Query 030447
Match_columns 177
No_of_seqs 161 out of 335
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 13:52:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030447.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030447hhsearch_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 1.4E-64 3.1E-69 422.9 13.4 142 36-177 6-208 (208)
2 PLN03111 DNA-directed RNA poly 100.0 1.5E-63 3.3E-68 418.2 13.7 146 32-177 1-206 (206)
3 PTZ00061 DNA-directed RNA poly 100.0 7.7E-62 1.7E-66 407.7 13.2 142 36-177 2-205 (205)
4 PF01191 RNA_pol_Rpb5_C: RNA p 100.0 3.2E-40 6.9E-45 239.4 6.3 74 104-177 1-74 (74)
5 PRK09570 rpoH DNA-directed RNA 100.0 4.2E-40 9.1E-45 241.5 7.0 75 103-177 3-77 (79)
6 COG2012 RPB5 DNA-directed RNA 100.0 3.4E-37 7.4E-42 226.3 7.0 79 99-177 2-80 (80)
7 PF03871 RNA_pol_Rpb5_N: RNA p 99.9 7.6E-24 1.7E-28 157.5 -0.9 64 35-98 3-69 (93)
8 PF13550 Phage-tail_3: Putativ 76.0 4.1 9E-05 30.9 3.8 56 115-175 103-159 (164)
9 KOG0975 Branched chain aminotr 56.2 5.2 0.00011 37.4 1.0 28 45-74 288-316 (379)
10 PRK05753 nucleoside diphosphat 55.2 23 0.00051 28.0 4.4 34 139-175 88-122 (137)
11 PF01272 GreA_GreB: Transcript 53.3 23 0.0005 24.8 3.7 34 139-176 39-73 (77)
12 KOG1232 Proteins containing th 51.7 10 0.00022 36.4 2.1 64 10-74 331-405 (511)
13 COG2002 AbrB Regulators of sta 46.9 20 0.00044 26.1 2.6 26 139-164 15-40 (89)
14 PRK05892 nucleoside diphosphat 46.2 34 0.00074 27.7 4.1 36 137-176 116-152 (158)
15 COG1034 NuoG NADH dehydrogenas 44.8 18 0.00038 36.3 2.6 64 11-78 50-118 (693)
16 PF04225 OapA: Opacity-associa 44.4 11 0.00025 27.5 1.0 47 119-165 9-56 (85)
17 TIGR01462 greA transcription e 43.7 46 0.001 26.4 4.4 34 139-176 114-148 (151)
18 TIGR03595 Obg_CgtA_exten Obg f 42.8 19 0.00041 25.5 1.9 14 148-161 50-63 (69)
19 PF01963 TraB: TraB family; I 42.7 11 0.00023 30.9 0.7 15 48-62 244-258 (259)
20 PRK01885 greB transcription el 42.5 42 0.00091 27.2 4.1 35 138-176 117-152 (157)
21 PF05920 Homeobox_KN: Homeobox 41.3 10 0.00022 24.4 0.3 24 114-137 7-30 (40)
22 PLN00045 photosystem I reactio 40.4 18 0.00039 28.2 1.6 17 148-164 36-52 (101)
23 TIGR03798 ocin_TIGR03798 bacte 40.3 31 0.00066 23.7 2.6 20 47-66 28-47 (64)
24 PF09269 DUF1967: Domain of un 40.2 19 0.0004 25.5 1.5 13 148-160 50-62 (69)
25 KOG4449 Translocase of outer m 39.6 23 0.00049 24.8 1.8 38 117-156 2-39 (53)
26 PRK08559 nusG transcription an 39.3 37 0.00081 27.0 3.3 31 117-163 76-106 (153)
27 TIGR01461 greB transcription e 39.3 54 0.0012 26.5 4.3 35 138-176 115-150 (156)
28 cd06573 PASTA PASTA domain. Th 38.0 56 0.0012 19.7 3.3 21 112-133 2-22 (53)
29 KOG3259 Peptidyl-prolyl cis-tr 37.6 34 0.00074 28.7 2.9 59 115-175 77-162 (163)
30 PF08479 POTRA_2: POTRA domain 37.6 29 0.00063 24.0 2.2 53 10-63 5-57 (76)
31 PF04014 Antitoxin-MazE: Antid 37.3 40 0.00086 21.6 2.6 20 145-164 14-33 (47)
32 cd02775 MopB_CT Molybdopterin- 37.1 26 0.00057 24.4 1.9 27 138-164 23-49 (101)
33 cd01900 YchF YchF subfamily. 37.0 16 0.00035 32.1 0.9 24 118-141 244-267 (274)
34 PF14085 DUF4265: Domain of un 35.8 55 0.0012 25.1 3.6 28 149-176 23-58 (117)
35 PF01568 Molydop_binding: Moly 35.6 33 0.00071 24.6 2.2 27 138-164 30-56 (110)
36 COG0782 Uncharacterized conser 35.3 65 0.0014 26.0 4.1 27 137-163 110-137 (151)
37 PRK06437 hypothetical protein; 35.2 32 0.0007 23.9 2.1 41 123-163 23-63 (67)
38 PF04023 FeoA: FeoA domain; I 35.2 30 0.00065 23.4 1.9 21 149-169 30-50 (74)
39 COG0250 NusG Transcription ant 35.1 54 0.0012 27.2 3.7 60 99-168 74-139 (178)
40 cd00988 PDZ_CTP_protease PDZ d 33.9 31 0.00068 23.3 1.8 19 140-159 20-38 (85)
41 PRK00226 greA transcription el 33.9 74 0.0016 25.3 4.2 34 139-176 119-153 (157)
42 cd02786 MopB_CT_3 The MopB_CT_ 33.6 37 0.0008 24.7 2.3 27 138-164 31-57 (116)
43 cd04459 Rho_CSD Rho_CSD: Rho p 33.0 45 0.00098 23.9 2.6 24 140-163 29-53 (68)
44 PRK06342 transcription elongat 32.4 70 0.0015 26.1 3.9 36 115-160 113-149 (160)
45 cd02788 MopB_CT_NDH-1_NuoG2-N7 32.0 45 0.00097 24.0 2.5 27 138-164 29-55 (96)
46 TIGR02328 conserved hypothetic 31.9 54 0.0012 26.4 3.1 41 16-62 29-70 (120)
47 CHL00142 rps17 ribosomal prote 31.5 66 0.0014 24.0 3.3 36 137-176 39-74 (84)
48 cd02787 MopB_CT_ydeP The MopB_ 31.4 54 0.0012 23.9 2.8 25 140-164 33-57 (112)
49 PF07653 SH3_2: Variant SH3 do 31.3 25 0.00055 22.8 1.0 12 150-161 16-27 (55)
50 cd02790 MopB_CT_Formate-Dh_H F 30.5 45 0.00098 24.0 2.3 28 137-164 34-61 (116)
51 cd00989 PDZ_metalloprotease PD 30.3 40 0.00087 22.4 1.9 17 145-161 23-39 (79)
52 COG4624 Iron only hydrogenase 29.4 43 0.00093 31.8 2.5 37 115-151 220-256 (411)
53 PF07957 DUF3294: Protein of u 29.1 16 0.00034 31.9 -0.4 34 116-153 175-208 (216)
54 cd02792 MopB_CT_Formate-Dh-Na- 28.8 42 0.00091 24.4 1.9 28 137-164 34-61 (122)
55 PF07862 Nif11: Nitrogen fixat 28.7 31 0.00066 22.3 1.0 20 47-66 30-49 (49)
56 TIGR02480 fliN flagellar motor 28.4 44 0.00094 23.7 1.8 19 145-163 22-40 (77)
57 cd00508 MopB_CT_Fdh-Nap-like T 28.2 48 0.001 23.9 2.1 27 138-164 35-61 (120)
58 cd02791 MopB_CT_Nitrate-R-NapA 27.8 40 0.00088 24.5 1.6 28 137-164 34-61 (122)
59 TIGR03784 marine_sortase sorta 27.8 78 0.0017 26.1 3.5 28 146-176 103-130 (174)
60 PRK00276 infA translation init 27.8 75 0.0016 22.3 3.0 23 152-175 47-71 (72)
61 PRK06033 hypothetical protein; 27.7 46 0.00099 24.4 1.9 19 145-163 21-39 (83)
62 cd02781 MopB_CT_Acetylene-hydr 27.5 49 0.0011 24.5 2.1 29 136-164 31-59 (130)
63 PF14250 AbrB-like: AbrB-like 27.3 39 0.00084 24.9 1.4 32 130-161 31-62 (71)
64 cd02794 MopB_CT_DmsA-EC The Mo 27.2 55 0.0012 24.2 2.3 25 140-164 32-56 (121)
65 PF01052 SpoA: Surface present 27.2 37 0.00081 23.4 1.3 19 145-163 22-40 (77)
66 PF08045 CDC14: Cell division 27.1 1.5E+02 0.0033 26.2 5.4 71 37-131 166-241 (257)
67 cd02789 MopB_CT_FmdC-FwdD The 26.9 47 0.001 24.6 1.9 26 139-164 32-57 (106)
68 PF03152 UFD1: Ubiquitin fusio 26.7 54 0.0012 27.4 2.4 31 144-174 78-108 (176)
69 smart00739 KOW KOW (Kyprides, 25.9 60 0.0013 17.8 1.8 17 152-169 2-18 (28)
70 cd03735 SOCS_SOCS1 SOCS (suppr 25.8 63 0.0014 21.4 2.1 33 43-77 8-40 (43)
71 cd02777 MopB_CT_DMSOR-like The 25.8 53 0.0011 24.5 2.0 27 138-164 34-60 (127)
72 PRK02220 4-oxalocrotonate taut 25.5 70 0.0015 20.8 2.3 35 118-164 12-46 (61)
73 cd02778 MopB_CT_Thiosulfate-R- 25.1 73 0.0016 23.3 2.6 27 138-164 30-56 (123)
74 cd00991 PDZ_archaeal_metallopr 25.1 54 0.0012 22.6 1.8 17 144-160 20-36 (79)
75 KOG2776 Metallopeptidase [Gene 24.9 48 0.001 31.3 1.9 14 149-162 100-113 (398)
76 PF01476 LysM: LysM domain; I 24.1 30 0.00065 21.0 0.3 37 121-160 7-43 (44)
77 PRK13622 psbV cytochrome c-550 23.5 1E+02 0.0022 26.2 3.5 82 41-128 67-153 (180)
78 TIGR00922 nusG transcription t 23.5 1.5E+02 0.0032 23.4 4.2 44 116-169 92-136 (172)
79 TIGR01312 XylB D-xylulose kina 23.4 79 0.0017 28.5 3.0 21 124-144 188-208 (481)
80 PRK11649 putative peptidase; P 23.4 71 0.0015 30.0 2.7 58 114-173 97-154 (439)
81 PF07497 Rho_RNA_bind: Rho ter 23.3 59 0.0013 24.0 1.8 32 139-170 30-62 (78)
82 smart00326 SH3 Src homology 3 23.2 96 0.0021 18.6 2.5 17 148-164 17-33 (58)
83 cd02782 MopB_CT_1 The MopB_CT_ 23.1 71 0.0015 23.7 2.2 27 138-164 33-59 (129)
84 PF11985 DUF3486: Protein of u 23.0 47 0.001 26.9 1.3 17 45-61 14-30 (180)
85 COG3655 Predicted transcriptio 22.9 32 0.00068 25.3 0.3 44 123-166 18-71 (73)
86 PF06130 PduL: Propanediol uti 22.8 1.7E+02 0.0037 21.1 4.1 16 147-162 18-33 (71)
87 PF00370 FGGY_N: FGGY family o 22.3 52 0.0011 26.9 1.5 46 102-158 179-232 (245)
88 PRK05609 nusG transcription an 22.3 1.9E+02 0.0041 22.8 4.7 43 117-169 101-143 (181)
89 COG5429 Uncharacterized secret 22.3 37 0.00081 30.4 0.7 108 69-177 59-203 (261)
90 CHL00125 psaE photosystem I su 22.0 57 0.0012 23.6 1.4 13 152-164 2-14 (64)
91 PRK02749 photosystem I reactio 21.7 57 0.0012 24.1 1.4 13 152-164 3-15 (71)
92 cd05829 Sortase_E Sortase E (S 21.5 1.3E+02 0.0029 23.5 3.6 28 145-175 66-93 (144)
93 KOG0790 Protein tyrosine phosp 21.5 67 0.0015 31.6 2.2 48 115-162 8-55 (600)
94 PRK14560 putative RNA-binding 21.3 1.1E+02 0.0024 24.3 3.2 30 134-163 73-118 (160)
95 PF03793 PASTA: PASTA domain; 21.1 81 0.0018 20.6 2.0 21 112-132 3-23 (63)
96 cd02780 MopB_CT_Tetrathionate_ 21.1 75 0.0016 24.3 2.1 27 138-164 30-56 (143)
97 cd02785 MopB_CT_4 The MopB_CT_ 20.9 87 0.0019 23.2 2.3 27 138-164 32-58 (124)
98 cd00565 ThiS ThiaminS ubiquiti 20.8 1.1E+02 0.0023 20.6 2.6 41 123-163 17-61 (65)
99 PRK09555 feoA ferrous iron tra 20.5 1E+02 0.0022 22.0 2.5 25 149-174 28-52 (74)
100 PRK05610 rpsQ 30S ribosomal pr 20.3 1.5E+02 0.0032 22.0 3.4 37 135-175 40-76 (84)
101 cd00992 PDZ_signaling PDZ doma 20.2 79 0.0017 20.9 1.8 21 140-161 33-53 (82)
102 TIGR01565 homeo_ZF_HD homeobox 20.0 58 0.0013 22.7 1.1 44 116-160 6-51 (58)
No 1
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=100.00 E-value=1.4e-64 Score=422.85 Aligned_cols=142 Identities=51% Similarity=0.924 Sum_probs=140.2
Q ss_pred hhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC-CCCCceeEeecCCCCCchh----------------
Q 030447 36 SRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKR---------------- 98 (177)
Q Consensus 36 ~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~~-~~r~~L~~~~~~~~dp~~k---------------- 98 (177)
+.|++|||++|||++||||||||.|+|+|++++|++|+++||+. |+|++|+|++.|++||++|
T Consensus 6 e~E~~rl~~ar~T~~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk~~ 85 (208)
T KOG3218|consen 6 EEEIYRLYLARKTAMQMLRDRGYTVTQEELDLTLEEFKARYGDKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVKTM 85 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCccccHHHhhhhHHHHHHHhccCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHHHH
Confidence 78999999999999999999999999999999999999999998 9999999999999999988
Q ss_pred --------------------------------------------hhhhhhcCCcccccCCceecCHHHHHHHHhhcCCCc
Q 030447 99 --------------------------------------------ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEE 134 (177)
Q Consensus 99 --------------------------------------------e~eLlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~ 134 (177)
|+||+||||+|+|||||.+||+|||++||++|++++
T Consensus 86 k~~~~~~~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l~e 165 (208)
T KOG3218|consen 86 KTYVIQMQSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKLKE 165 (208)
T ss_pred HHHHHHHHhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcCCc
Confidence 999999999999999999999999999999999999
Q ss_pred CCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447 135 KQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177 (177)
Q Consensus 135 ~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~ 177 (177)
+||||||.+||||||||||+||||||+|+|+|||+|+|||||+
T Consensus 166 ~qLPRIq~~DpvaRYyGLKrGqVVKI~r~setag~yitYR~v~ 208 (208)
T KOG3218|consen 166 TQLPRIQKKDPVARYYGLKRGQVVKIIRRSETAGRYITYRCVV 208 (208)
T ss_pred ccCCeeeccChHHhhhccccCcEEEEEecCccCcceEEEEEeC
Confidence 9999999999999999999999999999999999999999996
No 2
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=100.00 E-value=1.5e-63 Score=418.20 Aligned_cols=146 Identities=60% Similarity=0.947 Sum_probs=142.8
Q ss_pred CCCChhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceeEeecCCCCCchh-------------
Q 030447 32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKR------------- 98 (177)
Q Consensus 32 m~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~k------------- 98 (177)
|+.++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+.|+|++|+|++.+++||+++
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 4667889999999999999999999999999999999999999999999999999999999999988
Q ss_pred -----------------------------------------------hhhhhhcCCcccccCCceecCHHHHHHHHhhcC
Q 030447 99 -----------------------------------------------ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYS 131 (177)
Q Consensus 99 -----------------------------------------------e~eLlvNIt~H~LVPkH~vLs~eEk~~lL~~y~ 131 (177)
|+||+||||+|+|||||++||+|||++||++|+
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 999999999999999999999999999999999
Q ss_pred CCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447 132 IEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177 (177)
Q Consensus 132 i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~ 177 (177)
++++|||||+.+||||||||||+||||||+|+|+|||+||+||+|+
T Consensus 161 i~~~qLPrI~~~DPvary~g~k~G~vvkI~R~S~taG~~v~YR~vv 206 (206)
T PLN03111 161 VKETQLPRIQVSDPIARYYGLKRGQVVKIIRPSETAGRYVTYRCVV 206 (206)
T ss_pred CCHHHCCcccccChhhHhcCCCCCCEEEEEECCCCCCCceEEEEeC
Confidence 9999999999999999999999999999999999999999999996
No 3
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=7.7e-62 Score=407.65 Aligned_cols=142 Identities=43% Similarity=0.686 Sum_probs=137.6
Q ss_pred hhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC-CCCCceeEeecCCCCCchh----------------
Q 030447 36 SRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKR---------------- 98 (177)
Q Consensus 36 ~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~~-~~r~~L~~~~~~~~dp~~k---------------- 98 (177)
++++.||||+|||++|||+||||.|+++|+++|+++|+++||++ +.|++|+|++++.+||+++
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 47889999999999999999999999999999999999999987 4689999999999999766
Q ss_pred ---------------------------------------------hhhhhhcCCcccccCCceecCHHHHHHHHhhcCCC
Q 030447 99 ---------------------------------------------ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE 133 (177)
Q Consensus 99 ---------------------------------------------e~eLlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~ 133 (177)
|+||+||||+|+|||||++||+|||++||++|+++
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 99999999999999999999999999999999999
Q ss_pred cCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447 134 EKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177 (177)
Q Consensus 134 ~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~ 177 (177)
++|||||+.+||||||||||+||||||+|+|+|||+||+||+|+
T Consensus 162 ~~qLPrI~~~DPvary~g~k~G~vvkI~R~S~taG~~v~YR~vv 205 (205)
T PTZ00061 162 ESQLPRIQSADPVARYFGLSKGQVVKIIRPSETAGRYVTYRLVV 205 (205)
T ss_pred HHHCCcccccChhhHhcCCCCCCEEEEEECCCCCCcceEEEEeC
Confidence 99999999999999999999999999999999999999999996
No 4
>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=100.00 E-value=3.2e-40 Score=239.39 Aligned_cols=74 Identities=49% Similarity=0.793 Sum_probs=66.2
Q ss_pred hcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447 104 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177 (177)
Q Consensus 104 vNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~ 177 (177)
||||+|+|||||++||+||+++||++|+++++|||||+.+||+|||||+|+||||||+|+|+|||+|++||+||
T Consensus 1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~Vv 74 (74)
T PF01191_consen 1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSSDPVARYLGAKPGDVVKIIRKSETAGEYVTYRLVV 74 (74)
T ss_dssp S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETTSHHHHHTT--TTSEEEEEEEETTTSEEEEEEEEE
T ss_pred CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCcccccChhhhhcCCCCCCEEEEEecCCCCCCcEEEEEeC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999996
No 5
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=100.00 E-value=4.2e-40 Score=241.53 Aligned_cols=75 Identities=32% Similarity=0.589 Sum_probs=73.9
Q ss_pred hhcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447 103 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177 (177)
Q Consensus 103 lvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~ 177 (177)
.||||+|+|||+|++||+||+++||++|+++++|||||+.+||+|+||||++||||||+|+|+|||+|++||+|+
T Consensus 3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~Vv 77 (79)
T PRK09570 3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKIVRKSPTAGEAVYYRLVV 77 (79)
T ss_pred ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhcCCCCCCEEEEEECCCCCCccEEEEEEe
Confidence 589999999999999999999999999999999999999999999999999999999999999999999999996
No 6
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=100.00 E-value=3.4e-37 Score=226.25 Aligned_cols=79 Identities=34% Similarity=0.543 Sum_probs=76.9
Q ss_pred hhhhhhcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447 99 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177 (177)
Q Consensus 99 e~eLlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~ 177 (177)
++.+.||+++|+|||+|++||+||++++|++|+|+++|||||+.+||||+++|+|+||||||+|+|+|||++++||+|+
T Consensus 2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~DPva~~lgak~GdvVkIvRkS~TaGe~v~YR~Vv 80 (80)
T COG2012 2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKASDPVAKALGAKPGDVVKIVRKSPTAGESVYYRLVV 80 (80)
T ss_pred ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCcccccChhHHHccCCCCcEEEEEecCCCCCceEEEEEeC
Confidence 4578899999999999999999999999999999999999999999999999999999999999999999999999996
No 7
>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=99.87 E-value=7.6e-24 Score=157.51 Aligned_cols=64 Identities=45% Similarity=0.835 Sum_probs=52.7
Q ss_pred ChhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCC---CCCCCceeEeecCCCCCchh
Q 030447 35 GSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ---DPDVDRLRISISHQSDPSKR 98 (177)
Q Consensus 35 ~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~---~~~r~~L~~~~~~~~dp~~k 98 (177)
+++|++|||||||||+|||+||||.|+++|+++|+++|+++||+ .|+|++|+|++.+.+||+++
T Consensus 3 ~~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~ 69 (93)
T PF03871_consen 3 DDEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDK 69 (93)
T ss_dssp TTHHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--E
T ss_pred cHHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCe
Confidence 34899999999999999999999999999999999999999998 79999999999999999877
No 8
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=76.04 E-value=4.1 Score=30.92 Aligned_cols=56 Identities=14% Similarity=0.266 Sum_probs=35.4
Q ss_pred ceecCHHHHHHHHhhcCCCcCCCCC-cccCChhhhhhCCCCCCEEEEEecCCCCccceEEEE
Q 030447 115 HQVLTDQEKEKLLKKYSIEEKQLPR-MLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRC 175 (177)
Q Consensus 115 H~vLs~eEk~~lL~~y~i~~~QLPr-I~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~ 175 (177)
.-+++..+++.+-+++ +.....++ -..--=-..++.++|||||.|.-+ |....+|+
T Consensus 103 ~~v~~~~qA~r~a~~~-l~~~~~~r~t~~f~~~~~~~~l~pGDvi~l~~~----~~~~~~RI 159 (164)
T PF13550_consen 103 PGVTDASQAQRLAERL-LRRSRYERRTVSFTLPPDGLALEPGDVIALSDD----GRDMRFRI 159 (164)
T ss_pred eeECCHHHHHHHHHHH-HHHhhccceEEEEEEChhhccCCCCCEEEEEeC----CCceEEEE
Confidence 4467888888765443 33444444 222221234588999999999987 66777776
No 9
>KOG0975 consensus Branched chain aminotransferase BCAT1, pyridoxal phosphate enzymes type IV superfamily [Amino acid transport and metabolism]
Probab=56.19 E-value=5.2 Score=37.40 Aligned_cols=28 Identities=25% Similarity=0.657 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCC-CccChhhhccCHHHHHH
Q 030447 45 SRRTVLEMLKDRG-YAVALSEINLSVQDFRA 74 (177)
Q Consensus 45 ~rrTv~eMl~DRG-Y~V~~~el~~sl~~F~~ 74 (177)
.|++++|+.+|+| |.|.+ -++|++||.+
T Consensus 288 TR~sileLa~~~g~~~V~E--r~vtv~e~~~ 316 (379)
T KOG0975|consen 288 TRKSILELARDLGEFKVEE--RDVTVDELKT 316 (379)
T ss_pred cHHHHHHHHHHhCceEEEE--EEEeHHHhhh
Confidence 5899999999999 99987 5567788875
No 10
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=55.22 E-value=23 Score=27.95 Aligned_cols=34 Identities=12% Similarity=0.168 Sum_probs=26.2
Q ss_pred CcccCChhhhh-hCCCCCCEEEEEecCCCCccceEEEE
Q 030447 139 RMLKKDAIAQY-YGLERGQVVKVTYSGEITESHVTYRC 175 (177)
Q Consensus 139 rI~~sDPvary-~Glk~GdVVKI~R~SetaG~~v~YR~ 175 (177)
+|+..-|+++. +|.+.||+|.+.-+ .|....|++
T Consensus 88 ~ISi~SPlG~ALlG~~~Gd~v~v~~p---~G~~~~~~I 122 (137)
T PRK05753 88 QLSVLAPVGAALLGLSVGQSIDWPLP---GGKETHLEV 122 (137)
T ss_pred cCcccCHHHHHHcCCCCCCEEEEECC---CCCEEEEEE
Confidence 88899999996 59999999999865 344444544
No 11
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=53.30 E-value=23 Score=24.84 Aligned_cols=34 Identities=18% Similarity=0.351 Sum_probs=25.3
Q ss_pred CcccCChhhhhh-CCCCCCEEEEEecCCCCccceEEEEe
Q 030447 139 RMLKKDAIAQYY-GLERGQVVKVTYSGEITESHVTYRCV 176 (177)
Q Consensus 139 rI~~sDPvary~-Glk~GdVVKI~R~SetaG~~v~YR~V 176 (177)
+|+..-|+++.+ |.+.||.|.+.-+. | ...|++.
T Consensus 39 ~IS~~SPLG~ALlG~~~Gd~v~~~~~~---g-~~~~~I~ 73 (77)
T PF01272_consen 39 KISIDSPLGKALLGKKVGDEVEVELPG---G-ERKYEIL 73 (77)
T ss_dssp EEETTSHHHHHHTT-BTT-EEEEEETT---B-EEEEEEE
T ss_pred EEEecCHHHHHhcCCCCCCEEEEEeCC---c-eEEEEEE
Confidence 899999999875 99999999998764 2 4556653
No 12
>KOG1232 consensus Proteins containing the FAD binding domain [Energy production and conversion]
Probab=51.65 E-value=10 Score=36.36 Aligned_cols=64 Identities=22% Similarity=0.387 Sum_probs=48.9
Q ss_pred ccccccCCCCCCCc-----ccccccc------cCCCChhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHH
Q 030447 10 SMEMEGGNGYNGEP-----TESCLSG------FVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRA 74 (177)
Q Consensus 10 ~~~~~~~~~~~~~p-----~~~c~~~------~m~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~ 74 (177)
-+|-.|.|.=.+.- +.+|+.+ .+.++..+..++|++|..+=+-|..-|| |-.-++.+.|++|-.
T Consensus 331 LiETsGSn~dhD~eKl~afl~d~lek~lIsDGv~a~d~~~~~~lW~~Re~ip~a~~~~g~-vyKyDvSLpL~d~Y~ 405 (511)
T KOG1232|consen 331 LIETSGSNKDHDEEKLTAFLEDCLEKGLISDGVLAQDEAEAQKLWKIRESIPEALQKAGG-VYKYDVSLPLEDLYN 405 (511)
T ss_pred EEEecCCCccccHHHHHHHHHHhhhhcccccceecCCHHHHHHHHHHHhccHHHHHhcCC-EEEeeccccHHHHHH
Confidence 35666777655554 7788876 3667888999999999999999999994 455667778877754
No 13
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=46.86 E-value=20 Score=26.14 Aligned_cols=26 Identities=19% Similarity=0.512 Sum_probs=20.7
Q ss_pred CcccCChhhhhhCCCCCCEEEEEecC
Q 030447 139 RMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 139 rI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
+|-.--++-+.||+++||++.|+...
T Consensus 15 qIvIPkeiR~~lgi~~Gd~lei~~~~ 40 (89)
T COG2002 15 QIVIPKEIREALGIKEGDVLEIIVDG 40 (89)
T ss_pred eEEecHHHHHHhCCCCCCEEEEEEeC
Confidence 34444578899999999999998764
No 14
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=46.20 E-value=34 Score=27.74 Aligned_cols=36 Identities=11% Similarity=0.171 Sum_probs=28.2
Q ss_pred CCCcccCChhhhhh-CCCCCCEEEEEecCCCCccceEEEEe
Q 030447 137 LPRMLKKDAIAQYY-GLERGQVVKVTYSGEITESHVTYRCV 176 (177)
Q Consensus 137 LPrI~~sDPvary~-Glk~GdVVKI~R~SetaG~~v~YR~V 176 (177)
.-+|+..-|+++.+ |.+.||+|.+.-++. . ..|+++
T Consensus 116 ~~~IS~~SPlG~ALlGk~vGD~v~v~~p~g---~-~~~eI~ 152 (158)
T PRK05892 116 AETLTADSPLGQALAGHQAGDTVTYSTPQG---P-AQVELL 152 (158)
T ss_pred CCEEccCCHHHHHHhCCCCCCEEEEEcCCC---c-EEEEEE
Confidence 45899999999964 999999999976543 2 566654
No 15
>COG1034 NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]
Probab=44.84 E-value=18 Score=36.27 Aligned_cols=64 Identities=27% Similarity=0.279 Sum_probs=40.4
Q ss_pred cccccCCCCCCCcccccccccCCCC--hhhhHHHHHHHHHHHHHhcCCCCc---cChhhhccCHHHHHHHhCC
Q 030447 11 MEMEGGNGYNGEPTESCLSGFVDNG--SRDSLRYYLSRRTVLEMLKDRGYA---VALSEINLSVQDFRAIYGQ 78 (177)
Q Consensus 11 ~~~~~~~~~~~~p~~~c~~~~m~~~--~~e~~rl~r~rrTv~eMl~DRGY~---V~~~el~~sl~~F~~~y~~ 78 (177)
.|+||++ -|++.|++...+-+ .-.+..+|..|+.+||+|-...=. |=+.==+=-|+++...||-
T Consensus 50 VEveg~~----k~~~SC~tpv~dGM~I~T~s~~vk~~R~~vmE~LLiNHPlDCpiCD~gGeCeLQD~a~~~G~ 118 (693)
T COG1034 50 VEVEGAP----KLVASCATPVTDGMVISTNSEEVKKAREGVMEFLLINHPLDCPVCDKGGECELQDLAVKYGV 118 (693)
T ss_pred EEecCCC----ccccccccccCCCeEEecCCHHHHHHHHHHHHHHHhcCCCCCCccCCCCCchhHHHHHHhCC
Confidence 4778776 78999999765533 235678999999999998422100 0000012246777777763
No 16
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=44.43 E-value=11 Score=27.51 Aligned_cols=47 Identities=15% