDIDSFFSASGKSRFSRRLIISTTDKWSKNAEKAL 95 (129)
T ss_pred hhhhhHhhCCCCCCCCEeEEEEEcCCCcEEEEEEEeeCCCceEcHHHhhHHHHhcCCccccCcEEEEcCcHhhHHHHHHH
Confidence 456665554331111144444433321 11344444 55568999999999999887888877777664 6899999988
Q ss_pred Hhcc
Q 030846 115 QEIS 118 (170)
Q Consensus 115 ~~~~ 118 (170)
..-.
T Consensus 96 ~~q~ 99 (129)
T PF13156_consen 96 ENQS 99 (129)
T ss_pred HcCC
Confidence 7654
No 16
>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=59.90 E-value=59 Score=24.00 Aligned_cols=74 Identities=12% Similarity=0.081 Sum_probs=47.9
Q ss_pred HHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCCCe
Q 030846 18 VMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFR 97 (170)
Q Consensus 18 v~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~~~ 97 (170)
+.-|++..||.|..--.+.+.++|.+.-.+. +.+- +.+.+.. .-....++.+++.+.+.+...
T Consensus 19 ~~~~l~~~G~~vi~lG~~vp~e~~~~~a~~~-~~d~--------------V~iS~~~--~~~~~~~~~~~~~L~~~~~~~ 81 (122)
T cd02071 19 IARALRDAGFEVIYTGLRQTPEEIVEAAIQE-DVDV--------------IGLSSLS--GGHMTLFPEVIELLRELGAGD 81 (122)
T ss_pred HHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCE--------------EEEcccc--hhhHHHHHHHHHHHHhcCCCC
Confidence 4468999999998877778899998754322 1111 2222222 345667899999998888866
Q ss_pred EEEEEcCCCCH
Q 030846 98 AILVVQQNLTP 108 (170)
Q Consensus 98 ~IiV~q~~lt~ 108 (170)
..+++.+...+
T Consensus 82 i~i~~GG~~~~ 92 (122)
T cd02071 82 ILVVGGGIIPP 92 (122)
T ss_pred CEEEEECCCCH
Confidence 55566555433
No 17
>PRK09539 tRNA-splicing endonuclease subunit beta; Reviewed
Probab=59.60 E-value=59 Score=25.18 Aligned_cols=65 Identities=22% Similarity=0.154 Sum_probs=35.1
Q ss_pred HhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCCCeEEE
Q 030846 21 MLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAIL 100 (170)
Q Consensus 21 Ml~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~~~~Ii 100 (170)
=||+|||.|... . .||.- +... ..+...-+......+..+....|-.+......-+-+-.+=
T Consensus 43 DLR~RGyvVk~G-~---------kfg~~-------~~~~-~~~~s~ylV~Vl~E~~~is~~eL~~~vr~a~svrK~lVLA 104 (124)
T PRK09539 43 DLKQRGRKTIDG-I---------DEISL-------IIKD-KENKYTAMVLIVDENEKVSFKKILDKLHFSKSMNLELYLA 104 (124)
T ss_pred hHHhCCCeeccC-C---------ceeEE-------EEec-CCCCceEEEEEecCCCccCHHHHHHHHHHHhhccceeEEE
Confidence 489999999772 1 12211 1111 2233333333346667899999987766665444443443
Q ss_pred EEc
Q 030846 101 VVQ 103 (170)
Q Consensus 101 V~q 103 (170)
|+.
T Consensus 105 VVD 107 (124)
T PRK09539 105 IVD 107 (124)
T ss_pred EEc
Confidence 443
No 18
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=58.13 E-value=70 Score=24.55 Aligned_cols=74 Identities=18% Similarity=0.223 Sum_probs=49.3
Q ss_pred HHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCC
Q 030846 16 RTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV 95 (170)
Q Consensus 16 rTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~ 95 (170)
+-+.-|+++.||.|..-=.+.+.++|.+.-... +.+-+.++ +.. .-....++.+++.+.+.+.
T Consensus 21 ~iv~~~lr~~G~eVi~LG~~vp~e~i~~~a~~~-~~d~V~lS--------------~~~--~~~~~~~~~~~~~L~~~~~ 83 (137)
T PRK02261 21 KILDRALTEAGFEVINLGVMTSQEEFIDAAIET-DADAILVS--------------SLY--GHGEIDCRGLREKCIEAGL 83 (137)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEc--------------Ccc--ccCHHHHHHHHHHHHhcCC
Confidence 345569999999998877778899998854222 11122222 222 2467778889999988878
Q ss_pred CeEEEEEcCCC
Q 030846 96 FRAILVVQQNL 106 (170)
Q Consensus 96 ~~~IiV~q~~l 106 (170)
....+++.+.+
T Consensus 84 ~~~~i~vGG~~ 94 (137)
T PRK02261 84 GDILLYVGGNL 94 (137)
T ss_pred CCCeEEEECCC
Confidence 66666666666
No 19
>PRK08485 DNA polymerase III subunit delta'; Validated
Probab=56.82 E-value=29 Score=29.14 Aligned_cols=45 Identities=16% Similarity=0.171 Sum_probs=31.2
Q ss_pred EEeCCCCccchhHHHHHHHHHhh-cCCCeEEEEEcCCCCHHHHHHHH
Q 030846 70 VFFPDEQKVGVKTMKTYTNRMKS-ENVFRAILVVQQNLTPFARTCIQ 115 (170)
Q Consensus 70 VfF~~~~~vgvk~Ir~~~~~~~~-e~~~~~IiV~q~~lt~~Ar~~~~ 115 (170)
.+|+.+ .+|+..||.+++.+.- .+-.+.||.--..+|..|..++-
T Consensus 30 ~~f~~~-~i~Vd~iReii~~~~~~~~~~k~iI~~a~~l~~~A~NaLL 75 (206)
T PRK08485 30 RFFIKE-EFKIEDAKEVIAEAYIAESEEKIIVIAAPSYGIEAQNALL 75 (206)
T ss_pred EEECCC-CCCHHHHHHHHHHHhhCCCCcEEEEEchHhhCHHHHHHHH
Confidence 344443 6999999999999743 33445666666778988776553
No 20
>KOG0975 consensus Branched chain aminotransferase BCAT1, pyridoxal phosphate enzymes type IV superfamily [Amino acid transport and metabolism]
Probab=50.37 E-value=6.9 Score=35.60 Aligned_cols=29 Identities=17% Similarity=0.508 Sum_probs=23.8
Q ss_pred HHHHHHHHhcCCC-CCCChhhhccCHHHHHHH
Q 030846 14 IRRTVMQMLRDRG-YFVGDFEINMSKEQFIAK 44 (170)
Q Consensus 14 ~rrTv~eMl~DRG-Y~v~~~e~~~s~~~F~~~ 44 (170)
.|++++|+++|+| |.|.+ -++|.++|.+-
T Consensus 288 TR~sileLa~~~g~~~V~E--r~vtv~e~~~A 317 (379)
T KOG0975|consen 288 TRKSILELARDLGEFKVEE--RDVTVDELKTA 317 (379)
T ss_pred cHHHHHHHHHHhCceEEEE--EEEeHHHhhhh
Confidence 4899999999999 99987 45577788753
No 21
>COG1787 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]
Probab=49.87 E-value=42 Score=28.42 Aligned_cols=59 Identities=19% Similarity=0.154 Sum_probs=48.8
Q ss_pred CccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccccccc
Q 030846 76 QKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEH 138 (170)
Q Consensus 76 ~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni~~H 138 (170)
..|+.+.|+++....-.-++..+++|+.+..|-.|++. ...+ .+|+..-+++..++..-
T Consensus 157 ~aV~~kaiqEivask~~Y~~eka~vvTn~~yt~~aqkl-a~~n---sv~l~~r~~~~~f~~~~ 215 (217)
T COG1787 157 SAVSKKAIQEIVASKAYYGCEKAKVVTNGSYTYAAQKL-AQAN---SVELIDRDELSEFIREG 215 (217)
T ss_pred HhhhHHHHHHHHHhhhccCcceEEEecCCccchhHHHH-HHhh---cceEEecchHHhhhccc
Confidence 36899999999888888999999999999999999775 4333 68889999988887643
No 22
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=49.74 E-value=83 Score=27.37 Aligned_cols=96 Identities=15% Similarity=0.198 Sum_probs=55.4
Q ss_pred EEEEeCCCCccchhHHHHHHHHHh---hcCCCeEEEEEc-CCCCHHHHHHHHhc---ccccceeeeec---ccccccccc
Q 030846 68 IYVFFPDEQKVGVKTMKTYTNRMK---SENVFRAILVVQ-QNLTPFARTCIQEI---SAKFHLEVFQE---AELLVNIKE 137 (170)
Q Consensus 68 i~VfF~~~~~vgvk~Ir~~~~~~~---~e~~~~~IiV~q-~~lt~~Ar~~~~~~---~~~~~iE~F~e---~ELl~ni~~ 137 (170)
+....+++..+++..||..++.+. -++-.+.+||-. +.+|..|-.++-.. +|...+=+|.- ..|+-=|-.
T Consensus 80 ~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrS 159 (329)
T PRK08058 80 VHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILS 159 (329)
T ss_pred EEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHh
Confidence 344445567799999999999886 455567888877 66888665444322 22323322321 112111222
Q ss_pred ccccccccccCHHHHHHHHhhcCCCC
Q 030846 138 HVLVPEHQVLTNEEKKTLLKRYTVKE 163 (170)
Q Consensus 138 H~lVP~h~~l~~eE~~~ll~~y~~~~ 163 (170)
--.+=.-..+++++-.+.|++.++.+
T Consensus 160 Rc~~i~~~~~~~~~~~~~L~~~gi~~ 185 (329)
T PRK08058 160 RCQVVEFRPLPPESLIQRLQEEGISE 185 (329)
T ss_pred hceeeeCCCCCHHHHHHHHHHcCCCh
Confidence 22222345578888888888776654
No 23
>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=48.76 E-value=1.1e+02 Score=24.70 Aligned_cols=76 Identities=20% Similarity=0.236 Sum_probs=48.3
Q ss_pred HHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCC-
Q 030846 17 TVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV- 95 (170)
Q Consensus 17 Tv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~- 95 (170)
=+-.+++..||.|..--.+.+.++|.+.-... +.+-+.+++ ...-....++.+++.+.+.+.
