Query 029683
Match_columns 189
No_of_seqs 139 out of 340
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 16:50:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029683.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029683hhsearch_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 8.6E-65 1.9E-69 422.6 16.1 166 23-189 6-174 (208)
2 PLN03111 DNA-directed RNA poly 100.0 2.3E-63 5.1E-68 418.1 16.3 167 22-189 4-172 (206)
3 PTZ00061 DNA-directed RNA poly 100.0 1E-62 2.2E-67 413.8 16.5 166 23-189 2-171 (205)
4 PF03871 RNA_pol_Rpb5_N: RNA p 100.0 1.7E-33 3.7E-38 210.8 0.8 87 22-108 3-92 (93)
5 PRK09570 rpoH DNA-directed RNA 99.6 4.6E-17 1E-21 119.4 2.5 41 149-189 3-43 (79)
6 PF01191 RNA_pol_Rpb5_C: RNA p 99.6 1.1E-16 2.5E-21 116.0 2.4 40 150-189 1-40 (74)
7 COG2012 RPB5 DNA-directed RNA 99.6 4.4E-16 9.4E-21 113.7 2.5 45 145-189 2-46 (80)
8 PF04471 Mrr_cat: Restriction 96.6 0.0048 1E-07 45.0 5.2 75 72-148 36-111 (115)
9 TIGR00640 acid_CoA_mut_C methy 63.7 34 0.00074 26.8 6.7 87 33-137 19-105 (132)
10 PF13156 Mrr_cat_2: Restrictio 62.0 12 0.00025 30.0 3.7 92 56-148 16-110 (129)
11 PF03345 DDOST_48kD: Oligosacc 58.6 42 0.00091 31.8 7.4 97 33-148 14-120 (423)
12 PRK08485 DNA polymerase III su 53.9 31 0.00068 29.7 5.2 46 88-134 30-75 (206)
13 cd02072 Glm_B12_BD B12 binding 53.8 61 0.0013 25.7 6.6 75 34-126 17-91 (128)
14 COG1787 Predicted endonuclease 52.4 26 0.00056 30.5 4.5 96 41-155 120-215 (217)
15 PF08479 POTRA_2: POTRA domain 51.2 17 0.00037 25.3 2.7 25 26-50 33-57 (76)
16 KOG1150 Predicted molecular ch 49.1 28 0.00061 30.5 4.2 35 44-84 55-89 (250)
17 PRK09539 tRNA-splicing endonuc 45.2 1.2E+02 0.0025 24.2 6.9 66 38-122 42-107 (124)
18 PRK08058 DNA polymerase III su 44.8 89 0.0019 27.8 7.0 95 86-181 80-186 (329)
19 TIGR01501 MthylAspMutase methy 44.5 68 0.0015 25.6 5.5 75 33-125 18-92 (134)
20 cd02067 B12-binding B12 bindin 43.4 1.2E+02 0.0027 22.3 6.6 75 35-127 18-93 (119)
21 PF05920 Homeobox_KN: Homeobox 42.9 9.6 0.00021 24.3 0.4 24 160-183 7-30 (40)
22 PF01939 DUF91: Protein of unk 42.6 40 0.00086 29.4 4.2 58 85-145 149-210 (228)
23 cd02071 MM_CoA_mut_B12_BD meth 42.0 99 0.0021 23.4 6.0 74 36-127 19-92 (122)
24 KOG0975 Branched chain aminotr 41.5 12 0.00026 35.0 0.9 29 32-62 288-317 (379)
25 PRK02261 methylaspartate mutas 37.8 1.5E+02 0.0032 23.3 6.5 72 35-125 22-94 (137)
26 COG4889 Predicted helicase [Ge 37.1 48 0.001 35.2 4.3 80 72-153 61-155 (1518)
27 PF13607 Succ_CoA_lig: Succiny 36.1 64 0.0014 25.5 4.2 80 34-133 15-99 (138)
28 PRK03298 hypothetical protein; 35.7 56 0.0012 28.6 4.1 39 97-137 161-202 (224)
29 PRK05564 DNA polymerase III su 34.4 96 0.0021 27.1 5.4 41 92-133 69-113 (313)
30 cd01900 YchF YchF subfamily. 31.6 25 0.00055 31.0 1.3 24 164-187 244-267 (274)
31 PF01650 Peptidase_C13: Peptid 30.0 1.7E+02 0.0036 25.6 6.1 50 79-128 102-162 (256)
32 KOG4196 bZIP transcription fac 29.8 56 0.0012 26.5 2.8 43 2-48 15-67 (135)
33 PF11985 DUF3486: Protein of u 29.4 33 0.00071 28.0 1.6 36 32-72 14-52 (180)
34 PRK07993 DNA polymerase III su 29.3 1.5E+02 0.0032 26.8 5.9 95 86-181 76-185 (334)
35 COG1637 Predicted nuclease of 28.0 87 0.0019 27.9 4.0 57 86-144 175-238 (253)
36 cd02070 corrinoid_protein_B12- 27.7 2.8E+02 0.0061 22.7 6.9 76 35-129 101-179 (201)
37 TIGR00678 holB DNA polymerase 26.7 3E+02 0.0066 21.7 6.8 94 88-182 68-173 (188)
38 COG2938 Uncharacterized conser 26.6 56 0.0012 24.8 2.3 17 23-39 12-29 (94)
39 COG0135 TrpF Phosphoribosylant 25.0 3.9E+02 0.0084 22.9 7.3 68 87-176 28-97 (208)
40 TIGR03798 ocin_TIGR03798 bacte 24.4 62 0.0013 22.1 2.0 20 34-53 28-47 (64)
41 PRK06964 DNA polymerase III su 24.4 4.8E+02 0.01 23.8 8.3 83 95-179 111-206 (342)
42 PF11513 TA0956: Thermoplasma 23.7 1.9E+02 0.004 22.4 4.6 57 56-115 45-105 (110)
43 PRK06871 DNA polymerase III su 23.6 2.3E+02 0.0049 25.7 6.0 90 86-176 76-178 (325)
44 TIGR02370 pyl_corrinoid methyl 23.3 3.5E+02 0.0076 22.3 6.7 79 34-131 102-183 (197)
45 PF02938 GAD: GAD domain; Int 23.2 51 0.0011 24.1 1.5 20 164-183 61-80 (95)
46 PRK07132 DNA polymerase III su 21.3 5.2E+02 0.011 23.0 7.7 88 93-181 66-166 (299)
47 PF13167 GTP-bdg_N: GTP-bindin 20.8 1.2E+02 0.0026 22.8 3.1 53 96-152 41-93 (95)
48 PF05273 Pox_RNA_Pol_22: Poxvi 20.6 80 0.0017 26.6 2.2 122 38-189 18-146 (185)
49 PF13864 Enkurin: Calmodulin-b 20.6 62 0.0013 24.0 1.5 23 157-179 30-52 (98)
50 COG2344 AT-rich DNA-binding pr 20.5 1.5E+02 0.0033 25.7 4.0 68 96-167 130-198 (211)
51 PRK09545 znuA high-affinity zi 20.4 6E+02 0.013 22.5 9.3 45 91-137 231-275 (311)
52 KOG1885 Lysyl-tRNA synthetase 20.3 7.4E+02 0.016 24.5 8.8 133 23-170 51-207 (560)
53 TIGR02328 conserved hypothetic 20.3 91 0.002 24.8 2.4 70 26-114 47-118 (120)
54 KOG3451 Uncharacterized conser 20.3 1.3E+02 0.0029 21.8 3.0 55 113-177 3-65 (71)
No 1
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=100.00 E-value=8.6e-65 Score=422.63 Aligned_cols=166 Identities=36% Similarity=0.645 Sum_probs=163.4
Q ss_pred chHHHHHHHHHHHHHHHhcCCCCcCCcccccCCHHHHHHHhCCC-CCCCccEEEecCCCCCCCcEEEEecCCCccchhHH
Q 029683 23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK-CDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAI 101 (189)
Q Consensus 23 ~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~I 101 (189)
+.|++||||+|||++|||+||||.|+++|+++++++|+++||+. |+|++|+|+|.|++||+++||||||++++||+|+|
T Consensus 6 e~E~~rl~~ar~T~~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk~~ 85 (208)
T KOG3218|consen 6 EEEIYRLYLARKTAMQMLRDRGYTVTQEELDLTLEEFKARYGDKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVKTM 85 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCccccHHHhhhhHHHHHHHhccCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHHHH
Confidence 68999999999999999999999999999999999999999998 99999999999999999999999999999999999
Q ss_pred HHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC--ceEEeeeeccceeccccceecCcccccCHHHHHHHHHHcCCC
Q 029683 102 RGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIE 179 (189)
Q Consensus 102 r~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~--~~iE~F~e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~~~ 179 (189)
|.|+.+| .++|++++|+|+|+++||+|++++..++ |+||+|+|+||+||||+|+|||||++||+|||++||++|+++
T Consensus 86 k~~~~~~-~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l~ 164 (208)
T KOG3218|consen 86 KTYVIQM-QSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKLK 164 (208)
T ss_pred HHHHHHH-HhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcCC
Confidence 9999999 8899999999999999999999999998 999999999999999999999999999999999999999999
Q ss_pred CCCCcccccC
Q 029683 180 GKQVTILVKQ 189 (189)
Q Consensus 180 ~~qLP~i~~~ 189 (189)
++||||||.+
T Consensus 165 e~qLPRIq~~ 174 (208)
T KOG3218|consen 165 ETQLPRIQKK 174 (208)
T ss_pred cccCCeeecc
Confidence 9999999863
No 2
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=100.00 E-value=2.3e-63 Score=418.10 Aligned_cols=167 Identities=44% Similarity=0.732 Sum_probs=163.8
Q ss_pred CchHHHHHHHHHHHHHHHhcCCCCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHH
Q 029683 22 GSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAI 101 (189)
Q Consensus 22 ~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~I 101 (189)
++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+.|+|++|+|++++.+||+++|||||+++++||+|+|
T Consensus 4 ~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~r~~l~~~~~~~~d~~~~i~V~F~~~~kvgvk~i 83 (206)
T PLN03111 4 GSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPKRSDPSKKILVFFPEEEKVGVKTI 83 (206)
T ss_pred chHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHHcCCcCHHHcEeeeecCCCCCCcEEEEeCCCCccCHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC--ceEEeeeeccceeccccceecCcccccCHHHHHHHHHHcCCC
Q 029683 102 RGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIE 179 (189)
Q Consensus 102 r~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~--~~iE~F~e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~~~ 179 (189)
|.|+++| +++|++++|||+|+++||+|++++++++ ++||+|+|+||+||||+|+|||+|++||+|||++||++|+++
T Consensus 84 r~~~~~~-~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y~i~ 162 (206)
T PLN03111 84 KTYAERM-KDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVK 162 (206)
T ss_pred HHHHHHH-hhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHcCCC
Confidence 9999999 9999999999999999999999999995 899999999999999999999999999999999999999999
Q ss_pred CCCCcccccC
Q 029683 180 GKQVTILVKQ 189 (189)
Q Consensus 180 ~~qLP~i~~~ 189 (189)
++|||||+.+
T Consensus 163 ~~qLPrI~~~ 172 (206)
T PLN03111 163 ETQLPRIQVS 172 (206)
T ss_pred HHHCCccccc
Confidence 9999999874
No 3
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=1e-62 Score=413.80 Aligned_cols=166 Identities=28% Similarity=0.498 Sum_probs=160.7
Q ss_pred chHHHHHHHHHHHHHHHhcCCCCcCCcccccCCHHHHHHHhCCC-CCCCccEEEecCCCCCCCcEEEEecC-CCccchhH
Q 029683 23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK-CDLESLRLCLPLRSNPSKKMLVVYLG-TEEIRTQA 100 (189)
Q Consensus 23 ~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~ 100 (189)
++++.||||+|||++|||+||||.|+++|+++|+++|+++||+. +.|++|+|+|++.+||+++|||||++ +++||+|+
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 57899999999999999999999999999999999999999988 57899999999999999999999999 57999999
Q ss_pred HHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC--ceEEeeeeccceeccccceecCcccccCHHHHHHHHHHcCC
Q 029683 101 IRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKI 178 (189)
Q Consensus 101 Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~--~~iE~F~e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~~ 178 (189)
||.|+++| +++|++|||||+|+++||+|++++.+++ ++||+|+|+||+||||+|+|||+|++||+|||++||++|++
T Consensus 82 ir~~~~~~-~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i 160 (205)
T PTZ00061 82 IRELTEKM-EEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKV 160 (205)
T ss_pred HHHHHHHH-hhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCC
Confidence 99999999 9999999999999999999999999886 89999999999999999999999999999999999999999
Q ss_pred CCCCCcccccC
Q 029683 179 EGKQVTILVKQ 189 (189)
Q Consensus 179 ~~~qLP~i~~~ 189 (189)
+++|||||+.+
T Consensus 161 ~~~qLPrI~~~ 171 (205)
T PTZ00061 161 KESQLPRIQSA 171 (205)
T ss_pred CHHHCCccccc
Confidence 99999999874
No 4
>PF03871 RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal domain; InterPro: IPR005571 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region, plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) (IPR000783 from INTERPRO) [, , , ]. This entry represents the N-terminal domain of eukaryotic RPB5, which has a core structure consisting of 3 layers alpha/beta/alpha []. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure []. This module is important for positioning the downstream DNA.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3H0G_Q 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E 1I50_E ....
Probab=99.97 E-value=1.7e-33 Score=210.81 Aligned_cols=87 Identities=36% Similarity=0.583 Sum_probs=75.0
Q ss_pred CchHHHHHHHHHHHHHHHhcCCCCcCCcccccCCHHHHHHHhCC---CCCCCccEEEecCCCCCCCcEEEEecCCCccch
Q 029683 22 GSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD---KCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRT 98 (189)
Q Consensus 22 ~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~---~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgv 98 (189)
++.|++||||||||++|||+||||.|+++|+++|+++|+++||+ .|+|++|+|++.+.+||+++|+|||+++++||+
T Consensus 3 ~~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~kvgv 82 (93)
T PF03871_consen 3 DDEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDKIFVFFPEEPKVGV 82 (93)
T ss_dssp TTHHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--EEEEEE-SSSCESC
T ss_pred cHHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCeEEEEeCCCCCcCH
Confidence 46899999999999999999999999999999999999999998 799999999999999999999999999999999
Q ss_pred hHHHHHHHHH
Q 029683 99 QAIRGLYGQI 108 (189)
Q Consensus 99 k~Ir~~~~~~ 108 (189)
|+||.|+++|
T Consensus 83 k~Ir~~~~~m 92 (93)
T PF03871_consen 83 KTIRKYCERM 92 (93)
T ss_dssp CCCHHHCHHH
T ss_pred HHHHHHHHhc
Confidence 9999999998
No 5
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=99.65 E-value=4.6e-17 Score=119.37 Aligned_cols=41 Identities=37% Similarity=0.556 Sum_probs=39.4
Q ss_pred eeccccceecCcccccCHHHHHHHHHHcCCCCCCCcccccC
Q 029683 149 LVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ 189 (189)
Q Consensus 149 l~nit~H~lVPkH~~l~~eEk~~ll~~y~~~~~qLP~i~~~ 189 (189)
.||||+|+|||+|++||+||+++||++|+++++|||||+.+
T Consensus 3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~~~ 43 (79)
T PRK09570 3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKAS 43 (79)
T ss_pred ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCceecc
Confidence 58999999999999999999999999999999999999874
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=99.63 E-value=1.1e-16 Score=116.01 Aligned_cols=40 Identities=45% Similarity=0.745 Sum_probs=33.7
Q ss_pred eccccceecCcccccCHHHHHHHHHHcCCCCCCCcccccC
Q 029683 150 VNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ 189 (189)
Q Consensus 150 ~nit~H~lVPkH~~l~~eEk~~ll~~y~~~~~qLP~i~~~ 189 (189)
||||+|+|||+|++||+||+++||++|+++++|||||+.+
T Consensus 1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~ 40 (74)
T PF01191_consen 1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSS 40 (74)
T ss_dssp S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETT
T ss_pred CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCccccc
Confidence 7999999999999999999999999999999999999874
No 7
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=99.59 E-value=4.4e-16 Score=113.67 Aligned_cols=45 Identities=36% Similarity=0.448 Sum_probs=42.7
Q ss_pred eccceeccccceecCcccccCHHHHHHHHHHcCCCCCCCcccccC
Q 029683 145 ITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ 189 (189)
Q Consensus 145 e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~~~~~qLP~i~~~ 189 (189)
++.+.||+++|+|||+|++||+||++++|++|+|+++|||||+.+
T Consensus 2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~ 46 (80)
T COG2012 2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKAS 46 (80)
T ss_pred ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCccccc
Confidence 567899999999999999999999999999999999999999864
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=96.61 E-value=0.0048 Score=44.96 Aligned_cols=75 Identities=20% Similarity=0.262 Sum_probs=41.8
Q ss_pred cEEEecCCCCCCCcEEEEecC-CCccchhHHHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccCceEEeeeeccc
Q 029683 72 LRLCLPLRSNPSKKMLVVYLG-TEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDL 148 (189)
Q Consensus 72 L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~~~iE~F~e~EL 148 (189)
..+.+.+.+....+++|.+-. ..+++.+.|+.++..+ ...++..+|||+.+++|+.|++.+.... .|+++.-++|
T Consensus 36 iDi~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~-~~~~~~~~iivt~~~~t~~a~~~~~~~~-~I~l~d~~~L 111 (115)
T PF04471_consen 36 IDIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKA-KKYGADKGIIVTSSGFTPEAKEFAEKFK-NIELIDGEDL 111 (115)
T ss_dssp EEEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHH-GGGT-SEEEEE-SSEE-HHHHHHHH--------------
T ss_pred EEEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhh-hccCCCEEEEEECCcCCHHHHHHHHhhc-cccccccccc
Confidence 344444433233456666633 3579999999999999 8889999999999999999999988743 5766666655
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=63.66 E-value=34 Score=26.83 Aligned_cols=87 Identities=11% Similarity=0.129 Sum_probs=56.0
Q ss_pred HHHHHHHhcCCCCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhcc
Q 029683 33 RRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKE 112 (189)
Q Consensus 33 rrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~e 112 (189)
.+-+.-||++-||.|-+.-...|.++|.+..-+. +-+ . |.-|.-..-.+..++.+++.+ .++
T Consensus 19 ~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e~-~ad-i---------------i~iSsl~~~~~~~~~~~~~~L-~~~ 80 (132)
T TIGR00640 19 AKVIATAYADLGFDVDVGPLFQTPEEIARQAVEA-DVH-V---------------VGVSSLAGGHLTLVPALRKEL-DKL 80 (132)
T ss_pred HHHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHc-CCC-E---------------EEEcCchhhhHHHHHHHHHHH-Hhc
Confidence 3556789999999999988889999998875322 111 1 112222233456688888898 888
Q ss_pred CcceEEEEEcCCCCHHHHHhhcccC
Q 029683 113 ALHGLILILQSNMNTFARKEVLKFP 137 (189)
Q Consensus 113 ni~~~IiV~q~~lt~~Ar~~i~~~~ 137 (189)
+.....+++.+.+.+.-...+.+++
T Consensus 81 g~~~i~vivGG~~~~~~~~~l~~~G 105 (132)
T TIGR00640 81 GRPDILVVVGGVIPPQDFDELKEMG 105 (132)
T ss_pred CCCCCEEEEeCCCChHhHHHHHHCC
Confidence 8765556666656554444455554
No 10
>PF13156 Mrr_cat_2: Restriction endonuclease
Probab=61.99 E-value=12 Score=29.96 Aligned_cols=92 Identities=13% Similarity=0.171 Sum_probs=56.4
Q ss_pred HHHHHHHhCCCCCCCccEEEecCCCCCC-CcEEEEec-CCCccchhHHHHHHHHHhhccCcceEEEEEc-CCCCHHHHHh
Q 029683 56 LTEFRFTFGDKCDLESLRLCLPLRSNPS-KKMLVVYL-GTEEIRTQAIRGLYGQILNKEALHGLILILQ-SNMNTFARKE 132 (189)
Q Consensus 56 ~~eF~~~f~~~~~r~~L~~~~~~~~dp~-~~i~VfF~-~~~~vgvk~Ir~~~~~~~~~eni~~~IiV~q-~~lt~~Ar~~ 132 (189)
..+|-.+++....-.-+-+++...++.. -.|-+-|. .+.+|..+.|-.|+... ....+.+.|||.- .++++.|.++
T Consensus 16 w~dwp~~~~~~~~DtGIDLVA~~~~~g~~~AIQCKfY~~~~~I~k~didSF~s~s-gk~~f~~rliisTt~~~s~nAe~~ 94 (129)
T PF13156_consen 16 WSDWPERYGWGGKDTGIDLVARTRDGGEYWAIQCKFYDPDHTIQKSDIDSFFSAS-GKSRFSRRLIISTTDKWSKNAEKA 94 (129)
T ss_pred hhhhhHhhCCCCCCCCEeEEEEEcCCCcEEEEEEEeeCCCceEcHHHhhHHHHhc-CCccccCcEEEEcCcHhhHHHHHH
Confidence 3455544433211123455555443221 23555554 44689999999999998 8788888888854 4799999999
Q ss_pred hcccCceEEeeeeccc
Q 029683 133 VLKFPFKVEIFYITDL 148 (189)
Q Consensus 133 i~~~~~~iE~F~e~EL 148 (189)
+..-...+..+...+|
T Consensus 95 l~~q~~pv~ri~l~dl 110 (129)
T PF13156_consen 95 LENQSIPVSRIGLSDL 110 (129)
T ss_pred HHcCCCCeEEEcHHHH
Confidence 8765422333333333
No 11
>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=58.61 E-value=42 Score=31.76 Aligned_cols=97 Identities=14% Similarity=0.240 Sum_probs=55.0
Q ss_pred HHHHHHHhcCCCCcCCccccc-CCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhc
Q 029683 33 RRTVLQMLNDRGYAVPNSELT-RSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNK 111 (189)
Q Consensus 33 rrTv~eMl~DRGY~V~~~el~-~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~ 111 (189)
..+.++.|++|||.+.=...+ -++.=| +||+. ..+.|-+..++.+. |. +.++++.|-+|++.=
T Consensus 14 yS~Ff~~L~~rg~~l~~~~~~d~~l~L~--~~ge~-~YD~LIif~~~~k~--------~g--~~ls~~~ll~Fvd~G--- 77 (423)
T PF03345_consen 14 YSTFFNSLKERGYELTFKSADDESLSLF--KYGER-LYDHLIIFPPSVKE--------FG--GSLSPKTLLDFVDNG--- 77 (423)
T ss_pred HHHHHHHHHhCCCEEEEecCCCCCcchh--hCChh-hcceEEEeCCcccc--------cC--CCCCHHHHHHHHhCC---
Confidence 778899999999999632221 122222 23332 24445443332222 11 357777777775542
Q ss_pred cCcceEEEEEcCC-CCHHHHHhhcccC--------ceEEeeeeccc
Q 029683 112 EALHGLILILQSN-MNTFARKEVLKFP--------FKVEIFYITDL 148 (189)
Q Consensus 112 eni~~~IiV~q~~-lt~~Ar~~i~~~~--------~~iE~F~e~EL 148 (189)
...++++.+. ++...|..+.+++ .-|..|..+..
T Consensus 78 ---gNilv~~s~~~~~~~ir~~~~E~gi~~~~~~~~viDHf~~~~~ 120 (423)
T PF03345_consen 78 ---GNILVAGSSDAIPDSIREFANELGIEFDPKGSKVIDHFNYDSS 120 (423)
T ss_pred ---CcEEEEeCCCcCcHHHHHHHHHCCeEECCCCCEEEcCCCCccc
Confidence 2355666666 7888888888876 24555655444
No 12
>PRK08485 DNA polymerase III subunit delta'; Validated
Probab=53.87 E-value=31 Score=29.70 Aligned_cols=46 Identities=13% Similarity=0.242 Sum_probs=31.6
Q ss_pred EEecCCCccchhHHHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhc
Q 029683 88 VVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVL 134 (189)
Q Consensus 88 VfF~~~~~vgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~ 134 (189)
.||..+ .+|+..||.+++.+....+-.+.||.--..+|..|..++-
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 344433 7999999999999733444456666666778988876553
No 13
>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=53.85 E-value=61 Score=25.68 Aligned_cols=75 Identities=15% Similarity=0.218 Sum_probs=51.3
Q ss_pred HHHHHHhcCCCCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccC
Q 029683 34 RTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEA 113 (189)
Q Consensus 34 rTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~en 113 (189)
+-+.-||++.||.|-+--...+.++|.+..-+. +.+-+.+++ --.-.+..++..++.+ .+.+
T Consensus 17 niv~~~L~~~GfeVidLG~~v~~e~~v~aa~~~-~adiVglS~----------------L~t~~~~~~~~~~~~l-~~~g 78 (128)
T cd02072 17 KILDHAFTEAGFNVVNLGVLSPQEEFIDAAIET-DADAILVSS----------------LYGHGEIDCKGLREKC-DEAG 78 (128)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEec----------------cccCCHHHHHHHHHHH-HHCC
Confidence 445569999999999988889999998876332 111222221 1123466788888998 8899
Q ss_pred cceEEEEEcCCCC
Q 029683 114 LHGLILILQSNMN 126 (189)
Q Consensus 114 i~~~IiV~q~~lt 126 (189)
+....+++.+.+.
T Consensus 79 l~~v~vivGG~~~ 91 (128)
T cd02072 79 LKDILLYVGGNLV 91 (128)
T ss_pred CCCCeEEEECCCC
Confidence 9666677777753
No 14
>COG1787 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]
Probab=52.40 E-value=26 Score=30.46 Aligned_cols=96 Identities=11% Similarity=0.091 Sum_probs=64.5
Q ss_pred cCCCCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccCcceEEEE
Q 029683 41 NDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILI 120 (189)
Q Consensus 41 ~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~eni~~~IiV 120 (189)
..-||.++ .+..-.+|.+.--..++.....+.+.+.. ..|+.+.|+++.... -.-++..+++|
T Consensus 120 t~~g~~~t---~Tqks~D~GADlia~~~g~~v~vQaKR~~-------------~aV~~kaiqEivask-~~Y~~eka~vv 182 (217)
T COG1787 120 TEKGFRIT---STQKSSDFGADLIAAKDGKKVAVQAKRYI-------------SAVSKKAIQEIVASK-AYYGCEKAKVV 182 (217)
T ss_pred HhcCeEEE---eeeccccchhHHHhccCCcEEeehhhHHH-------------HhhhHHHHHHHHHhh-hccCcceEEEe
Confidence 33466666 23334455444333344444444433211 369999999999887 88999999999
Q ss_pred EcCCCCHHHHHhhcccCceEEeeeeccceeccccc
Q 029683 121 LQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKH 155 (189)
Q Consensus 121 ~q~~lt~~Ar~~i~~~~~~iE~F~e~ELl~nit~H 155 (189)
+.+..|-.|++.-. . ..+|...-+++..++..-
T Consensus 183 Tn~~yt~~aqkla~-~-nsv~l~~r~~~~~f~~~~ 215 (217)
T COG1787 183 TNGSYTYAAQKLAQ-A-NSVELIDRDELSEFIREG 215 (217)
T ss_pred cCCccchhHHHHHH-h-hcceEEecchHHhhhccc
Confidence 99999998887622 2 478889999988887543
No 15
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=51.17 E-value=17 Score=25.30 Aligned_cols=25 Identities=8% Similarity=0.119 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCcCCcc
Q 029683 26 SYRYFLSRRTVLQMLNDRGYAVPNS 50 (189)
Q Consensus 26 ~~rL~rvrrTv~eMl~DRGY~V~~~ 50 (189)
...|..+.+.+-+.++++||..+.-
T Consensus 33 ~~~l~~~~~~l~~~y~~~GY~~s~v 57 (76)
T PF08479_consen 33 LADLQQLADALTNYYREKGYITSRV 57 (76)
T ss_dssp HHHHHHHHHHHHHHHHHTT-TT-EE
T ss_pred HHHHHHHHHHHHHHHHHcCceEEEE
Confidence 4667788999999999999998754
No 16
>KOG1150 consensus Predicted molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=49.07 E-value=28 Score=30.45 Aligned_cols=35 Identities=11% Similarity=0.225 Sum_probs=27.3
Q ss_pred CCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCC
Q 029683 44 GYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSK 84 (189)
Q Consensus 44 GY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~ 84 (189)
-|.|.+-+..++.++-+.+| ..|++++.+..||.+
T Consensus 55 pfeVLqIdpev~~edikkry------RklSilVHPDKN~Dd 89 (250)
T KOG1150|consen 55 PFEVLQIDPEVTDEDIKKRY------RKLSILVHPDKNPDD 89 (250)
T ss_pred hHHHHhcCCCCCHHHHHHHH------HhhheeecCCCCccc
Confidence 48888888899999999998 357777776666653
No 17
>PRK09539 tRNA-splicing endonuclease subunit beta; Reviewed
Probab=45.22 E-value=1.2e+02 Score=24.21 Aligned_cols=66 Identities=15% Similarity=0.142 Sum_probs=36.1
Q ss_pred HHhcCCCCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccCcceE
Q 029683 38 QMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGL 117 (189)
Q Consensus 38 eMl~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~eni~~~ 117 (189)
.=||+|||.|... . .| |. + +... ..+...-++....++..+....|-.+.... ..-+-+-.
T Consensus 42 kDLR~RGyvVk~G-~-----kf----g~------~-~~~~-~~~~s~ylV~Vl~E~~~is~~eL~~~vr~a-~svrK~lV 102 (124)
T PRK09539 42 VDLKQRGRKTIDG-I-----DE----IS------L-IIKD-KENKYTAMVLIVDENEKVSFKKILDKLHFS-KSMNLELY 102 (124)
T ss_pred hhHHhCCCeeccC-C-----ce----eE------E-EEec-CCCCceEEEEEecCCCccCHHHHHHHHHHH-hhccceeE
Confidence 3489999999773 1 12 11 0 1111 123333344444666889999998887776 43343333
Q ss_pred EEEEc
Q 029683 118 ILILQ 122 (189)
Q Consensus 118 IiV~q 122 (189)
+=|+.
T Consensus 103 LAVVD 107 (124)
T PRK09539 103 LAIVD 107 (124)
T ss_pred EEEEc
Confidence 33443
No 18
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=44.85 E-value=89 Score=27.83 Aligned_cols=95 Identities=14% Similarity=0.114 Sum_probs=54.8
Q ss_pred EEEEecCCCccchhHHHHHHHHHhh---ccCcceEEEEEc-CCCCHHHHHhh----cccCceEEeeeec----cceeccc
Q 029683 86 MLVVYLGTEEIRTQAIRGLYGQILN---KEALHGLILILQ-SNMNTFARKEV----LKFPFKVEIFYIT----DLLVNVT 153 (189)
Q Consensus 86 i~VfF~~~~~vgvk~Ir~~~~~~~~---~eni~~~IiV~q-~~lt~~Ar~~i----~~~~~~iE~F~e~----ELl~nit 153 (189)
+...+++...+++..||.+++.+ . -++-.+.|||-. +.+|..|..++ .+.+-.+-.+..+ .|+-=|-
T Consensus 80 ~~~i~~~~~~i~id~ir~l~~~~-~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIr 158 (329)
T PRK08058 80 VHLVAPDGQSIKKDQIRYLKEEF-SKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTIL 158 (329)
T ss_pred EEEeccccccCCHHHHHHHHHHH-hhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHH
Confidence 44444556789999999999987 5 455567888866 66788665444 3333122122211 1111122
Q ss_pred cceecCcccccCHHHHHHHHHHcCCCCC
Q 029683 154 KHILQPKHEVLSAGERDKLMKKYKIEGK 181 (189)
Q Consensus 154 ~H~lVPkH~~l~~eEk~~ll~~y~~~~~ 181 (189)
.--.+=.-..+++++..+.|++.++.++
T Consensus 159 SRc~~i~~~~~~~~~~~~~L~~~gi~~~ 186 (329)
T PRK08058 159 SRCQVVEFRPLPPESLIQRLQEEGISES 186 (329)
T ss_pred hhceeeeCCCCCHHHHHHHHHHcCCChH
Confidence 2222223355788888888887766544
No 19
>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=44.51 E-value=68 Score=25.55 Aligned_cols=75 Identities=15% Similarity=0.236 Sum_probs=50.1
Q ss_pred HHHHHHHhcCCCCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhcc
Q 029683 33 RRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKE 112 (189)
Q Consensus 33 rrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~e 112 (189)
.+-+.-||++.||.|-+-=...|.++|.+..-+. +.+-+.++.- ---.+..++.+.+.+ .++
T Consensus 18 k~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~~~-~adiVglS~l----------------~~~~~~~~~~~~~~l-~~~ 79 (134)
T TIGR01501 18 NKILDHAFTNAGFNVVNLGVLSPQEEFIKAAIET-KADAILVSSL----------------YGHGEIDCKGLRQKC-DEA 79 (134)
T ss_pred HHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc-CCCEEEEecc----------------cccCHHHHHHHHHHH-HHC
Confidence 3566779999999999877888999998875322 1122222210 023345688888898 889
Q ss_pred CcceEEEEEcCCC
Q 029683 113 ALHGLILILQSNM 125 (189)
Q Consensus 113 ni~~~IiV~q~~l 125 (189)
++....+|+.+.+
T Consensus 80 gl~~~~vivGG~~ 92 (134)
T TIGR01501 80 GLEGILLYVGGNL 92 (134)
T ss_pred CCCCCEEEecCCc
Confidence 8866666676653
No 20
>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=43.40 E-value=1.2e+02 Score=22.31 Aligned_cols=75 Identities=12% Similarity=0.158 Sum_probs=45.4
Q ss_pred HHHHHhcCCCCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccCc
Q 029683 35 TVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEAL 114 (189)
Q Consensus 35 Tv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~eni 114 (189)
-+..+++..||.|..-..+.+.++|.+..... +|. + |.++....-....++.+++.+ .+.+-
T Consensus 18 ~~~~~l~~~G~~V~~lg~~~~~~~l~~~~~~~--------------~pd--v-V~iS~~~~~~~~~~~~~i~~l-~~~~~ 79 (119)
T cd02067 18 IVARALRDAGFEVIDLGVDVPPEEIVEAAKEE--------------DAD--A-IGLSGLLTTHMTLMKEVIEEL-KEAGL 79 (119)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHc--------------CCC--E-EEEeccccccHHHHHHHHHHH-HHcCC
Confidence 45578999999998766778888887764211 111 1 122222223457788888898 66655
Q ss_pred -ceEEEEEcCCCCH
Q 029683 115 -HGLILILQSNMNT 127 (189)
Q Consensus 115 -~~~IiV~q~~lt~ 127 (189)
+-.|+|-....+.
T Consensus 80 ~~~~i~vGG~~~~~ 93 (119)
T cd02067 80 DDIPVLVGGAIVTR 93 (119)
T ss_pred CCCeEEEECCCCCh
Confidence 3335554444444
No 21
>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=42.93 E-value=9.6 Score=24.26 Aligned_cols=24 Identities=25% Similarity=0.350 Sum_probs=18.0
Q ss_pred cccccCHHHHHHHHHHcCCCCCCC
Q 029683 160 KHEVLSAGERDKLMKKYKIEGKQV 183 (189)
Q Consensus 160 kH~~l~~eEk~~ll~~y~~~~~qL 183 (189)
.|+--|++||++|.+..++...|+
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 567789999999999999887764
No 22
>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=42.61 E-value=40 Score=29.36 Aligned_cols=58 Identities=10% Similarity=0.024 Sum_probs=34.9
Q ss_pred cEEEEecCC-C-ccchhHHHHHHHHHhhccC--cceEEEEEcCCCCHHHHHhhcccCceEEeeee
Q 029683 85 KMLVVYLGT-E-EIRTQAIRGLYGQILNKEA--LHGLILILQSNMNTFARKEVLKFPFKVEIFYI 145 (189)
Q Consensus 85 ~i~VfF~~~-~-~vgvk~Ir~~~~~~~~~en--i~~~IiV~q~~lt~~Ar~~i~~~~~~iE~F~e 145 (189)
-+.|..--. . .=.+.++..|++.+..+.+ --|+|||.++ +|+.|+..+.+.+ +|+...
T Consensus 149 ~VVIElKR~~a~~~aV~QL~rY~~~l~~~~~~~~VRGilvA~~-i~~~a~~ll~~~g--lef~~l 210 (228)
T PF01939_consen 149 LVVIELKRRRADRDAVEQLLRYVELLKRDPGLEPVRGILVAPS-ITPQARELLEDRG--LEFVEL 210 (228)
T ss_dssp EEEEEE-SS-B-HHHHHHHHHHHHHHHHHH--S-EEEEEEES--B-HHHHHHHHHHT---EEEE-
T ss_pred EEEEEEEeccCCHHHHHHHHHHHHHHhhccCCCceeEEEECCC-CCHHHHHHHHHcC--CEEEEe
Confidence 366666443 2 2347777788888833332 3379999877 9999999988765 555543
No 23
>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=42.00 E-value=99 Score=23.36 Aligned_cols=74 Identities=9% Similarity=0.083 Sum_probs=46.5
Q ss_pred HHHHhcCCCCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccCcc
Q 029683 36 VLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALH 115 (189)
Q Consensus 36 v~eMl~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~eni~ 115 (189)
+.-|++..||.|..--.+.+.++|.+.-.+. +| +-+.+.+.. .-....++.+++.+ .+.+..
T Consensus 19 ~~~~l~~~G~~vi~lG~~vp~e~~~~~a~~~--------------~~-d~V~iS~~~--~~~~~~~~~~~~~L-~~~~~~ 80 (122)
T cd02071 19 IARALRDAGFEVIYTGLRQTPEEIVEAAIQE--------------DV-DVIGLSSLS--GGHMTLFPEVIELL-RELGAG 80 (122)
T ss_pred HHHHHHHCCCEEEECCCCCCHHHHHHHHHHc--------------CC-CEEEEcccc--hhhHHHHHHHHHHH-HhcCCC
Confidence 3458999999998877777888887764221 11 112222222 34456688999998 777776
Q ss_pred eEEEEEcCCCCH
Q 029683 116 GLILILQSNMNT 127 (189)
Q Consensus 116 ~~IiV~q~~lt~ 127 (189)
...+++.+...+
T Consensus 81 ~i~i~~GG~~~~ 92 (122)
T cd02071 81 DILVVGGGIIPP 92 (122)
T ss_pred CCEEEEECCCCH
Confidence 555556554443
No 24
>KOG0975 consensus Branched chain aminotransferase BCAT1, pyridoxal phosphate enzymes type IV superfamily [Amino acid transport and metabolism]
Probab=41.50 E-value=12 Score=34.96 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCC-CcCCcccccCCHHHHHHH
Q 029683 32 SRRTVLQMLNDRG-YAVPNSELTRSLTEFRFT 62 (189)
Q Consensus 32 vrrTv~eMl~DRG-Y~V~~~el~~s~~eF~~~ 62 (189)
.|++++|+.+|+| |.|.+. +.|.+||++.
T Consensus 288 TR~sileLa~~~g~~~V~Er--~vtv~e~~~A 317 (379)
T KOG0975|consen 288 TRKSILELARDLGEFKVEER--DVTVDELKTA 317 (379)
T ss_pred cHHHHHHHHHHhCceEEEEE--EEeHHHhhhh
Confidence 4899999999999 999874 5567788754
No 25
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=37.84 E-value=1.5e+02 Score=23.31 Aligned_cols=72 Identities=24% Similarity=0.266 Sum_probs=47.3
Q ss_pred HHHHHhcCCCCcCCcccccCCHHHHHHHhCCC-CCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccC
Q 029683 35 TVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK-CDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEA 113 (189)
Q Consensus 35 Tv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~en 113 (189)
-+.-|+++.||.|..-=...+.++|.+.-... |+ - +.+.+.. .-....++.+++.+ .+.+
T Consensus 22 iv~~~lr~~G~eVi~LG~~vp~e~i~~~a~~~~~d--~--------------V~lS~~~--~~~~~~~~~~~~~L-~~~~ 82 (137)
T PRK02261 22 ILDRALTEAGFEVINLGVMTSQEEFIDAAIETDAD--A--------------ILVSSLY--GHGEIDCRGLREKC-IEAG 82 (137)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCC--E--------------EEEcCcc--ccCHHHHHHHHHHH-HhcC
Confidence 34468999999998866677889997764221 22 1 2222222 24567788888888 8787
Q ss_pred cceEEEEEcCCC
Q 029683 114 LHGLILILQSNM 125 (189)
Q Consensus 114 i~~~IiV~q~~l 125 (189)
.....+++.+.+
T Consensus 83 ~~~~~i~vGG~~ 94 (137)
T PRK02261 83 LGDILLYVGGNL 94 (137)
T ss_pred CCCCeEEEECCC
Confidence 766666666766
No 26
>COG4889 Predicted helicase [General function prediction only]
Probab=37.12 E-value=48 Score=35.17 Aligned_cols=80 Identities=14% Similarity=0.215 Sum_probs=62.4
Q ss_pred cEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC--------------
Q 029683 72 LRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP-------------- 137 (189)
Q Consensus 72 L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~-------------- 137 (189)
+.+++...++.-..|.+-|.. .+++...|..|...+ ..-++++++||.-...++-|.+++....
T Consensus 61 idlva~~d~g~ytaiQcKFy~-nslak~di~sF~t~l-gkt~f~~gliiSTtdw~sNA~~aieq~~~~~~~Iglsei~es 138 (1518)
T COG4889 61 IDLVAREDNGNYTAIQCKFYQ-NSLAKGDIDSFFTAL-GKTGFKNGLIISTTDWTSNAEKAIEQQRSPGMRIGLSEIAES 138 (1518)
T ss_pred eeEEEEccCCCeEEEEeeeec-cccccccccHHHHHh-ccccccCceEEEecccchhHHHHHHhhhCccceecHHHHhcC
Confidence 455555433333557777765 679999999999999 9999999999987889999999987653
Q ss_pred -ceEEeeeeccceeccc
Q 029683 138 -FKVEIFYITDLLVNVT 153 (189)
Q Consensus 138 -~~iE~F~e~ELl~nit 153 (189)
...++|...||..|++
T Consensus 139 ~IDW~~f~p~e~~~nl~ 155 (1518)
T COG4889 139 PIDWDIFDPTELQDNLP 155 (1518)
T ss_pred CCChhhcCccccccccc
Confidence 2457788899999986
No 27
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=36.07 E-value=64 Score=25.55 Aligned_cols=80 Identities=15% Similarity=0.312 Sum_probs=38.7
Q ss_pred HHHHHHhcCCCCcCC-----cccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHH
Q 029683 34 RTVLQMLNDRGYAVP-----NSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQI 108 (189)
Q Consensus 34 rTv~eMl~DRGY~V~-----~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~ 108 (189)
-++++++.+||.-++ =.+..++..++.+.|.+ ||..++.+.|.+. ++.=+.|++.+
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 356788888987775 23457778888887754 4445566666552 22236666666
Q ss_pred hhccCcceEEEEEcCCCCHHHHHhh
Q 029683 109 LNKEALHGLILILQSNMNTFARKEV 133 (189)
Q Consensus 109 ~~~eni~~~IiV~q~~lt~~Ar~~i 133 (189)
..-...+=|++++.+-|+..+++.
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 444444778888888776655443
No 28
>PRK03298 hypothetical protein; Provisional
Probab=35.74 E-value=56 Score=28.56 Aligned_cols=39 Identities=13% Similarity=0.076 Sum_probs=31.7
Q ss_pred chhHHHHHHHHHhhcc---CcceEEEEEcCCCCHHHHHhhcccC
Q 029683 97 RTQAIRGLYGQILNKE---ALHGLILILQSNMNTFARKEVLKFP 137 (189)
Q Consensus 97 gvk~Ir~~~~~~~~~e---ni~~~IiV~q~~lt~~Ar~~i~~~~ 137 (189)
+|.++..|++.+ ..+ .-=|||||.|+ +||.|+..+.+-+
T Consensus 161 aV~QL~RYve~l-~rd~~~~~VRGIlvAp~-It~~Ar~Ll~drG 202 (224)
T PRK03298 161 GVEQLTRYLELL-NRDPLLAPVRGVFAAQE-IKPQARTLAEDRG 202 (224)
T ss_pred HHHHHHHHHHHH-hhCcCcCCceEEEECCc-CCHHHHHHHHHcC
Confidence 799999999999 544 23589999765 9999999998766
No 29
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=34.35 E-value=96 Score=27.06 Aligned_cols=41 Identities=22% Similarity=0.353 Sum_probs=31.0
Q ss_pred CCCccchhHHHHHHHHHhh---ccCcceEEEEEc-CCCCHHHHHhh
Q 029683 92 GTEEIRTQAIRGLYGQILN---KEALHGLILILQ-SNMNTFARKEV 133 (189)
Q Consensus 92 ~~~~vgvk~Ir~~~~~~~~---~eni~~~IiV~q-~~lt~~Ar~~i 133 (189)
+...+++..||.+++.+ . -++-.+.+||.. ..+|..|..++
T Consensus 69 ~~~~i~v~~ir~~~~~~-~~~p~~~~~kv~iI~~ad~m~~~a~naL 113 (313)
T PRK05564 69 NKKSIGVDDIRNIIEEV-NKKPYEGDKKVIIIYNSEKMTEQAQNAF 113 (313)
T ss_pred cCCCCCHHHHHHHHHHH-hcCcccCCceEEEEechhhcCHHHHHHH
Confidence 55679999999999966 4 345578888887 78898766544
No 30
>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=31.57 E-value=25 Score=31.01 Aligned_cols=24 Identities=17% Similarity=0.347 Sum_probs=21.7
Q ss_pred cCHHHHHHHHHHcCCCCCCCcccc
Q 029683 164 LSAGERDKLMKKYKIEGKQVTILV 187 (189)
Q Consensus 164 l~~eEk~~ll~~y~~~~~qLP~i~ 187 (189)
|++||+++.|+.|+++++.||||-
T Consensus 244 l~~ee~~~fl~~~gi~es~l~riI 267 (274)
T cd01900 244 LDEEEAAEFLEELGLEESGLDRLI 267 (274)
T ss_pred CCHHHHHHHHHHcCCccccHHHHH
Confidence 678999999999999999999873
No 31
>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=29.98 E-value=1.7e+02 Score=25.58 Aligned_cols=50 Identities=10% Similarity=0.291 Sum_probs=37.6
Q ss_pred CCCCCCcEEEEec-----------CCCccchhHHHHHHHHHhhccCcceEEEEEcCCCCHH
Q 029683 79 RSNPSKKMLVVYL-----------GTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTF 128 (189)
Q Consensus 79 ~~dp~~~i~VfF~-----------~~~~vgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~ 128 (189)
.+++++.+||||. +.+.+..+.++..++.|..+....+++||+...-+.+
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 3677788999883 4567888899999999955666688888877665543
No 32
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=29.75 E-value=56 Score=26.47 Aligned_cols=43 Identities=35% Similarity=0.541 Sum_probs=28.4
Q ss_pred CCCCCCCCcccccc---cCC-------CCCCchHHHHHHHHHHHHHHHhcCCCCcCC
Q 029683 2 GGSGGGGECITRSS---HVM-------EGGGSLESYRYFLSRRTVLQMLNDRGYAVP 48 (189)
Q Consensus 2 ~~~~~~~~~~~~~~---m~~-------~~~~~~e~~rL~rvrrTv~eMl~DRGY~V~ 48 (189)
|+||-+|.|+|-+. |+. .|.+-.|+.||=.-|||+ +.|||.-+
T Consensus 15 ~~~~~~~d~lsDd~LvsmSVReLNr~LrG~~reEVvrlKQrRRTL----KNRGYA~s 67 (135)
T KOG4196|consen 15 GESGEGGDRLSDDELVSMSVRELNRHLRGLSREEVVRLKQRRRTL----KNRGYAQS 67 (135)
T ss_pred cCCCCCCCCcCHHHHHHhhHHHHHHHhcCCCHHHHHHHHHHHHHH----hhhhHHHH
Confidence 56777889993332 321 111346788888888885 67999876
No 33
>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=29.43 E-value=33 Score=28.04 Aligned_cols=36 Identities=25% Similarity=0.294 Sum_probs=23.5
Q ss_pred HHHHHHHHhcCCCCcCCcccccCCHHHHHHHh---CCCCCCCcc
Q 029683 32 SRRTVLQMLNDRGYAVPNSELTRSLTEFRFTF---GDKCDLESL 72 (189)
Q Consensus 32 vrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f---~~~~~r~~L 72 (189)
+|..+.+||+|+||.-.+. +++|.+.. |..++|+.+
T Consensus 14 ir~~l~~~L~~~~~t~~ei-----~~~~~~~~~~~g~~iSrSav 52 (180)
T PF11985_consen 14 IREWLDQMLRDGGFTQYEI-----LAEWLEELAEEGYDISRSAV 52 (180)
T ss_pred HHHHHHHHHHhCCCChHHH-----HHHHHHhhhccCCCcCHHHH
Confidence 7788999999999765542 45666665 444444433
No 34
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=29.30 E-value=1.5e+02 Score=26.75 Aligned_cols=95 Identities=9% Similarity=0.092 Sum_probs=56.0
Q ss_pred EEEEecCC--CccchhHHHHHHHHHh--hccCcceEEEEEc-CCCCHHHHHhhc----ccC----ceEEeeeeccceecc
Q 029683 86 MLVVYLGT--EEIRTQAIRGLYGQIL--NKEALHGLILILQ-SNMNTFARKEVL----KFP----FKVEIFYITDLLVNV 152 (189)
Q Consensus 86 i~VfF~~~--~~vgvk~Ir~~~~~~~--~~eni~~~IiV~q-~~lt~~Ar~~i~----~~~----~~iE~F~e~ELl~ni 152 (189)
+++.+++. ..+++..||.+.+.+. ..++-.+.+||.+ +.||..|..++- +-+ +.+-.-..+.|+--|
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 56666765 4599999999998872 2456677777754 668987765543 323 222222333454332
Q ss_pred -ccceecCcccccCHHHHHHHHH-HcCCCCC
Q 029683 153 -TKHILQPKHEVLSAGERDKLMK-KYKIEGK 181 (189)
Q Consensus 153 -t~H~lVPkH~~l~~eEk~~ll~-~y~~~~~ 181 (189)
.+-..+ .-..+++++..+.|. ++++.+.
T Consensus 156 rSRCq~~-~~~~~~~~~~~~~L~~~~~~~~~ 185 (334)
T PRK07993 156 RSRCRLH-YLAPPPEQYALTWLSREVTMSQD 185 (334)
T ss_pred Hhccccc-cCCCCCHHHHHHHHHHccCCCHH
Confidence 222222 233578888888775 4565544
No 35
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=27.98 E-value=87 Score=27.87 Aligned_cols=57 Identities=12% Similarity=0.054 Sum_probs=41.8
Q ss_pred EEEEecCC--CccchhHHHHHHHHHhhccCcc--eEEEEEcCCCCHHHHHhhcccC---ceEEeee
Q 029683 86 MLVVYLGT--EEIRTQAIRGLYGQILNKEALH--GLILILQSNMNTFARKEVLKFP---FKVEIFY 144 (189)
Q Consensus 86 i~VfF~~~--~~vgvk~Ir~~~~~~~~~eni~--~~IiV~q~~lt~~Ar~~i~~~~---~~iE~F~ 144 (189)
+.|..--. .-..+.+++.|.+.+ .++... |||||.++ +|+.|++.+.+-+ .++|-+.
T Consensus 175 viiElKR~ka~~~Av~QL~RYv~~l-~~~~~~~VRGiLvAp~-it~~a~~ll~~~GLef~kle~~~ 238 (253)
T COG1637 175 VIIELKRRKAGLSAVSQLKRYVELL-REDTGDKVRGILVAPS-ITEQARRLLEDEGLEFVKLEPPK 238 (253)
T ss_pred EEEEEecccCCchHHHHHHHHHHHc-ccccCceEEEEEEccc-ccHHHHHHHHHcCceEEEcCCch
Confidence 45555333 235688999999999 877777 99999865 8999999998755 3555544
No 36
>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=27.68 E-value=2.8e+02 Score=22.74 Aligned_cols=76 Identities=16% Similarity=0.148 Sum_probs=47.1
Q ss_pred HHHHHhcCCCCcCCcccccCCHHHHHHHhCC-CCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccC
Q 029683 35 TVLQMLNDRGYAVPNSELTRSLTEFRFTFGD-KCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEA 113 (189)
Q Consensus 35 Tv~eMl~DRGY~V~~~el~~s~~eF~~~f~~-~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~en 113 (189)
-+-.+++..||.|..--.+.+.++|.+.... .|+ - |.+.+.. .-....++.+++.+ .+.+
T Consensus 101 ~v~~~l~~~G~~vi~lG~~~p~~~l~~~~~~~~~d--~--------------v~lS~~~--~~~~~~~~~~i~~l-r~~~ 161 (201)
T cd02070 101 LVATMLEANGFEVIDLGRDVPPEEFVEAVKEHKPD--I--------------LGLSALM--TTTMGGMKEVIEAL-KEAG 161 (201)
T ss_pred HHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCC--E--------------EEEeccc--cccHHHHHHHHHHH-HHCC
Confidence 3456888899999765567778888776422 122 1 2222222 23467789999999 7776
Q ss_pred c--ceEEEEEcCCCCHHH
Q 029683 114 L--HGLILILQSNMNTFA 129 (189)
Q Consensus 114 i--~~~IiV~q~~lt~~A 129 (189)
. +--|+|-...+++..
T Consensus 162 ~~~~~~i~vGG~~~~~~~ 179 (201)
T cd02070 162 LRDKVKVMVGGAPVNQEF 179 (201)
T ss_pred CCcCCeEEEECCcCCHHH
Confidence 5 444666666666643
No 37
>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=26.72 E-value=3e+02 Score=21.72 Aligned_cols=94 Identities=16% Similarity=0.157 Sum_probs=49.0
Q ss_pred EEecCCCccchhHHHHHHHHHhhc---cCcceEEEEEc-CCCCHHHHHhh----cccC-ceEEeeeecc---ceeccccc
Q 029683 88 VVYLGTEEIRTQAIRGLYGQILNK---EALHGLILILQ-SNMNTFARKEV----LKFP-FKVEIFYITD---LLVNVTKH 155 (189)
Q Consensus 88 VfF~~~~~vgvk~Ir~~~~~~~~~---eni~~~IiV~q-~~lt~~Ar~~i----~~~~-~~iE~F~e~E---Ll~nit~H 155 (189)
++.+....+++..|+.+++.+ .. .+-.+.|||-. ..+++.|...+ .+.+ ..+=+|.-.. |+=-|...
T Consensus 68 ~~~~~~~~~~~~~i~~i~~~~-~~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr 146 (188)
T TIGR00678 68 RLEPEGQSIKVDQVRELVEFL-SRTPQESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSR 146 (188)
T ss_pred EeccccCcCCHHHHHHHHHHH-ccCcccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhh
Confidence 334444568999999888877 54 34445555433 45666544333 2222 1222222211 11112222
Q ss_pred eecCcccccCHHHHHHHHHHcCCCCCC
Q 029683 156 ILQPKHEVLSAGERDKLMKKYKIEGKQ 182 (189)
Q Consensus 156 ~lVPkH~~l~~eEk~~ll~~y~~~~~q 182 (189)
-.+=.-..++++|..+.|++.++++.+
T Consensus 147 ~~~~~~~~~~~~~~~~~l~~~gi~~~~ 173 (188)
T TIGR00678 147 CQVLPFPPLSEEALLQWLIRQGISEEA 173 (188)
T ss_pred cEEeeCCCCCHHHHHHHHHHcCCCHHH
Confidence 222234557888888888887665544
No 38
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=26.59 E-value=56 Score=24.82 Aligned_cols=17 Identities=24% Similarity=0.321 Sum_probs=11.7
Q ss_pred chHHHH-HHHHHHHHHHH
Q 029683 23 SLESYR-YFLSRRTVLQM 39 (189)
Q Consensus 23 ~~e~~r-L~rvrrTv~eM 39 (189)
+....| .||+||=+.||
T Consensus 12 d~~~~RL~~rsrRGmrEl 29 (94)
T COG2938 12 DARKARLRWRSRRGMREL 29 (94)
T ss_pred HHHHHHHHHHHHhccHHH
Confidence 344445 89999877665
No 39
>COG0135 TrpF Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]
Probab=24.99 E-value=3.9e+02 Score=22.88 Aligned_cols=68 Identities=9% Similarity=0.076 Sum_probs=45.2
Q ss_pred EEEecCC-CccchhHHHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC-ceEEeeeeccceeccccceecCccccc
Q 029683 87 LVVYLGT-EEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP-FKVEIFYITDLLVNVTKHILQPKHEVL 164 (189)
Q Consensus 87 ~VfF~~~-~~vgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~-~~iE~F~e~ELl~nit~H~lVPkH~~l 164 (189)
+||++.. ..|...+.+.+...+ .. + ..+-|+.+.-.......+...+ ..|++ |--.
T Consensus 28 ~If~~~SpR~Vs~~~a~~i~~~v-~~--~-~~VgVf~n~~~~~i~~i~~~~~ld~VQl------------------HG~e 85 (208)
T COG0135 28 FIFVPKSPRYVSPEQAREIASAV-PK--V-KVVGVFVNESIEEILEIAEELGLDAVQL------------------HGDE 85 (208)
T ss_pred EEEcCCCCCcCCHHHHHHHHHhC-CC--C-CEEEEECCCCHHHHHHHHHhcCCCEEEE------------------CCCC
Confidence 5566634 689999999999888 43 3 3777887777677777777665 34443 3335
Q ss_pred CHHHHHHHHHHc
Q 029683 165 SAGERDKLMKKY 176 (189)
Q Consensus 165 ~~eEk~~ll~~y 176 (189)
+++..++|-++|
T Consensus 86 ~~~~~~~l~~~~ 97 (208)
T COG0135 86 DPEYIDQLKEEL 97 (208)
T ss_pred CHHHHHHHHhhc
Confidence 566666666555
No 40
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=24.43 E-value=62 Score=22.09 Aligned_cols=20 Identities=10% Similarity=0.393 Sum_probs=17.0
Q ss_pred HHHHHHhcCCCCcCCccccc
Q 029683 34 RTVLQMLNDRGYAVPNSELT 53 (189)
Q Consensus 34 rTv~eMl~DRGY~V~~~el~ 53 (189)
.-+++..+..||.++.+|+.
T Consensus 28 e~~~~lA~~~Gf~ft~~el~ 47 (64)
T TIGR03798 28 EDRVAIAKEAGFEFTGEDLK 47 (64)
T ss_pred HHHHHHHHHcCCCCCHHHHH
Confidence 45778899999999999884
No 41
>PRK06964 DNA polymerase III subunit delta'; Validated
Probab=24.37 E-value=4.8e+02 Score=23.80 Aligned_cols=83 Identities=14% Similarity=0.160 Sum_probs=49.0
Q ss_pred ccchhHHHHHHHHHhhc---cCcceEEEEEc-CCCCHHHHHhh----cccC----ceEEeeeeccceeccc-cceecCcc
Q 029683 95 EIRTQAIRGLYGQILNK---EALHGLILILQ-SNMNTFARKEV----LKFP----FKVEIFYITDLLVNVT-KHILQPKH 161 (189)
Q Consensus 95 ~vgvk~Ir~~~~~~~~~---eni~~~IiV~q-~~lt~~Ar~~i----~~~~----~~iE~F~e~ELl~nit-~H~lVPkH 161 (189)
.+++..||.+++.+ .. ++-.+.+||.+ ..||+.|..++ ++-+ +.+-.-..+.|+--|. .-..+ .-
T Consensus 111 ~I~idqiR~l~~~~-~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i-~~ 188 (342)
T PRK06964 111 EIKIEQVRALLDFC-GVGTHRGGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQF-PM 188 (342)
T ss_pred ccCHHHHHHHHHHh-ccCCccCCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEE-Ee
Confidence 58999999998887 42 34466666644 45888776554 3333 2222333344443322 11122 23
Q ss_pred cccCHHHHHHHHHHcCCC
Q 029683 162 EVLSAGERDKLMKKYKIE 179 (189)
Q Consensus 162 ~~l~~eEk~~ll~~y~~~ 179 (189)
..+++++..+.|.+..+.
T Consensus 189 ~~~~~~~~~~~L~~~~~~ 206 (342)
T PRK06964 189 TVPAPEAAAAWLAAQGVA 206 (342)
T ss_pred cCCCHHHHHHHHHHcCCC
Confidence 367889999999876654
No 42
>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=23.72 E-value=1.9e+02 Score=22.42 Aligned_cols=57 Identities=12% Similarity=0.211 Sum_probs=34.2
Q ss_pred HHHHHHHhCC--C--CCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccCcc
Q 029683 56 LTEFRFTFGD--K--CDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALH 115 (189)
Q Consensus 56 ~~eF~~~f~~--~--~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~eni~ 115 (189)
+.+|.++|.- . |.-+..-|++- +...+-+-|-|++-..==.+.|++.++.. .+.|.+
T Consensus 45 lmdFIsryARTDEImPEDKTvGFvvi--N~dKK~mSvsFsdideNmK~~i~ei~kky-kd~Gyk 105 (110)
T PF11513_consen 45 LMDFISRYARTDEIMPEDKTVGFVVI--NKDKKMMSVSFSDIDENMKNSIEEIVKKY-KDSGYK 105 (110)
T ss_dssp HHHHHHHH---S---TTSEEEEEEEE--ETTTTEEEEEE-S--CCHHHHHHHHHHHH-HCCS-E
T ss_pred HHHHHHHhhcccccCCCCceeEEEEE--ecCCeEEEEEecchhHHHHHHHHHHHHHh-hcCCce
Confidence 8899999963 3 55555555553 33334578899865332277888888888 666654
No 43
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=23.61 E-value=2.3e+02 Score=25.71 Aligned_cols=90 Identities=9% Similarity=0.071 Sum_probs=50.3
Q ss_pred EEEEec-CCCccchhHHHHHHHHHh--hccCcceEEEEE-cCCCCHHHHHhhccc----Cc----eEEeeeeccceeccc
Q 029683 86 MLVVYL-GTEEIRTQAIRGLYGQIL--NKEALHGLILIL-QSNMNTFARKEVLKF----PF----KVEIFYITDLLVNVT 153 (189)
Q Consensus 86 i~VfF~-~~~~vgvk~Ir~~~~~~~--~~eni~~~IiV~-q~~lt~~Ar~~i~~~----~~----~iE~F~e~ELl~nit 153 (189)
+++..+ +...+|+..||.+++.+. ..++-.+.+||- -..||..|..++-.. +- .+-.-..+.|+--|.
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 346799999999988862 245666777664 456898777555332 31 222222333443322
Q ss_pred -cceecCcccccCHHHHHHHHHHc
Q 029683 154 -KHILQPKHEVLSAGERDKLMKKY 176 (189)
Q Consensus 154 -~H~lVPkH~~l~~eEk~~ll~~y 176 (189)
+-..+ .-..+++++..+.|++-
T Consensus 156 SRC~~~-~~~~~~~~~~~~~L~~~ 178 (325)
T PRK06871 156 SRCQTW-LIHPPEEQQALDWLQAQ 178 (325)
T ss_pred hhceEE-eCCCCCHHHHHHHHHHH
Confidence 11122 23456777777777653
No 44
>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=23.33 E-value=3.5e+02 Score=22.26 Aligned_cols=79 Identities=11% Similarity=0.053 Sum_probs=50.5
Q ss_pred HHHHHHhcCCCCcCCcccccCCHHHHHHHhCC-CCCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhcc
Q 029683 34 RTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD-KCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKE 112 (189)
Q Consensus 34 rTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~-~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~e 112 (189)
+-+..|++..||.|..--.+.+.++|.+..-. +|+ -+.+++ .. .-.+..++.+++.+ .+.
T Consensus 102 ~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~~~~~pd--~v~lS~--------------~~--~~~~~~~~~~i~~l-~~~ 162 (197)
T TIGR02370 102 NIVVTMLRANGFDVIDLGRDVPIDTVVEKVKKEKPL--MLTGSA--------------LM--TTTMYGQKDINDKL-KEE 162 (197)
T ss_pred HHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHcCCC--EEEEcc--------------cc--ccCHHHHHHHHHHH-HHc
Confidence 44567899999999887778888999877522 232 222222 11 23355688899998 777
Q ss_pred Ccc--eEEEEEcCCCCHHHHH
Q 029683 113 ALH--GLILILQSNMNTFARK 131 (189)
Q Consensus 113 ni~--~~IiV~q~~lt~~Ar~ 131 (189)
+.. --|+|-...+++.-.+
T Consensus 163 ~~~~~v~i~vGG~~~~~~~~~ 183 (197)
T TIGR02370 163 GYRDSVKFMVGGAPVTQDWAD 183 (197)
T ss_pred CCCCCCEEEEEChhcCHHHHH
Confidence 664 3466666667764433
No 45
>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=23.17 E-value=51 Score=24.14 Aligned_cols=20 Identities=20% Similarity=0.278 Sum_probs=16.1
Q ss_pred cCHHHHHHHHHHcCCCCCCC
Q 029683 164 LSAGERDKLMKKYKIEGKQV 183 (189)
Q Consensus 164 l~~eEk~~ll~~y~~~~~qL 183 (189)
|+++++++|++++++++..+
T Consensus 61 l~e~~~~~l~~~~~a~~GD~ 80 (95)
T PF02938_consen 61 LSEEELKALIERLGAKPGDL 80 (95)
T ss_dssp CHHHHHHHHHHHTT--TTEE
T ss_pred CCHHHHHHHHHHhCCCCCCE
Confidence 89999999999999988654
No 46
>PRK07132 DNA polymerase III subunit delta'; Validated
Probab=21.33 E-value=5.2e+02 Score=23.03 Aligned_cols=88 Identities=3% Similarity=-0.007 Sum_probs=51.8
Q ss_pred CCccchhHHHHHHHHHhhcc----CcceEEEEEc-CCCCHHHHH----hhcccC-ceEEeeeec--ccee-ccccceecC
Q 029683 93 TEEIRTQAIRGLYGQILNKE----ALHGLILILQ-SNMNTFARK----EVLKFP-FKVEIFYIT--DLLV-NVTKHILQP 159 (189)
Q Consensus 93 ~~~vgvk~Ir~~~~~~~~~e----ni~~~IiV~q-~~lt~~Ar~----~i~~~~-~~iE~F~e~--ELl~-nit~H~lVP 159 (189)
+..+++..|+..++.+ .-. +-.+.+||-. +++|..|.. .+.+.+ ..+=+|..+ +-++ -|.+.-.+=
T Consensus 66 g~~i~vd~Ir~l~~~~-~~~~~~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~ 144 (299)
T PRK07132 66 DKDLSKSEFLSAINKL-YFSSFVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVF 144 (299)
T ss_pred CCcCCHHHHHHHHHHh-ccCCcccCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEE
Confidence 4679999999999998 433 4677888866 778886654 444444 333333222 1111 122222222
Q ss_pred cccccCHHHHHHHHHHcCCCCC
Q 029683 160 KHEVLSAGERDKLMKKYKIEGK 181 (189)
Q Consensus 160 kH~~l~~eEk~~ll~~y~~~~~ 181 (189)
+-..+++++..+.|.+-++.+.
T Consensus 145 ~f~~l~~~~l~~~l~~~~~~~~ 166 (299)
T PRK07132 145 NVKEPDQQKILAKLLSKNKEKE 166 (299)
T ss_pred ECCCCCHHHHHHHHHHcCCChh
Confidence 3456788888877776555443
No 47
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=20.84 E-value=1.2e+02 Score=22.80 Aligned_cols=53 Identities=11% Similarity=0.257 Sum_probs=36.1
Q ss_pred cchhHHHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccCceEEeeeeccceecc
Q 029683 96 IRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNV 152 (189)
Q Consensus 96 vgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~~~iE~F~e~ELl~ni 152 (189)
+|.--+.++.+.+ ...++. .+|+.+.+||.-.+.+.... .++++.-..|+.+|
T Consensus 41 iG~GK~eei~~~~-~~~~~d--~vvfd~~Lsp~Q~rNLe~~~-~~~V~DRt~LIL~I 93 (95)
T PF13167_consen 41 IGSGKVEEIKELI-EELDAD--LVVFDNELSPSQQRNLEKAL-GVKVIDRTQLILEI 93 (95)
T ss_pred echhHHHHHHHHH-hhcCCC--EEEECCCCCHHHHHHHHHHH-CCeeeccccHHHHH
Confidence 4444466666666 556663 55667889999888887653 67778877777665
No 48
>PF05273 Pox_RNA_Pol_22: Poxvirus RNA polymerase 22 kDa subunit; InterPro: IPR007937 Vaccinia viral RNA synthesis is carried out by a virus coded, multi-subunit, eukaryotic-like RNA polymerase. RNA polymerase subunits are synthesized throughout infection and the assembled RNA polymerase is packaged into nascent virions late in infection. The RNA polymerase exists in two different forms, one specific for early genes and one specific for late genes. Both forms of the RNA polymerase have in common eight subunits, ranging in size from 147 to 7 kDa This family consists of several poxvirus DNA-dependent RNA polymerase 22 kDa subunits.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=20.64 E-value=80 Score=26.64 Aligned_cols=122 Identities=18% Similarity=0.284 Sum_probs=73.0
Q ss_pred HHhcCCCCcCCcccccCCHHHHHHHhCCCCCCCccE--EEecCCCCCCCcEEEEecCCCccchhHHHHHHHHHhhccCcc
Q 029683 38 QMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLR--LCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALH 115 (189)
Q Consensus 38 eMl~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~--~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~eni~ 115 (189)
|.++ .-|.|-..+ -..+|.-.....+|. +.+.|+-|.+..+|=.|.+ .+|.-.++. ...-
T Consensus 18 Ei~r-~PyavIsk~-------~~~~Y~~~v~YgDlvt~itv~hkid~~~tVfQvFnE-ssV~YsP~e---------~DYG 79 (185)
T PF05273_consen 18 EILR-DPYAVISKD-------ILSRYDTDVEYGDLVTIITVTHKIDSSKTVFQVFNE-SSVNYSPLE---------DDYG 79 (185)
T ss_pred HHhc-CCceeeeHH-------HHhhheeeeeeCcEEEEEEEEEEccCCceeeeeecc-cceeecccc---------ccCC
Confidence 4444 467765543 334554444444443 3345666666666666654 446655554 2333
Q ss_pred eEEEEEcCCCCHHHHHhhcccCceEEeeeeccceeccccceecCcccccCHHHHHHHHHHcCCCCCC-----CcccccC
Q 029683 116 GLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQ-----VTILVKQ 189 (189)
Q Consensus 116 ~~IiV~q~~lt~~Ar~~i~~~~~~iE~F~e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~~~~~q-----LP~i~~~ 189 (189)
--|||+ ++....-.. |..+=|-+++-.-.|.|+...|+++|..-+-.=+.+.+.. |||++.|
T Consensus 80 ePIiiT-----s~lq~gHnK-------fPi~~lyIDvVaSDlFP~F~Rlt~~e~~vv~svl~~gd~kE~~lkLPkmleT 146 (185)
T PF05273_consen 80 EPIIIT-----SFLQPGHNK-------FPINMLYIDVVASDLFPKFVRLTPDEIAVVNSVLQIGDRKEQSLKLPKMLET 146 (185)
T ss_pred CcEEEE-----ecccccccc-------cceeeEEeeeeecccccccccCChhhhhHhhhhhccCCCccceeecchhhhh
Confidence 346665 332222332 5556677788888899999999999998865555555443 8988753
No 49
>PF13864 Enkurin: Calmodulin-binding
Probab=20.56 E-value=62 Score=23.96 Aligned_cols=23 Identities=30% Similarity=0.442 Sum_probs=18.8
Q ss_pred ecCcccccCHHHHHHHHHHcCCC
Q 029683 157 LQPKHEVLSAGERDKLMKKYKIE 179 (189)
Q Consensus 157 lVPkH~~l~~eEk~~ll~~y~~~ 179 (189)
.-|.|..|+++|+.++|+.++-+
T Consensus 30 ~~~~~~~l~eeER~~lL~~Lk~~ 52 (98)
T PF13864_consen 30 CPPGMRLLSEEERQELLEGLKKN 52 (98)
T ss_pred CccccccCCHHHHHHHHHHHHHH
Confidence 34789999999999999876543
No 50
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=20.49 E-value=1.5e+02 Score=25.66 Aligned_cols=68 Identities=15% Similarity=0.125 Sum_probs=38.0
Q ss_pred cchhHHHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC-ceEEeeeeccceeccccceecCcccccCHH
Q 029683 96 IRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP-FKVEIFYITDLLVNVTKHILQPKHEVLSAG 167 (189)
Q Consensus 96 vgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~-~~iE~F~e~ELl~nit~H~lVPkH~~l~~e 167 (189)
+.+..+..+-..+ .+..+.-+||-++..-.-.+...+-+.+ ..|=-|.--.| ++.+|+.| +|+-||.|
T Consensus 130 v~V~~~d~le~~v-~~~dv~iaiLtVPa~~AQ~vad~Lv~aGVkGIlNFtPv~l--~~pe~V~V-~~iDLt~e 198 (211)
T COG2344 130 VPVYDLDDLEKFV-KKNDVEIAILTVPAEHAQEVADRLVKAGVKGILNFTPVRL--QVPEGVIV-ENIDLTAE 198 (211)
T ss_pred eeeechHHHHHHH-HhcCccEEEEEccHHHHHHHHHHHHHcCCceEEeccceEe--cCCCCcEE-EEeehHHH
Confidence 3355666777777 7789999999886643322333333333 34544544333 45555444 45555544
No 51
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=20.44 E-value=6e+02 Score=22.45 Aligned_cols=45 Identities=4% Similarity=-0.085 Sum_probs=29.7
Q ss_pred cCCCccchhHHHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC
Q 029683 91 LGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP 137 (189)
Q Consensus 91 ~~~~~vgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~ 137 (189)
..+...+.+.|.++++.+ +++++. +|++=.+.-+..++...++.+
T Consensus 231 ~~~~eps~~~l~~l~~~i-k~~~v~-~If~e~~~~~~~~~~la~e~g 275 (311)
T PRK09545 231 NPEIQPGAQRLHEIRTQL-VEQKAT-CVFAEPQFRPAVIESVAKGTS 275 (311)
T ss_pred CCCCCCCHHHHHHHHHHH-HHcCCC-EEEecCCCChHHHHHHHHhcC
Confidence 344567899999999999 989986 555544444444444444444
No 52
>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=20.34 E-value=7.4e+02 Score=24.48 Aligned_cols=133 Identities=15% Similarity=0.097 Sum_probs=74.2
Q ss_pred chHHHHHHHHHHHHHHHhcCCCCcCCc--ccccCCHHHHHHHhCCC-----CCCCcc----------------EEEecCC
Q 029683 23 SLESYRYFLSRRTVLQMLNDRGYAVPN--SELTRSLTEFRFTFGDK-----CDLESL----------------RLCLPLR 79 (189)
Q Consensus 23 ~~e~~rL~rvrrTv~eMl~DRGY~V~~--~el~~s~~eF~~~f~~~-----~~r~~L----------------~~~~~~~ 79 (189)
+.....+|..|.-.++-|+.-|-..-. -...+|+.+|.++|... .+...+ .|..-+.
T Consensus 51 ~~d~~qy~~~R~r~i~~l~~s~~~Pyphkf~vs~si~~fieky~~l~~ge~~~n~~~svaGRI~s~R~sGsKL~Fydl~~ 130 (560)
T KOG1885|consen 51 TSDPEQYFKIRSRAIEELRASGLNPYPHKFHVSISIPDFIEKYLHLATGEHLDNEIVSVAGRIHSKRESGSKLVFYDLHG 130 (560)
T ss_pred cCCHHHHHHHHHHHHHHHhhcCCCCCcchhhccccHHHHHHHhcCcccccccccceeeeeeeEeeeeccCCceEEEEEec
Confidence 344577899988888888877655543 35788999999999641 111112 2222222
Q ss_pred CCCCCcEEEEecCCCccchhHHHHHHHHHhhccCcceEEEE-EcCCCCHHHHHhhcccCceEEeeeeccceeccccceec
Q 029683 80 SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILI-LQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQ 158 (189)
Q Consensus 80 ~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~~eni~~~IiV-~q~~lt~~Ar~~i~~~~~~iE~F~e~ELl~nit~H~lV 158 (189)
+ ..++.|.+......+-. .|.+.+ +.+.||=|| +.+.+.-+-+. + +-+|--+=.+...--|.|=
T Consensus 131 ~--g~klQvm~~~~~~~~~~---~F~~~~---~~lkrGDiig~~G~pgrt~~g---E----LSi~~~~~~lLspcLh~lP 195 (560)
T KOG1885|consen 131 D--GVKLQVMANAKKITSEE---DFEQLH---KFLKRGDIIGVSGYPGRTKSG---E----LSIIPNEIILLSPCLHMLP 195 (560)
T ss_pred C--CeEEEEEEehhhcCCHH---HHHHHH---hhhhccCEEeeecCCCcCCCc---e----EEEeecchheecchhccCC
Confidence 2 22344444332221111 244444 566677444 55554332222 2 3334444466677888888
Q ss_pred CcccccCHHHHH
Q 029683 159 PKHEVLSAGERD 170 (189)
Q Consensus 159 PkH~~l~~eEk~ 170 (189)
++|..|++.|++
T Consensus 196 ~~~~gLkD~EtR 207 (560)
T KOG1885|consen 196 HEHFGLKDKETR 207 (560)
T ss_pred hhhcCCCcHHHH
Confidence 899999997754
No 53
>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=20.34 E-value=91 Score=24.80 Aligned_cols=70 Identities=16% Similarity=0.310 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCcCCcccccCCHHHHHHHhCCC--CCCCccEEEecCCCCCCCcEEEEecCCCccchhHHHH
Q 029683 26 SYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK--CDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRG 103 (189)
Q Consensus 26 ~~rL~rvrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~--~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~ 103 (189)
...||.--.-|++-|..|||.|+.+ ++...|-+. +...+|.- ...++| | |+ .=+-..+.+
T Consensus 47 ~~~L~~yH~lv~~EM~~RGY~~~~~-------W~d~~yRG~~~~~y~~l~~--~~~~~P---i---Y~---eHd~~Yl~e 108 (120)
T TIGR02328 47 PYKLFAYHLLVMEEMATRGYHVSKQ-------WLDPNYRGQNCPNYDLLEE--IKLTTP---I---YP---EHNDDYLNE 108 (120)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCChh-------hcCccccCCcCCcccccch--hhcCCC---C---Ch---hhhHHHHHH
Confidence 4678888888888888899999984 665556333 33333321 122333 1 22 233455666
Q ss_pred HHHHHhhccCc
Q 029683 104 LYGQILNKEAL 114 (189)
Q Consensus 104 ~~~~~~~~eni 114 (189)
.++.+ .+.||
T Consensus 109 Cl~NL-~~KgI 118 (120)
T TIGR02328 109 CLANL-RAKGI 118 (120)
T ss_pred HHHHH-HHcCc
Confidence 77776 66554
No 54
>KOG3451 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.27 E-value=1.3e+02 Score=21.75 Aligned_cols=55 Identities=16% Similarity=0.215 Sum_probs=34.7
Q ss_pred CcceEEEEEcCCCCHHHHHhhcccC--------ceEEeeeeccceeccccceecCcccccCHHHHHHHHHHcC
Q 029683 113 ALHGLILILQSNMNTFARKEVLKFP--------FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYK 177 (189)
Q Consensus 113 ni~~~IiV~q~~lt~~Ar~~i~~~~--------~~iE~F~e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~ 177 (189)
|+..|++|... |.-++.+-.|. +.||...++-|+||...-+. =+.|...+|++-+
T Consensus 3 na~KGvlV~cD---p~~kqlilnmd~sm~~~skfii~eLDdthLfV~p~~vem-------vk~~le~~le~n~ 65 (71)
T KOG3451|consen 3 NAKKGVLVTCD---PAFKQLILNMDDSMQLGSKFIIEELDDTHLFVNPSIVEM-------VKNELERILENNN 65 (71)
T ss_pred ccccceEEecC---hhHHHHhhhccccCCCCCCeeEEEeccceeeecHHHHHH-------HHHHHHHHHHhcC
Confidence 56677788655 44566654442 78899999888888544333 3455566666543
Done!