T Consensus 101 ~v~~~l~~~G~~vi~lG~~~p~~~l~~~~~~~-~~d~v~lS~----------------~~~~~~~~~~~~i~~lr~~~~~ 163 (201)
T cd02070 101 LVATMLEANGFEVIDLGRDVPPEEFVEAVKEH-KPDILGLSA----------------LMTTTMGGMKEVIEALKEAGLR 163 (201)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEec----------------cccccHHHHHHHHHHHHHCCCC
Confidence 34568888999997655678888888854222 111222222 122356788999999988876
Q ss_pred -CeEEEEEcCCCCHH
Q 030846 96 -FRAILVVQQNLTPF 109 (170)
Q Consensus 96 -~~~IiV~q~~lt~~ 109 (170)
+--|+|-....++.
T Consensus 164 ~~~~i~vGG~~~~~~ 178 (201)
T cd02070 164 DKVKVMVGGAPVNQE 178 (201)
T ss_pred cCCeEEEECCcCCHH
Confidence 44566666666654
No 24
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=47.33 E-value=41 Score=24.68 Aligned_cols=53 Identities=13% Similarity=0.338 Sum_probs=39.1
Q ss_pred cchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeecccccccc
Q 030846 78 VGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNI 135 (170)
Q Consensus 78 vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni 135 (170)
+|.--+..+.+.+...++. .+|+.+.+||...+.+.... .++++.-..|+..|
T Consensus 41 iG~GK~eei~~~~~~~~~d--~vvfd~~Lsp~Q~rNLe~~~---~~~V~DRt~LIL~I 93 (95)
T PF13167_consen 41 IGSGKVEEIKELIEELDAD--LVVFDNELSPSQQRNLEKAL---GVKVIDRTQLILEI 93 (95)
T ss_pred echhHHHHHHHHHhhcCCC--EEEECCCCCHHHHHHHHHHH---CCeeeccccHHHHH
Confidence 4555666666766667774 45667889999988888764 68888888887766
No 25
>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=46.95 E-value=1.1e+02 Score=24.62 Aligned_cols=77 Identities=19% Similarity=0.188 Sum_probs=50.7
Q ss_pred HHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCC
Q 030846 16 RTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV 95 (170)
Q Consensus 16 rTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~ 95 (170)
+-+..|++..||.|..--.+.+.++|.+..-.. +.+-+.+++. -.-.+..++.+++.+.+.+.
T Consensus 102 ~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~~~~-~pd~v~lS~~----------------~~~~~~~~~~~i~~l~~~~~ 164 (197)
T TIGR02370 102 NIVVTMLRANGFDVIDLGRDVPIDTVVEKVKKE-KPLMLTGSAL----------------MTTTMYGQKDINDKLKEEGY 164 (197)
T ss_pred HHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHc-CCCEEEEccc----------------cccCHHHHHHHHHHHHHcCC
Confidence 345678999999998877788899998864222 1222333332 12345678999999998877
Q ss_pred C--eEEEEEcCCCCHH
Q 030846 96 F--RAILVVQQNLTPF 109 (170)
Q Consensus 96 ~--~~IiV~q~~lt~~ 109 (170)
. --|+|-...+|+.
T Consensus 165 ~~~v~i~vGG~~~~~~ 180 (197)
T TIGR02370 165 RDSVKFMVGGAPVTQD 180 (197)
T ss_pred CCCCEEEEEChhcCHH
Confidence 5 3466666666664
No 26
>COG4889 Predicted helicase [General function prediction only]
Probab=46.86 E-value=41 Score=34.77 Aligned_cols=82 Identities=12% Similarity=0.208 Sum_probs=61.3
Q ss_pred eEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcc-cc------------
Q 030846 54 LVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS-AK------------ 120 (170)
Q Consensus 54 L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~-~~------------ 120 (170)
+...+...++.--.|-+-|-. .+++...|..|...+..-++++++||.-...|+-|.+++.... +-
T Consensus 61 idlva~~d~g~ytaiQcKFy~-nslak~di~sF~t~lgkt~f~~gliiSTtdw~sNA~~aieq~~~~~~~Iglsei~es~ 139 (1518)
T COG4889 61 IDLVAREDNGNYTAIQCKFYQ-NSLAKGDIDSFFTALGKTGFKNGLIISTTDWTSNAEKAIEQQRSPGMRIGLSEIAESP 139 (1518)
T ss_pred eeEEEEccCCCeEEEEeeeec-cccccccccHHHHHhccccccCceEEEecccchhHHHHHHhhhCccceecHHHHhcCC
Confidence 444444322222346666654 6899999999999999999999999998889999999987653 11
Q ss_pred cceeeeeccccccccc
Q 030846 121 FHLEVFQEAELLVNIK 136 (170)
Q Consensus 121 ~~iE~F~e~ELl~ni~ 136 (170)
...++|...||..|++
T Consensus 140 IDW~~f~p~e~~~nl~ 155 (1518)
T COG4889 140 IDWDIFDPTELQDNLP 155 (1518)
T ss_pred CChhhcCccccccccc
Confidence 3457788899999986
No 27
>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=46.32 E-value=35 Score=28.95 Aligned_cols=59 Identities=22% Similarity=0.354 Sum_probs=35.2
Q ss_pred CcEEEEeCCC-C-ccchhHHHHHHHHHhhcC---CCeEEEEEcCCCCHHHHHHHHhcccccceeeeecc
Q 030846 66 DQIYVFFPDE-Q-KVGVKTMKTYTNRMKSEN---VFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEA 129 (170)
Q Consensus 66 ~~i~VfF~~~-~-~vgvk~Ir~~~~~~~~e~---~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ 129 (170)
+-+.|..--. . .=++.++..|++.+.++. -=|||+|.++ +|+.|+..+.+ ..||+...+
T Consensus 148 ~~VVIElKR~~a~~~aV~QL~rY~~~l~~~~~~~~VRGilvA~~-i~~~a~~ll~~----~glef~~ld 211 (228)
T PF01939_consen 148 NLVVIELKRRRADRDAVEQLLRYVELLKRDPGLEPVRGILVAPS-ITPQARELLED----RGLEFVELD 211 (228)
T ss_dssp -EEEEEE-SS-B-HHHHHHHHHHHHHHHHHH--S-EEEEEEES--B-HHHHHHHHH----HT-EEEE--
T ss_pred CEEEEEEEeccCCHHHHHHHHHHHHHHhhccCCCceeEEEECCC-CCHHHHHHHHH----cCCEEEEec
Confidence 3466666443 2 236777777888886533 2389999865 99999988865 357766544
No 28
>TIGR00689 rpiB_lacA_lacB sugar-phosphate isomerases, RpiB/LacA/LacB family. Proteins of known function in this family act as sugar (pentose and/or hexose)-phosphate isomerases, including the LacA and LacB subunits of galactose-6-phosphate isomerases from Gram-positive bacteria and RpiB. RpiB is the second ribose phosphate isomerase of E. coli. It lacks homology to RpiA, its inducer is unknown (but is not ribose), and it can be replaced by the homologous galactose-6-phosphate isomerase of Streptococcus mutans, all of which suggests that the ribose phosphate isomerase activity of RpiB is a secondary function. On the other hand, there appear to be a significant number of species which contain rpiB, lack rpiA and seem to require rpi activity in order to copplete the pentose phosphate pathway.
Probab=42.84 E-value=60 Score=25.59 Aligned_cols=58 Identities=21% Similarity=0.395 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHh
Q 030846 12 FRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMK 91 (170)
Q Consensus 12 ~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~ 91 (170)
|.-+..+.+.|+++||.|.+ +|... +++ +-||+ .-....+.+.
T Consensus 10 ~~lK~~l~~~L~~~g~eV~D-------------~G~~~------------~~~-----~dYpd-------~a~~va~~V~ 52 (144)
T TIGR00689 10 LELKSEIIEHLKQKGHEVID-------------CGTLY------------DER-----VDYPD-------YAKLVADKVV 52 (144)
T ss_pred HHHHHHHHHHHHHCCCEEEE-------------cCCCC------------CCC-----CChHH-------HHHHHHHHHH
Confidence 45677899999999999977 33321 111 11332 1234555566
Q ss_pred hcCCCeEEEEEcCCC
Q 030846 92 SENVFRAILVVQQNL 106 (170)
Q Consensus 92 ~e~~~~~IiV~q~~l 106 (170)
+...++||+|+..++
T Consensus 53 ~g~~~~GIliCGtGi 67 (144)
T TIGR00689 53 AGEVSLGILICGTGI 67 (144)
T ss_pred cCCCceEEEEcCCcH
Confidence 677888998888876
No 29
>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=42.75 E-value=1e+02 Score=25.46 Aligned_cols=78 Identities=15% Similarity=0.162 Sum_probs=52.3
Q ss_pred HHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCC
Q 030846 16 RTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV 95 (170)
Q Consensus 16 rTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~ 95 (170)
+=+.-||+.+||.|..--.+.+.++|.+...+. +.+-+.+++ ...-++..++.+++.+.+.+.
T Consensus 106 ~iv~~~l~~~G~~Vi~LG~~vp~e~~v~~~~~~-~~~~V~lS~----------------~~~~~~~~~~~~i~~L~~~~~ 168 (213)
T cd02069 106 NLVGVILSNNGYEVIDLGVMVPIEKILEAAKEH-KADIIGLSG----------------LLVPSLDEMVEVAEEMNRRGI 168 (213)
T ss_pred HHHHHHHHhCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEcc----------------chhccHHHHHHHHHHHHhcCC
Confidence 345678999999998877788999998865332 122222222 123467788999999988888
Q ss_pred CeEEEEEcCCCCHHH
Q 030846 96 FRAILVVQQNLTPFA 110 (170)
Q Consensus 96 ~~~IiV~q~~lt~~A 110 (170)
+--|+|-....|...
T Consensus 169 ~~~i~vGG~~~~~~~ 183 (213)
T cd02069 169 KIPLLIGGAATSRKH 183 (213)
T ss_pred CCeEEEEChhcCHHH
Confidence 555666655666543
No 30
>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=42.20 E-value=9.3 Score=23.63 Aligned_cols=24 Identities=25% Similarity=0.342 Sum_probs=18.0
Q ss_pred cccccCHHHHHHHHhhcCCCCCCC
Q 030846 143 EHQVLTNEEKKTLLKRYTVKETQV 166 (170)
Q Consensus 143 ~h~~l~~eE~~~ll~~y~~~~~ql 166 (170)
.|+--|++||++|.+..++...|+
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 467789999999999999987775
No 31
>PRK07132 DNA polymerase III subunit delta'; Validated
Probab=39.33 E-value=1.8e+02 Score=25.36 Aligned_cols=88 Identities=7% Similarity=0.051 Sum_probs=51.9
Q ss_pred CCccchhHHHHHHHHHhhc----CCCeEEEEEc-CCCCHHHHHHH----Hhcccccceeeeeccc--ccc-ccccccccc
Q 030846 75 EQKVGVKTMKTYTNRMKSE----NVFRAILVVQ-QNLTPFARTCI----QEISAKFHLEVFQEAE--LLV-NIKEHVLVP 142 (170)
Q Consensus 75 ~~~vgvk~Ir~~~~~~~~e----~~~~~IiV~q-~~lt~~Ar~~~----~~~~~~~~iE~F~e~E--Ll~-ni~~H~lVP 142 (170)
+..+++..|+..++.+.-. |-.+.+||-. +++|..|..++ .+. |...+=+|..+. -++ -|.+.-.+=
T Consensus 66 g~~i~vd~Ir~l~~~~~~~~~~~~~~KvvII~~~e~m~~~a~NaLLK~LEEP-p~~t~~il~~~~~~kll~TI~SRc~~~ 144 (299)
T PRK07132 66 DKDLSKSEFLSAINKLYFSSFVQSQKKILIIKNIEKTSNSLLNALLKTIEEP-PKDTYFLLTTKNINKVLPTIVSRCQVF 144 (299)
T ss_pred CCcCCHHHHHHHHHHhccCCcccCCceEEEEecccccCHHHHHHHHHHhhCC-CCCeEEEEEeCChHhChHHHHhCeEEE
Confidence 4679999999999998532 5677888877 67888665443 443 334444443221 111 122222222
Q ss_pred cccccCHHHHHHHHhhcCCCC
Q 030846 143 EHQVLTNEEKKTLLKRYTVKE 163 (170)
Q Consensus 143 ~h~~l~~eE~~~ll~~y~~~~ 163 (170)
+-..+++++..+.|.+-++.+
T Consensus 145 ~f~~l~~~~l~~~l~~~~~~~ 165 (299)
T PRK07132 145 NVKEPDQQKILAKLLSKNKEK 165 (299)
T ss_pred ECCCCCHHHHHHHHHHcCCCh
Confidence 345678888887777655543
No 32
>PRK03298 hypothetical protein; Provisional
Probab=39.20 E-value=60 Score=27.62 Aligned_cols=50 Identities=20% Similarity=0.313 Sum_probs=35.5
Q ss_pred cEEEEeCCCC-ccchhHHHHHHHHHhhc-C--CCeEEEEEcCCCCHHHHHHHHhc
Q 030846 67 QIYVFFPDEQ-KVGVKTMKTYTNRMKSE-N--VFRAILVVQQNLTPFARTCIQEI 117 (170)
Q Consensus 67 ~i~VfF~~~~-~vgvk~Ir~~~~~~~~e-~--~~~~IiV~q~~lt~~Ar~~~~~~ 117 (170)
-++|..--.. -=++.++..|++.+..+ + -=|||||. +.+||.|+..+.+-
T Consensus 148 ~V~vEvKRr~~idaV~QL~RYve~l~rd~~~~~VRGIlvA-p~It~~Ar~Ll~dr 201 (224)
T PRK03298 148 TVAVEIKRRGEIDGVEQLTRYLELLNRDPLLAPVRGVFAA-QEIKPQARTLAEDR 201 (224)
T ss_pred EEEEEEEecCCccHHHHHHHHHHHHhhCcCcCCceEEEEC-CcCCHHHHHHHHHc
Confidence 3455552222 22899999999999765 2 35899986 67899999988764
No 33
>PRK12399 tagatose 1,6-diphosphate aldolase; Reviewed
Probab=36.75 E-value=70 Score=28.67 Aligned_cols=101 Identities=15% Similarity=0.256 Sum_probs=54.2
Q ss_pred cEEEEeCCC-Cc-c---chhHHHHHHHHHhhcCCCeE--EEEEcCCCCH------------HHHHHHHhcc-cccceeee
Q 030846 67 QIYVFFPDE-QK-V---GVKTMKTYTNRMKSENVFRA--ILVVQQNLTP------------FARTCIQEIS-AKFHLEVF 126 (170)
Q Consensus 67 ~i~VfF~~~-~~-v---gvk~Ir~~~~~~~~e~~~~~--IiV~q~~lt~------------~Ar~~~~~~~-~~~~iE~F 126 (170)
|++|+|..+ +. + ....|+.+-+....+++-.. |++++..+.. ....++.+++ +.|.+.++
T Consensus 123 K~Llyy~pD~~~~in~~k~a~vervg~eC~a~dipf~lE~ltY~~~~~d~~~~~yak~kP~~V~~a~kefs~~~~gvDVl 202 (324)
T PRK12399 123 KFLLYYDVDEPDEINEQKKAYIERIGSECVAEDIPFFLEILTYDEKIADNGSVEYAKVKPHKVNEAMKVFSKPRFGVDVL 202 (324)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCeEEEEeeccCcccccccHHHHhhChHHHHHHHHHhccCCCCCcEE
Confidence 689999544 32 2 33444445555566777655 5676655522 1123444443 23555554
Q ss_pred ecccccccc--ccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846 127 QEAELLVNI--KEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF 170 (170)
Q Consensus 127 ~e~ELl~ni--~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~ 170 (170)
..+ .=+|. .+= +=+.-.+.|.+|..+.+++..-- +.+||||
T Consensus 203 KvE-vPvn~~~veG-~~~~e~~yt~~eA~~~f~~~~~~-~~~P~i~ 245 (324)
T PRK12399 203 KVE-VPVNMKYVEG-FAEGEVVYTKEEAAQHFKEQDAA-THLPYIY 245 (324)
T ss_pred EEe-cccccccccc-cCcccccccHHHHHHHHHHHhhc-cCCCEEE
Confidence 431 11111 000 11224577999999988776554 7899885
No 34
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=36.70 E-value=1.5e+02 Score=20.93 Aligned_cols=97 Identities=18% Similarity=0.165 Sum_probs=54.3
Q ss_pred HHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCC
Q 030846 16 RTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV 95 (170)
Q Consensus 16 rTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~ 95 (170)
..+..+|+..||.|.--+.+.+.+++.+.-... ..+-+.+++. ..-+....+.+++.+++.+-
T Consensus 18 ~~la~~l~~~G~~v~~~d~~~~~~~l~~~~~~~-~pd~V~iS~~----------------~~~~~~~~~~l~~~~k~~~p 80 (121)
T PF02310_consen 18 LYLAAYLRKAGHEVDILDANVPPEELVEALRAE-RPDVVGISVS----------------MTPNLPEAKRLARAIKERNP 80 (121)
T ss_dssp HHHHHHHHHTTBEEEEEESSB-HHHHHHHHHHT-TCSEEEEEES----------------SSTHHHHHHHHHHHHHTTCT
T ss_pred HHHHHHHHHCCCeEEEECCCCCHHHHHHHHhcC-CCcEEEEEcc----------------CcCcHHHHHHHHHHHHhcCC
Confidence 467789999999998766677777887743222 1222333331 12355666777777655544
Q ss_pred CeEEEEEcCC-CCHHHHHHHHhcccccceeeeecccc
Q 030846 96 FRAILVVQQN-LTPFARTCIQEISAKFHLEVFQEAEL 131 (170)
Q Consensus 96 ~~~IiV~q~~-lt~~Ar~~~~~~~~~~~iE~F~e~EL 131 (170)
+ .++|+.+. .|......++... .+..=++.|.|.
T Consensus 81 ~-~~iv~GG~~~t~~~~~~l~~~~-~~D~vv~GegE~ 115 (121)
T PF02310_consen 81 N-IPIVVGGPHATADPEEILREYP-GIDYVVRGEGEE 115 (121)
T ss_dssp T-SEEEEEESSSGHHHHHHHHHHH-TSEEEEEETTSS
T ss_pred C-CEEEEECCchhcChHHHhccCc-CcceecCCChHH
Confidence 4 44455554 4666555555422 234445666553
No 35
>PRK05571 ribose-5-phosphate isomerase B; Provisional
Probab=36.69 E-value=88 Score=24.74 Aligned_cols=20 Identities=25% Similarity=0.471 Sum_probs=16.7
Q ss_pred HHHHHHHHHHhcCCCCCCCh
Q 030846 12 FRIRRTVMQMLRDRGYFVGD 31 (170)
Q Consensus 12 ~r~rrTv~eMl~DRGY~v~~ 31 (170)
|-.+..+.++|++.||.|.+
T Consensus 12 ~~lK~~l~~~L~~~g~eV~D 31 (148)
T PRK05571 12 FELKEEIIEHLEELGHEVID 31 (148)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 45677889999999999976
No 36
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=35.05 E-value=98 Score=26.40 Aligned_cols=86 Identities=15% Similarity=0.266 Sum_probs=48.5
Q ss_pred CCCccchhHHHHHHHHHhh---cCCCeEEEEEc-CCCCHHHHHHHHhc---ccccceeeeecc--cccc-cccccccccc
Q 030846 74 DEQKVGVKTMKTYTNRMKS---ENVFRAILVVQ-QNLTPFARTCIQEI---SAKFHLEVFQEA--ELLV-NIKEHVLVPE 143 (170)
Q Consensus 74 ~~~~vgvk~Ir~~~~~~~~---e~~~~~IiV~q-~~lt~~Ar~~~~~~---~~~~~iE~F~e~--ELl~-ni~~H~lVP~ 143 (170)
++..+++..||..++.+.. ++-.+.+||.. +.+|..|-.++-.. +|...+=+|.-+ +-+. -|...-.+=.
T Consensus 69 ~~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~ 148 (313)
T PRK05564 69 NKKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYK 148 (313)
T ss_pred cCCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeee
Confidence 4567999999999997743 56678888888 78898766554332 222333223211 1111 1111111112
Q ss_pred ccccCHHHHHHHHhhc
Q 030846 144 HQVLTNEEKKTLLKRY 159 (170)
Q Consensus 144 h~~l~~eE~~~ll~~y 159 (170)
-..+++++....|++.
T Consensus 149 ~~~~~~~~~~~~l~~~ 164 (313)
T PRK05564 149 LNRLSKEEIEKFISYK 164 (313)
T ss_pred CCCcCHHHHHHHHHHH
Confidence 3456778877777653
No 37
>COG1715 Mrr Restriction endonuclease [Defense mechanisms]
Probab=34.91 E-value=1.2e+02 Score=26.94 Aligned_cols=53 Identities=19% Similarity=0.344 Sum_probs=43.2
Q ss_pred CcEEEEe-CCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcc
Q 030846 66 DQIYVFF-PDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS 118 (170)
Q Consensus 66 ~~i~VfF-~~~~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~ 118 (170)
+.|||-= .-+..||...|++|..-+.-....+|++|+-++.|+.|+...+.+.
T Consensus 214 d~iyiQAKR~~~tv~rpEIq~FagaL~g~kA~~GVFitTS~fs~~A~~~a~~i~ 267 (308)
T COG1715 214 DRIYVQAKRWKNTVGRPEIQEFAGALEGHKAKRGVFITTSGFSAGARAYAERIL 267 (308)
T ss_pred eeEEEEeeecCCCcCCHHHHHHHHHhhhhccCCcEEEECCCCCHHHHHHHHhcc
Confidence 4566543 2245799999999999999999999999999999999987766544
No 38
>TIGR01120 rpiB ribose 5-phosphate isomerase B. Involved in the non-oxidative branch of the pentose phospate pathway.
Probab=34.78 E-value=98 Score=24.34 Aligned_cols=20 Identities=30% Similarity=0.479 Sum_probs=16.8
Q ss_pred HHHHHHHHHHhcCCCCCCCh
Q 030846 12 FRIRRTVMQMLRDRGYFVGD 31 (170)
Q Consensus 12 ~r~rrTv~eMl~DRGY~v~~ 31 (170)
|.-+..+.+.|+++||.|.+
T Consensus 11 ~~lK~~l~~~L~~~g~eV~D 30 (143)
T TIGR01120 11 FILKEEIKAFLVERGVKVID 30 (143)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 45678899999999999976
No 39
>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=34.17 E-value=44 Score=22.23 Aligned_cols=20 Identities=5% Similarity=0.255 Sum_probs=17.2
Q ss_pred HHHHHHhcCCCCCCChhhhc
Q 030846 16 RTVMQMLRDRGYFVGDFEIN 35 (170)
Q Consensus 16 rTv~eMl~DRGY~v~~~e~~ 35 (170)
.-+++..+..||.++.+|+.
T Consensus 28 e~~~~lA~~~Gf~ft~~el~ 47 (64)
T TIGR03798 28 EDRVAIAKEAGFEFTGEDLK 47 (64)
T ss_pred HHHHHHHHHcCCCCCHHHHH
Confidence 45778899999999999984
No 40
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=33.95 E-value=67 Score=27.85 Aligned_cols=49 Identities=20% Similarity=0.314 Sum_probs=38.3
Q ss_pred EEEEeCCC--CccchhHHHHHHHHHhhcCCC--eEEEEEcCCCCHHHHHHHHhc
Q 030846 68 IYVFFPDE--QKVGVKTMKTYTNRMKSENVF--RAILVVQQNLTPFARTCIQEI 117 (170)
Q Consensus 68 i~VfF~~~--~~vgvk~Ir~~~~~~~~e~~~--~~IiV~q~~lt~~Ar~~~~~~ 117 (170)
+.|...-. .-.++.+++.|.+.+.+.... |||||. ..+|+.|++.+..-
T Consensus 175 viiElKR~ka~~~Av~QL~RYv~~l~~~~~~~VRGiLvA-p~it~~a~~ll~~~ 227 (253)
T COG1637 175 VIIELKRRKAGLSAVSQLKRYVELLREDTGDKVRGILVA-PSITEQARRLLEDE 227 (253)
T ss_pred EEEEEecccCCchHHHHHHHHHHHcccccCceEEEEEEc-ccccHHHHHHHHHc
Confidence 55555333 246889999999999888877 999997 67899999988763
No 41
>PRK12615 galactose-6-phosphate isomerase subunit LacB; Reviewed
Probab=33.61 E-value=1.1e+02 Score=24.99 Aligned_cols=20 Identities=30% Similarity=0.416 Sum_probs=17.1
Q ss_pred HHHHHHHHHHhcCCCCCCCh
Q 030846 12 FRIRRTVMQMLRDRGYFVGD 31 (170)
Q Consensus 12 ~r~rrTv~eMl~DRGY~v~~ 31 (170)
|-.+..+.+.|+++||.|.+
T Consensus 12 ~~lK~~l~~~L~~~G~eV~D 31 (171)
T PRK12615 12 TNEKMAVSDFLKSKGYDVID 31 (171)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 55678899999999999976
No 42
>TIGR01232 lacD tagatose 1,6-diphosphate aldolase. This family consists of Gram-positive proteins. Tagatose 1,6-diphosphate aldolase is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation.
Probab=33.29 E-value=72 Score=28.59 Aligned_cols=97 Identities=16% Similarity=0.283 Sum_probs=49.9
Q ss_pred cEEEEeCCCCccc-----hhHHHHHHHHHhhcCCCeE--EEEEcCCCCH-----HHHHHHHhcccc---cceeeeecccc
Q 030846 67 QIYVFFPDEQKVG-----VKTMKTYTNRMKSENVFRA--ILVVQQNLTP-----FARTCIQEISAK---FHLEVFQEAEL 131 (170)
Q Consensus 67 ~i~VfF~~~~~vg-----vk~Ir~~~~~~~~e~~~~~--IiV~q~~lt~-----~Ar~~~~~~~~~---~~iE~F~e~EL 131 (170)
|++|+|..+..=. ...|+.+-+....+++-.. |++++..+++ +|+. .|. -.++.|.....
T Consensus 124 K~Llyy~pD~~~ein~~k~a~vervg~ec~a~dipf~lE~ltYd~~~~~~~~~~yak~-----kP~~V~~a~kefs~~~~ 198 (325)
T TIGR01232 124 KFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKV-----KPRKVNEAMKLFSEPRF 198 (325)
T ss_pred EEEEEeCCCCChHHHHHHHHHHHHHHHHHHHCCCCeEEEEeccCCCCCCCCcHHHHHh-----ChHHHHHHHHHhccCCC
Confidence 6899996553222 3333444444455677655 4555433311 2211 011 02334444444
Q ss_pred ccccccccccccc-----------cccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846 132 LVNIKEHVLVPEH-----------QVLTNEEKKTLLKRYTVKETQVSDKF 170 (170)
Q Consensus 132 l~ni~~H~lVP~h-----------~~l~~eE~~~ll~~y~~~~~qlP~~~ 170 (170)
=+++.|=+ ||=+ .+-|.+|..+.++...-- +.+||||
T Consensus 199 gvDVlKvE-vPvn~~~veG~~~~e~~yt~~eA~~~f~eq~~~-~~~P~i~ 246 (325)
T TIGR01232 199 NVDVLKVE-VPVNVKYVEGFAEGEVVYTKEEAAQHFKDQDAA-THLPYIY 246 (325)
T ss_pred CCcEEEEe-cccccccccccCcccccccHHHHHHHHHHHhhc-cCCCEEE
Confidence 44444433 3322 334889999988875443 7899875
No 43
>PRK04280 arginine repressor; Provisional
Probab=31.70 E-value=1.7e+02 Score=22.92 Aligned_cols=25 Identities=16% Similarity=0.361 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCCCCChhhhccCHHH
Q 030846 16 RTVMQMLRDRGYFVGDFEINMSKEQ 40 (170)
Q Consensus 16 rTv~eMl~DRGY~v~~~e~~~s~~~ 40 (170)
.-+.+.|+++|+.|+|+.+.-.+.+
T Consensus 22 eeL~~~L~~~Gi~vTQATiSRDike 46 (148)
T PRK04280 22 DELVDRLREEGFNVTQATVSRDIKE 46 (148)
T ss_pred HHHHHHHHHcCCCeehHHHHHHHHH
Confidence 3467899999999999888544433
No 44
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=31.02 E-value=1.2e+02 Score=26.79 Aligned_cols=95 Identities=16% Similarity=0.198 Sum_probs=55.1
Q ss_pred EEEEeCCC--CccchhHHHHHHHHHh---hcCCCeEEEEEc-CCCCHHHHHHHHhc---ccccce---eeeecccccccc
Q 030846 68 IYVFFPDE--QKVGVKTMKTYTNRMK---SENVFRAILVVQ-QNLTPFARTCIQEI---SAKFHL---EVFQEAELLVNI 135 (170)
Q Consensus 68 i~VfF~~~--~~vgvk~Ir~~~~~~~---~e~~~~~IiV~q-~~lt~~Ar~~~~~~---~~~~~i---E~F~e~ELl~ni 135 (170)
+.+.+++. ..+++..||.+.+.+. .+|-.+.+||.+ +.||..|..++-.. +|...+ -.-..+.|+-=|
T Consensus 76 ~~~i~p~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI 155 (334)
T PRK07993 76 YYTLTPEKGKSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATL 155 (334)
T ss_pred EEEEecccccccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHH
Confidence 55566665 4599999999999885 356667777764 56898766544322 233222 111223344332
Q ss_pred c-cccccccccccCHHHHHHHHh-hcCCCC
Q 030846 136 K-EHVLVPEHQVLTNEEKKTLLK-RYTVKE 163 (170)
Q Consensus 136 ~-~H~lVP~h~~l~~eE~~~ll~-~y~~~~ 163 (170)
. +-..+ .-..+++++..+.|. ++++.+
T Consensus 156 rSRCq~~-~~~~~~~~~~~~~L~~~~~~~~ 184 (334)
T PRK07993 156 RSRCRLH-YLAPPPEQYALTWLSREVTMSQ 184 (334)
T ss_pred Hhccccc-cCCCCCHHHHHHHHHHccCCCH
Confidence 2 23333 333578888888774 446553
No 45
>TIGR02133 RPI_actino ribose 5-phosphate isomerase. This family is a member of the RpiB/LacA/LacB subfamily (TIGR00689) but lies outside the RpiB equivalog (TIGR01120) which is also a member of that subfamily. Ribose 5-phosphate isomerase is an essential enzyme of the pentose phosphate pathway; a pathway that appears to be present in the actinobacteria. The only candidates for ribose 5-phosphate isomerase in the Actinobacteria are members of this family.
Probab=29.30 E-value=73 Score=25.14 Aligned_cols=20 Identities=20% Similarity=0.145 Sum_probs=16.9
Q ss_pred HHHHHHHHHHhcCCCCCCCh
Q 030846 12 FRIRRTVMQMLRDRGYFVGD 31 (170)
Q Consensus 12 ~r~rrTv~eMl~DRGY~v~~ 31 (170)
|..+..+.+.|+.+||.|.+
T Consensus 12 ~~lK~~l~~~L~~~g~eV~D 31 (148)
T TIGR02133 12 FEYKEALWLDLAAHEPEVCD 31 (148)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 55678899999999999976
No 46
>PTZ00215 ribose 5-phosphate isomerase; Provisional
Probab=29.24 E-value=1.6e+02 Score=23.40 Aligned_cols=20 Identities=15% Similarity=0.664 Sum_probs=16.6
Q ss_pred HHHHHHHHHHhcC--CCCCCCh
Q 030846 12 FRIRRTVMQMLRD--RGYFVGD 31 (170)
Q Consensus 12 ~r~rrTv~eMl~D--RGY~v~~ 31 (170)
|.-+..+.+.|++ +||.|.+
T Consensus 14 ~~lK~~l~~~L~~~~~g~eV~D 35 (151)
T PTZ00215 14 FDLKNEIIDYIKNKGKEYKIED 35 (151)
T ss_pred HHHHHHHHHHHHhccCCCEEEE
Confidence 4567788999999 9999977
No 47
>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=28.94 E-value=2.7e+02 Score=21.48 Aligned_cols=96 Identities=16% Similarity=0.201 Sum_probs=50.3
Q ss_pred EEeCCCCccchhHHHHHHHHHhh---cCCCeEEEEEc-CCCCHHHHHHHHhc---ccccceeeeecccc---cccccccc
Q 030846 70 VFFPDEQKVGVKTMKTYTNRMKS---ENVFRAILVVQ-QNLTPFARTCIQEI---SAKFHLEVFQEAEL---LVNIKEHV 139 (170)
Q Consensus 70 VfF~~~~~vgvk~Ir~~~~~~~~---e~~~~~IiV~q-~~lt~~Ar~~~~~~---~~~~~iE~F~e~EL---l~ni~~H~ 139 (170)
...+....+++..|+.+++.+.. .+-.+.|||-. +.+++.|..++... .+...+=+|.-... .=-|...-
T Consensus 68 ~~~~~~~~~~~~~i~~i~~~~~~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~ 147 (188)
T TIGR00678 68 RLEPEGQSIKVDQVRELVEFLSRTPQESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRC 147 (188)
T ss_pred EeccccCcCCHHHHHHHHHHHccCcccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhc
Confidence 33444457899999998888754 34445454433 45676554333222 12222323322211 11122222
Q ss_pred ccccccccCHHHHHHHHhhcCCCCCC
Q 030846 140 LVPEHQVLTNEEKKTLLKRYTVKETQ 165 (170)
Q Consensus 140 lVP~h~~l~~eE~~~ll~~y~~~~~q 165 (170)
.+=.-..++.+|..+.|++.++.+.+
T Consensus 148 ~~~~~~~~~~~~~~~~l~~~gi~~~~ 173 (188)
T TIGR00678 148 QVLPFPPLSEEALLQWLIRQGISEEA 173 (188)
T ss_pred EEeeCCCCCHHHHHHHHHHcCCCHHH
Confidence 23244567888888888887665443
No 48
>PRK05917 DNA polymerase III subunit delta'; Validated
Probab=28.59 E-value=1.6e+02 Score=25.71 Aligned_cols=48 Identities=15% Similarity=0.210 Sum_probs=33.9
Q ss_pred EEEEeCCCC--ccchhHHHHHHHHHhh---cCCCeEEEEE-cCCCCHHHHHHHH
Q 030846 68 IYVFFPDEQ--KVGVKTMKTYTNRMKS---ENVFRAILVV-QQNLTPFARTCIQ 115 (170)
Q Consensus 68 i~VfF~~~~--~vgvk~Ir~~~~~~~~---e~~~~~IiV~-q~~lt~~Ar~~~~ 115 (170)
+++.+|++. .+++.+||.+.+.+.. ++-.+.+||. .+.||+.|..++-
T Consensus 63 ~~~i~p~~~~~~I~idqiR~l~~~~~~~p~e~~~kv~ii~~ad~mt~~AaNaLL 116 (290)
T PRK05917 63 IHEFSPQGKGRLHSIETPRAIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFL 116 (290)
T ss_pred EEEEecCCCCCcCcHHHHHHHHHHHhhCccCCCceEEEEechhhcCHHHHHHHH
Confidence 666677664 3899999999998853 4556676655 4668987765553
No 49
>TIGR02328 conserved hypothetical protein. Members of this protein are found in a small number of taxonomically well separated species, yet are strongly conserved, suggesting lateral gene transfer. Members are found in Treponema denticola, Clostridium acetobutylicum, and several of the Firmicutes. The function of this protein is unknown.
Probab=27.75 E-value=60 Score=25.06 Aligned_cols=23 Identities=35% Similarity=0.585 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCh
Q 030846 9 KRLFRIRRTVMQMLRDRGYFVGD 31 (170)
Q Consensus 9 ~rl~r~rrTv~eMl~DRGY~v~~ 31 (170)
..||.--.-|++-|..|||.|+.
T Consensus 48 ~~L~~yH~lv~~EM~~RGY~~~~ 70 (120)
T TIGR02328 48 YKLFAYHLLVMEEMATRGYHVSK 70 (120)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCh
Confidence 56777777778778889999988
No 50
>PRK08622 galactose-6-phosphate isomerase subunit LacB; Reviewed
Probab=27.56 E-value=1.5e+02 Score=24.10 Aligned_cols=20 Identities=25% Similarity=0.220 Sum_probs=16.7
Q ss_pred HHHHHHHHHHhcCCCCCCCh
Q 030846 12 FRIRRTVMQMLRDRGYFVGD 31 (170)
Q Consensus 12 ~r~rrTv~eMl~DRGY~v~~ 31 (170)
|-.+..+.+.|++.||.|.+
T Consensus 12 ~~lK~~l~~~L~~~G~eV~D 31 (171)
T PRK08622 12 TDEKMAVSDYLKSKGHEVID 31 (171)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 45677899999999999976
No 51
>PF08011 DUF1703: Protein of unknown function (DUF1703); InterPro: IPR012547 This family contains many hypothetical bacterial proteins.
Probab=27.55 E-value=1.5e+02 Score=21.32 Aligned_cols=44 Identities=18% Similarity=0.164 Sum_probs=28.2
Q ss_pred HHHHHhc-CCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeC
Q 030846 17 TVMQMLR-DRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFP 73 (170)
Q Consensus 17 Tv~eMl~-DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~ 73 (170)
.++-||. +.||.|..+ .-.+.+|-+|.+. .+.+.+...+.+.|-
T Consensus 9 ~~~~~l~~~~~y~v~sE------------~e~~~Gr~Dl~l~-~~~~~~~~~~IiElK 53 (105)
T PF08011_consen 9 FLLGYLSLSSGYEVKSE------------RESGKGRIDLVLE-PPKPTPKYIYIIELK 53 (105)
T ss_pred HHHHHHHHcCCcEEEEE------------ecCCCCeEEEEEE-EccCCCCeEEEEEEE
Confidence 4566777 889988662 2234458888887 344455556777775
No 52
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=27.39 E-value=1.3e+02 Score=20.69 Aligned_cols=48 Identities=10% Similarity=0.098 Sum_probs=33.5
Q ss_pred hHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeecc
Q 030846 81 KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEA 129 (170)
Q Consensus 81 k~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ 129 (170)
++++.++....+. ...+-.+.-.+|++.-|+.+.++...++|+...+.
T Consensus 16 ~~l~~la~~~~~~-~~~~~~~~l~PM~~~eR~iIH~la~~~~l~S~S~G 63 (74)
T cd02643 16 KDLIELVESVNKG-KQTSRSHSFPPMNREKRRIVHELAEHFGIESVSYD 63 (74)
T ss_pred HHHHHHHHHHHhc-cccCCeeECCCCCHHHHHHHHHHHhhCCCEEEecC
Confidence 3455566655444 45555677899999999999888765677766654
No 53
>PRK04161 tagatose 1,6-diphosphate aldolase; Reviewed
Probab=27.21 E-value=1.2e+02 Score=27.20 Aligned_cols=102 Identities=12% Similarity=0.210 Sum_probs=50.7
Q ss_pred cEEEEeCCCCcc-----chhHHHHHHHHHhhcCCCeE--EEEEcCCCCHHHHHHHHhccccc---ceeeeeccccccccc
Q 030846 67 QIYVFFPDEQKV-----GVKTMKTYTNRMKSENVFRA--ILVVQQNLTPFARTCIQEISAKF---HLEVFQEAELLVNIK 136 (170)
Q Consensus 67 ~i~VfF~~~~~v-----gvk~Ir~~~~~~~~e~~~~~--IiV~q~~lt~~Ar~~~~~~~~~~---~iE~F~e~ELl~ni~ 136 (170)
|++|+|..+..- ....|+.+-+....+++-.. |++++..+.......-..+.|.. .+..|...+.=+++.
T Consensus 125 K~Llyy~pD~~~ein~~k~a~vervg~eC~a~dipf~lE~l~Yd~~~~d~~~~eyak~kP~~V~~amkefs~~~~gvDVl 204 (329)
T PRK04161 125 KFLLYYDVDGDEEINDQKQAYIERIGSECTAEDIPFFLELLTYDERISDNNSAAYAKLKPHKVNGAMKVFSDKRFGVDVL 204 (329)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCeEEEEeccCCcccccccHHHHhhChHHHHHHHHHhccCCCCCcEE
Confidence 689999555322 33344444444566777655 45665444321000000000100 223344333444444
Q ss_pred ccccccc-----------ccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846 137 EHVLVPE-----------HQVLTNEEKKTLLKRYTVKETQVSDKF 170 (170)
Q Consensus 137 ~H~lVP~-----------h~~l~~eE~~~ll~~y~~~~~qlP~~~ 170 (170)
|=+ ||= -.+-|.+|..+.+++..-- +.+||||
T Consensus 205 KvE-vPvn~~~veG~~~g~~~yt~~eA~~~f~~~~~~-~~~P~i~ 247 (329)
T PRK04161 205 KVE-VPVNMAYVEGFTEGEVVYSQEEAIKAFKDQEAA-THLPYIY 247 (329)
T ss_pred EEe-cccccccccccCcccccccHHHHHHHHHHHhcc-cCCCEEE
Confidence 332 333 3456788888888776544 7899885
No 54
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=26.95 E-value=37 Score=21.27 Aligned_cols=19 Identities=26% Similarity=0.485 Sum_probs=15.5
Q ss_pred HHHHHHhcCCCCCCChhhh
Q 030846 16 RTVMQMLRDRGYFVGDFEI 34 (170)
Q Consensus 16 rTv~eMl~DRGY~v~~~e~ 34 (170)
.-+..+-++.||.++.+|+
T Consensus 30 ~e~~~lA~~~Gy~ft~~el 48 (49)
T PF07862_consen 30 EEVVALAREAGYDFTEEEL 48 (49)
T ss_pred HHHHHHHHHcCCCCCHHHh
Confidence 4467788999999998876
No 55
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=26.60 E-value=1.8e+02 Score=25.72 Aligned_cols=90 Identities=13% Similarity=0.182 Sum_probs=49.6
Q ss_pred EEEEeC-CCCccchhHHHHHHHHHh---hcCCCeEEEEE-cCCCCHHHHHHHHhc---ccccceeee---eccccccccc
Q 030846 68 IYVFFP-DEQKVGVKTMKTYTNRMK---SENVFRAILVV-QQNLTPFARTCIQEI---SAKFHLEVF---QEAELLVNIK 136 (170)
Q Consensus 68 i~VfF~-~~~~vgvk~Ir~~~~~~~---~e~~~~~IiV~-q~~lt~~Ar~~~~~~---~~~~~iE~F---~e~ELl~ni~ 136 (170)
+++..+ ++..+|+..||.+++.+. .+|-.+.+||- -+.||..|..++-.. +|...+=++ ..+.|+--|.
T Consensus 76 ~~~i~p~~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~ 155 (325)
T PRK06871 76 FHILEPIDNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIY 155 (325)
T ss_pred EEEEccccCCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHH
Confidence 444456 345799999999998875 35666776665 356888776554332 233222111 1233332222
Q ss_pred -cccccccccccCHHHHHHHHhh
Q 030846 137 -EHVLVPEHQVLTNEEKKTLLKR 158 (170)
Q Consensus 137 -~H~lVP~h~~l~~eE~~~ll~~ 158 (170)
+...+ .-..+++++..+.|++
T Consensus 156 SRC~~~-~~~~~~~~~~~~~L~~ 177 (325)
T PRK06871 156 SRCQTW-LIHPPEEQQALDWLQA 177 (325)
T ss_pred hhceEE-eCCCCCHHHHHHHHHH
Confidence 11222 2345667777766665
No 56
>PLN02559 chalcone--flavonone isomerase
Probab=26.29 E-value=49 Score=28.27 Aligned_cols=74 Identities=16% Similarity=0.268 Sum_probs=41.5
Q ss_pred ccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCcc---chhHHHH--HHHHHhhcCCCeEEEEEcCCCCHH
Q 030846 35 NMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKV---GVKTMKT--YTNRMKSENVFRAILVVQQNLTPF 109 (170)
Q Consensus 35 ~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~v---gvk~Ir~--~~~~~~~e~~~~~IiV~q~~lt~~ 109 (170)
.-.++.|.+-|-+..-..--.+..... |..++-+-|+.+.++ +...|.+ +++-+ ...+ |-..+.+|+
T Consensus 128 ~~aLekF~~~Fk~~~fp~Gs~I~ft~s--p~g~L~isfs~dg~ipe~~~~~Ienk~l~eAv-----~e~~-IG~~~VSP~ 199 (230)
T PLN02559 128 AKAVEKFKEAFKEETFPPGSSILFTHS--PTGSLTVAFSKDSSVPEVGNAVIENKLLCEAV-----LESI-IGKHGVSPA 199 (230)
T ss_pred HHHHHHHHHHhcCCCCCCCCEEEEEEC--CCCcEEEEEecCCCCCccceEEEechHHHHHH-----HHHH-ccCCCCCHH
Confidence 346889999887653332233333333 556788888766432 2222221 22222 1122 477889999
Q ss_pred HHHHHHh
Q 030846 110 ARTCIQE 116 (170)
Q Consensus 110 Ar~~~~~ 116 (170)
||+.+..
T Consensus 200 aK~slA~ 206 (230)
T PLN02559 200 AKLSLAA 206 (230)
T ss_pred HHHHHHH
Confidence 9988754
No 57
>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=25.76 E-value=2e+02 Score=24.43 Aligned_cols=49 Identities=12% Similarity=0.379 Sum_probs=35.5
Q ss_pred CCCCCCcEEEEeC-----------CCCccchhHHHHHHHHHhh-cCCCeEEEEEcCCCCHH
Q 030846 61 RNDSSDQIYVFFP-----------DEQKVGVKTMKTYTNRMKS-ENVFRAILVVQQNLTPF 109 (170)
Q Consensus 61 ~~dp~~~i~VfF~-----------~~~~vgvk~Ir~~~~~~~~-e~~~~~IiV~q~~lt~~ 109 (170)
.+++++.++|||. +...+..+.++..++.|.. ....++++|+...-+.+
T Consensus 102 ~s~~~D~vfiy~~~HG~~~~l~~~~~~~l~~~~L~~~L~~m~~~~~y~~lv~~veaC~SGs 162 (256)
T PF01650_consen 102 NSTENDNVFIYFTGHGGPGFLKFPDGEELTADDLADALDKMHEKKRYKKLVFVVEACYSGS 162 (256)
T ss_pred cCCCCCeEEEEEeccCCCCcccCCCcccccHHHHHHHHHHHHhhCCcceEEEEEecccccc
Confidence 3567777888873 4566788899999999965 55578888877665443
No 58
>KOG0373 consensus Serine/threonine specific protein phosphatase involved in cell cycle control, PP2A-related [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=25.36 E-value=32 Score=29.88 Aligned_cols=81 Identities=22% Similarity=0.365 Sum_probs=52.4
Q ss_pred cCCCCCCChhhhccCHHHHHHHhcCCCC-CcceEEEe-ecCCCCCCcEEEEeCCC-CccchhHHHHHHHHH-----hhcC
Q 030846 23 RDRGYFVGDFEINMSKEQFIAKFGENMK-REDLVINK-ALRNDSSDQIYVFFPDE-QKVGVKTMKTYTNRM-----KSEN 94 (170)
Q Consensus 23 ~DRGY~v~~~e~~~s~~~F~~~~~~~~~-r~~L~~~~-~~~~dp~~~i~VfF~~~-~~vgvk~Ir~~~~~~-----~~e~ 94 (170)
-||||. |++.|.--+.-... ...++... +|.+..-.++|-||.+= .|-|-.+.-+||-++ ...-
T Consensus 83 VDRGyy--------SLEtfT~l~~LkaryP~~ITLlRGNHEsRqitqVYGFydECq~KYGnan~wkycckVFD~LtlaAi 154 (306)
T KOG0373|consen 83 VDRGYY--------SLETFTLLLLLKARYPAKITLLRGNHESRQITQVYGFYDECQNKYGNANVWKYCCKVFDFLTLAAI 154 (306)
T ss_pred cccccc--------cHHHHHHHHHHhhcCCceeEEeeccchhhhhhhhhhhHHHHHhhcCCchHHHHHHHHHhhhhHHHH
Confidence 488887 45567655444333 34455543 34444445678887433 477888887777665 2455
Q ss_pred CCeEEEEEcCCCCHHHH
Q 030846 95 VFRAILVVQQNLTPFAR 111 (170)
Q Consensus 95 ~~~~IiV~q~~lt~~Ar 111 (170)
++.-|+-+.++++|..|
T Consensus 155 ID~~vLCVHGGLSPdir 171 (306)
T KOG0373|consen 155 IDEKVLCVHGGLSPDIR 171 (306)
T ss_pred hcCcEEEEcCCCCccce
Confidence 67789999999999875
No 59
>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=24.89 E-value=35 Score=27.22 Aligned_cols=17 Identities=47% Similarity=0.546 Sum_probs=13.7
Q ss_pred HHHHHHHHhcCCCCCCC
Q 030846 14 IRRTVMQMLRDRGYFVG 30 (170)
Q Consensus 14 ~rrTv~eMl~DRGY~v~ 30 (170)
+|..+.+||+|+||.-.
T Consensus 14 ir~~l~~~L~~~~~t~~ 30 (180)
T PF11985_consen 14 IREWLDQMLRDGGFTQY 30 (180)
T ss_pred HHHHHHHHHHhCCCChH
Confidence 67788999999987654
No 60
>PRK03094 hypothetical protein; Provisional
Probab=24.63 E-value=31 Score=24.81 Aligned_cols=15 Identities=40% Similarity=0.583 Sum_probs=12.8
Q ss_pred HHHHHhcCCCCCCCh
Q 030846 17 TVMQMLRDRGYFVGD 31 (170)
Q Consensus 17 Tv~eMl~DRGY~v~~ 31 (170)
-|.|.|+.|||.|-+
T Consensus 12 ~i~~~L~~~GYeVv~ 26 (80)
T PRK03094 12 DVQQALKQKGYEVVQ 26 (80)
T ss_pred HHHHHHHHCCCEEEe
Confidence 467899999999966
No 61
>TIGR01119 lacB galactose-6-phosphate isomerase, LacB subunit. This family contains four members from low GC gram-positive bacteria. Galactose-6-phosphate isomerase is involved in lactose catabolism by the tagatose-6-phosphate pathway.
Probab=24.26 E-value=1.9e+02 Score=23.53 Aligned_cols=20 Identities=30% Similarity=0.516 Sum_probs=16.7
Q ss_pred HHHHHHHHHHhcCCCCCCCh
Q 030846 12 FRIRRTVMQMLRDRGYFVGD 31 (170)
Q Consensus 12 ~r~rrTv~eMl~DRGY~v~~ 31 (170)
|-.+..+.+.|+..||.|.+
T Consensus 12 ~~lK~~l~~~L~~~G~eV~D 31 (171)
T TIGR01119 12 TDVKMEVSEFLKSKGYEVLD 31 (171)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 45678889999999999976
No 62
>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=24.02 E-value=28 Score=29.96 Aligned_cols=23 Identities=22% Similarity=0.359 Sum_probs=20.5
Q ss_pred cCHHHHHHHHhhcCCCCCCCCCC
Q 030846 147 LTNEEKKTLLKRYTVKETQVSDK 169 (170)
Q Consensus 147 l~~eE~~~ll~~y~~~~~qlP~~ 169 (170)
|+++|+++.|+.|+++++.||++
T Consensus 244 l~~ee~~~fl~~~gi~es~l~ri 266 (274)
T cd01900 244 LDEEEAAEFLEELGLEESGLDRL 266 (274)
T ss_pred CCHHHHHHHHHHcCCccccHHHH
Confidence 57899999999999999888875
No 63
>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=23.83 E-value=85 Score=28.57 Aligned_cols=62 Identities=18% Similarity=0.245 Sum_probs=39.3
Q ss_pred ccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHH--HHHHhcccccceeeeeccccccccccccccccc
Q 030846 77 KVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFAR--TCIQEISAKFHLEVFQEAELLVNIKEHVLVPEH 144 (170)
Q Consensus 77 ~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar--~~~~~~~~~~~iE~F~e~ELl~ni~~H~lVP~h 144 (170)
+|.|| ++.|++.|+...=.+-.-|..++.--.++ +.+. .|.+-.|-.+|| |-+...+--|.|
T Consensus 117 sv~MK-mkyY~~Ym~~~RddsPLYiFDssFgE~~~~rkLl~----dY~VPk~F~dDl-F~y~g~e~RPpy 180 (407)
T KOG2130|consen 117 SVKMK-MKYYIEYMKSTRDDSPLYIFDSSFGEHAPRRKLLE----DYSVPKYFRDDL-FQYLGEERRPPY 180 (407)
T ss_pred ceeee-HHHHHHHHhccccCCCeEEecchhhcccchhhhhh----hcCcchhhhHHH-HHhcCcccCCCc
Confidence 56666 68899999877777778888877654444 4333 366666666664 444444444444
No 64
>COG1137 YhbG ABC-type (unclassified) transport system, ATPase component [General function prediction only]
Probab=23.32 E-value=1.6e+02 Score=25.26 Aligned_cols=40 Identities=15% Similarity=0.396 Sum_probs=30.9
Q ss_pred eCCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhc
Q 030846 72 FPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEI 117 (170)
Q Consensus 72 F~~~~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~ 117 (170)
|.+-+.+.+..|++++..+.+.|+ ||+|+.... |..+.-.
T Consensus 167 FAGVDPiaV~dIq~iI~~L~~rgi--GvLITDHNV----REtL~i~ 206 (243)
T COG1137 167 FAGVDPIAVIDIQRIIKHLKDRGI--GVLITDHNV----RETLDIC 206 (243)
T ss_pred ccCCCchhHHHHHHHHHHHHhCCc--eEEEccccH----HHHHhhh
Confidence 666678999999999999998877 788887663 5555443
No 65
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=23.17 E-value=4.9e+02 Score=22.46 Aligned_cols=81 Identities=11% Similarity=0.125 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHH
Q 030846 11 LFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRM 90 (170)
Q Consensus 11 l~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~ 90 (170)
|-.-.+..+.-+.+|.+.+... .+.-|.++||-.. .. .+-...+...+.+.|.++++.+
T Consensus 190 l~~~~~~~l~~~~~~~~i~~H~----af~Yf~~~ygl~~-------~~----------~~~~~~~~eps~~~l~~l~~~i 248 (311)
T PRK09545 190 TDKQIGNQLAPVKGKGYFVFHD----AYGYFEKHYGLTP-------LG----------HFTVNPEIQPGAQRLHEIRTQL 248 (311)
T ss_pred HHHHHHHHhhccCCCcEEEECc----hHHHHHHhCCCce-------ee----------eeccCCCCCCCHHHHHHHHHHH
Confidence 3333344444455666655432 4556777775431 11 0112334467899999999999
Q ss_pred hhcCCCeEEEEEcCCCCHHHHHH
Q 030846 91 KSENVFRAILVVQQNLTPFARTC 113 (170)
Q Consensus 91 ~~e~~~~~IiV~q~~lt~~Ar~~ 113 (170)
+++++. +|++=.+.-+..++..
T Consensus 249 k~~~v~-~If~e~~~~~~~~~~l 270 (311)
T PRK09545 249 VEQKAT-CVFAEPQFRPAVIESV 270 (311)
T ss_pred HHcCCC-EEEecCCCChHHHHHH
Confidence 999998 4444444434444333
No 66
>PRK07276 DNA polymerase III subunit delta'; Validated
Probab=23.00 E-value=2.8e+02 Score=24.19 Aligned_cols=94 Identities=13% Similarity=0.162 Sum_probs=52.8
Q ss_pred EEEEeCCCCccchhHHHHHHHHHhh---cCCCeEEEEE-cCCCCHHHHHHHHhc---ccccceeee---eccccccccc-
Q 030846 68 IYVFFPDEQKVGVKTMKTYTNRMKS---ENVFRAILVV-QQNLTPFARTCIQEI---SAKFHLEVF---QEAELLVNIK- 136 (170)
Q Consensus 68 i~VfF~~~~~vgvk~Ir~~~~~~~~---e~~~~~IiV~-q~~lt~~Ar~~~~~~---~~~~~iE~F---~e~ELl~ni~- 136 (170)
++++.+.+..+++..||.+.+.+.. +|-.+.+||- -+.||+.|..++-.. +|...+=++ ..+.|+=-|-
T Consensus 74 ~~~i~p~~~~I~idqIR~l~~~~~~~p~~~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~S 153 (290)
T PRK07276 74 VTVIEPQGQVIKTDTIRELVKNFSQSGYEGKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKS 153 (290)
T ss_pred eeeecCCCCcCCHHHHHHHHHHHhhCcccCCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHH
Confidence 6666677778999999999988853 5556666665 356888766544322 232222111 1223333222
Q ss_pred cccccccccccCHHHHHHHHhhcCCCC
Q 030846 137 EHVLVPEHQVLTNEEKKTLLKRYTVKE 163 (170)
Q Consensus 137 ~H~lVP~h~~l~~eE~~~ll~~y~~~~ 163 (170)
+-..+|= .. ++++-.++|++.++..
T Consensus 154 Rcq~i~f-~~-~~~~~~~~L~~~g~~~ 178 (290)
T PRK07276 154 RTQIFHF-PK-NEAYLIQLLEQKGLLK 178 (290)
T ss_pred cceeeeC-CC-cHHHHHHHHHHcCCCh
Confidence 2222221 12 5677777777776654
No 67
>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=22.81 E-value=2.1e+02 Score=21.43 Aligned_cols=58 Identities=10% Similarity=0.150 Sum_probs=34.0
Q ss_pred HHHHHHHhcCC----CCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhhcCCCe
Q 030846 38 KEQFIAKFGEN----MKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFR 97 (170)
Q Consensus 38 ~~~F~~~~~~~----~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~e~~~~ 97 (170)
+.+|.++|.-- |.-...-|.+-+++ .+-+-|-|++-..=-.+.|+.+++..++.|++.
T Consensus 45 lmdFIsryARTDEImPEDKTvGFvviN~d--KK~mSvsFsdideNmK~~i~ei~kkykd~Gykv 106 (110)
T PF11513_consen 45 LMDFISRYARTDEIMPEDKTVGFVVINKD--KKMMSVSFSDIDENMKNSIEEIVKKYKDSGYKV 106 (110)
T ss_dssp HHHHHHHH---S---TTSEEEEEEEEETT--TTEEEEEE-S--CCHHHHHHHHHHHHHCCS-EE
T ss_pred HHHHHHHhhcccccCCCCceeEEEEEecC--CeEEEEEecchhHHHHHHHHHHHHHhhcCCcee
Confidence 78999999743 22344555554332 345788998654323778888888888777653
No 68
>PRK09426 methylmalonyl-CoA mutase; Reviewed
Probab=22.66 E-value=3.3e+02 Score=26.87 Aligned_cols=88 Identities=14% Similarity=0.016 Sum_probs=56.9
Q ss_pred HHHHH-HHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHh
Q 030846 13 RIRRT-VMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMK 91 (170)
Q Consensus 13 r~rrT-v~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~ 91 (170)
.+|.+ +..|+++-||.|.......|.++|.+-.-+.. -+ .|..|....-....+..+++.++
T Consensus 596 ~~ra~fv~~~l~~~GfeV~~~~~~~s~e~~v~aa~~~~--a~---------------ivvlcs~d~~~~e~~~~l~~~Lk 658 (714)
T PRK09426 596 DRGAKVIATAFADLGFDVDIGPLFQTPEEAARQAVEND--VH---------------VVGVSSLAAGHKTLVPALIEALK 658 (714)
T ss_pred hHhHHHHHHHHHhCCeeEecCCCCCCHHHHHHHHHHcC--CC---------------EEEEeccchhhHHHHHHHHHHHH
Confidence 34443 45789999999965555578888888763321 11 23334444456667888999999
Q ss_pred hcCCCeEEEEEcCCCCHHHHHHHHhc
Q 030846 92 SENVFRAILVVQQNLTPFARTCIQEI 117 (170)
Q Consensus 92 ~e~~~~~IiV~q~~lt~~Ar~~~~~~ 117 (170)
+.|.....+++.+.+.|.....+.++
T Consensus 659 ~~G~~~v~vl~GG~~~~~~~~~l~~a 684 (714)
T PRK09426 659 KLGREDIMVVVGGVIPPQDYDFLYEA 684 (714)
T ss_pred hcCCCCcEEEEeCCCChhhHHHHHhC
Confidence 99977776677777666544455544
No 69
>PF13864 Enkurin: Calmodulin-binding
Probab=21.66 E-value=56 Score=23.60 Aligned_cols=23 Identities=26% Similarity=0.444 Sum_probs=18.8
Q ss_pred ccccccccCHHHHHHHHhhcCCC
Q 030846 140 LVPEHQVLTNEEKKTLLKRYTVK 162 (170)
Q Consensus 140 lVP~h~~l~~eE~~~ll~~y~~~ 162 (170)
.-|-|..|+++|+.++|+.++-+
T Consensus 30 ~~~~~~~l~eeER~~lL~~Lk~~ 52 (98)
T PF13864_consen 30 CPPGMRLLSEEERQELLEGLKKN 52 (98)
T ss_pred CccccccCCHHHHHHHHHHHHHH
Confidence 34789999999999999876543
No 70
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=21.28 E-value=2.4e+02 Score=18.58 Aligned_cols=53 Identities=21% Similarity=0.268 Sum_probs=31.1
Q ss_pred CCCCChhhh-----ccCHHHHHHHhcCCCC----CcceEEEeecCCC-----CCCcEEEEeCCCCcc
Q 030846 26 GYFVGDFEI-----NMSKEQFIAKFGENMK----REDLVINKALRND-----SSDQIYVFFPDEQKV 78 (170)
Q Consensus 26 GY~v~~~e~-----~~s~~~F~~~~~~~~~----r~~L~~~~~~~~d-----p~~~i~VfF~~~~~v 78 (170)
||.++++.+ .||.++-.+..|.... ...-+.-+..... ....+.|.|.++..|
T Consensus 1 G~~~~~~~~~~i~~GmTk~qV~~lLG~P~~~~~~~~~~W~Y~~~~~~~~~~~~~~~l~V~Fd~~~~v 67 (71)
T PF04355_consen 1 GNVLTQEQLAQIKPGMTKDQVRALLGSPSLRDPFDPNRWYYVYSKRRGNGANEQRQLKVYFDDDGVV 67 (71)
T ss_dssp TSCTTSHHHTTT-TTSBHHHHHHHHTS-SEE-CTTSSEEEEEEEETTCSSSSCEEEEEEEECTTSBE
T ss_pred CCcCCHHHHHhhcCCCCHHHHHHhcCCCCccccccCCEEEEEEEEecCCCccEEEEEEEEEcCCCEE
Confidence 667766555 5999999999997633 1122222222211 235688999877654
No 71
>PLN00062 TATA-box-binding protein; Provisional
Probab=21.24 E-value=4.5e+02 Score=21.28 Aligned_cols=89 Identities=10% Similarity=0.032 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCChhhh-------------ccCHHHHHHHhcCCCCCc--ceEEEeecCCCCCCcEEEEe
Q 030846 8 IKRLFRIRRTVMQMLRDRGYFVGDFEI-------------NMSKEQFIAKFGENMKRE--DLVINKALRNDSSDQIYVFF 72 (170)
Q Consensus 8 ~~rl~r~rrTv~eMl~DRGY~v~~~e~-------------~~s~~~F~~~~~~~~~r~--~L~~~~~~~~dp~~~i~VfF 72 (170)
...+.++.+.+..||++-||.+...+. .+.|+.+...+.++..++ .--..+=+-.+|.-.+.||-
T Consensus 66 ~e~a~~a~~~~~~~L~~lg~~~~~~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~ 145 (179)
T PLN00062 66 EHDSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFV 145 (179)
T ss_pred HHHHHHHHHHHHHHHHHcCCCcCCCccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeC
Confidence 345677888888999999997753222 477888876555443322 21111212345544455554
Q ss_pred CCCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccc
Q 030846 73 PDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119 (170)
Q Consensus 73 ~~~~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~ 119 (170)
++ =|+|+..+....+++|+..+-|
T Consensus 146 sG-----------------------kvvitGaks~~~~~~ai~~i~p 169 (179)
T PLN00062 146 SG-----------------------KIVITGAKVREEIYTAFENIYP 169 (179)
T ss_pred CC-----------------------EEEEEecCCHHHHHHHHHHHHH
Confidence 43 2456666655666666665543
No 72
>KOG1232 consensus Proteins containing the FAD binding domain [Energy production and conversion]
Probab=21.03 E-value=79 Score=29.51 Aligned_cols=40 Identities=20% Similarity=0.488 Sum_probs=31.9
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHH
Q 030846 2 TLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFI 42 (170)
Q Consensus 2 ~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~ 42 (170)
+-|..+..++|+.|..+=+-|..-|| |-..++.+.+++|-
T Consensus 365 a~d~~~~~~lW~~Re~ip~a~~~~g~-vyKyDvSLpL~d~Y 404 (511)
T KOG1232|consen 365 AQDEAEAQKLWKIRESIPEALQKAGG-VYKYDVSLPLEDLY 404 (511)
T ss_pred cCCHHHHHHHHHHHhccHHHHHhcCC-EEEeeccccHHHHH
Confidence 44677899999999999999999994 45666777777663
No 73
>PF12641 Flavodoxin_3: Flavodoxin domain
Probab=20.90 E-value=2.6e+02 Score=22.04 Aligned_cols=52 Identities=10% Similarity=0.089 Sum_probs=33.6
Q ss_pred CcEEEEeCCCCccchhHHHHHH----HHHhhcCCCeEEEEEcCCCCHHHHHHHHhc
Q 030846 66 DQIYVFFPDEQKVGVKTMKTYT----NRMKSENVFRAILVVQQNLTPFARTCIQEI 117 (170)
Q Consensus 66 ~~i~VfF~~~~~vgvk~Ir~~~----~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~ 117 (170)
++|++|=.....-+....+.++ .-+.+.|.--+-+++|++++|..+.....+
T Consensus 68 KkV~lF~T~G~~~~s~~~~~~~~~~~~~~~~~~~~lg~f~CqGk~~~~~~e~~~~~ 123 (160)
T PF12641_consen 68 KKVALFGTAGAGPDSEYAKKILKNVEALLPKGNEILGTFMCQGKMDPKVIEKYKKM 123 (160)
T ss_pred CeEEEEEecCCCCchHHHHHHHHHHHHhhccCCeecceEEeCCcCCHHHHHHHHhc
Confidence 4577766443333334444443 334445566688999999999998888776
No 74
>PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D.
Probab=20.72 E-value=59 Score=23.21 Aligned_cols=19 Identities=37% Similarity=0.518 Sum_probs=15.5
Q ss_pred cCHHHHHHHHhhcCCCCCC
Q 030846 147 LTNEEKKTLLKRYTVKETQ 165 (170)
Q Consensus 147 l~~eE~~~ll~~y~~~~~q 165 (170)
|+++++++|++++++++..
T Consensus 61 l~e~~~~~l~~~~~a~~GD 79 (95)
T PF02938_consen 61 LSEEELKALIERLGAKPGD 79 (95)
T ss_dssp CHHHHHHHHHHHTT--TTE
T ss_pred CCHHHHHHHHHHhCCCCCC
Confidence 8999999999999998764
No 75
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=20.50 E-value=1.2e+02 Score=23.59 Aligned_cols=31 Identities=26% Similarity=0.531 Sum_probs=24.1
Q ss_pred HHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCC
Q 030846 13 RIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM 49 (170)
Q Consensus 13 r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~ 49 (170)
-.|+.|.+|+.+ |+ +++|+ ++.|.++||+..
T Consensus 61 dmR~~Vr~~i~~-G~--Sd~eI---~~~~v~RYG~~V 91 (126)
T TIGR03147 61 DLRHEVYSMVNE-GK--SNQQI---IDFMTARFGDFV 91 (126)
T ss_pred HHHHHHHHHHHc-CC--CHHHH---HHHHHHhcCCeE
Confidence 357888899974 65 67777 789999999863
No 76
>COG4624 Iron only hydrogenase large subunit, C-terminal domain [General function prediction only]
Probab=20.41 E-value=70 Score=29.53 Aligned_cols=26 Identities=27% Similarity=0.339 Sum_probs=23.8
Q ss_pred ccccCHHHHHHHHhhcCCCCCCCCCC
Q 030846 144 HQVLTNEEKKTLLKRYTVKETQVSDK 169 (170)
Q Consensus 144 h~~l~~eE~~~ll~~y~~~~~qlP~~ 169 (170)
-.+||.+|-.++|+..+++..+||+.
T Consensus 220 D~vLTtrEL~~ml~~l~id~~~lp~~ 245 (411)
T COG4624 220 DFVLTTRELVKMLKELRIDFARLPDG 245 (411)
T ss_pred eEEecHHHHHHHHHHhCCCHhHCCCC
Confidence 45899999999999999999999974
No 77
>PRK05818 DNA polymerase III subunit delta'; Validated
Probab=20.06 E-value=2.1e+02 Score=24.79 Aligned_cols=47 Identities=11% Similarity=0.267 Sum_probs=32.7
Q ss_pred EEEEeCCCCccchhHHHHHHHHHhhc----CCCeEEEEE-cCCCCHHHHHHH
Q 030846 68 IYVFFPDEQKVGVKTMKTYTNRMKSE----NVFRAILVV-QQNLTPFARTCI 114 (170)
Q Consensus 68 i~VfF~~~~~vgvk~Ir~~~~~~~~e----~~~~~IiV~-q~~lt~~Ar~~~ 114 (170)
+++.|+....+++..||.+.+.+... +-.+.+||. .+.||+.|..++
T Consensus 57 l~~i~p~~~~I~id~ir~l~~~l~~~s~e~~~~KV~II~~ae~m~~~AaNaL 108 (261)
T PRK05818 57 FYLIFDQKNPIKKEDALSIINKLNRPSVESNGKKIYIIYGIEKLNKQSANSL 108 (261)
T ss_pred EEEecCCcccCCHHHHHHHHHHHccCchhcCCCEEEEeccHhhhCHHHHHHH
Confidence 56667877789999999999988543 334555554 456887666444
Done!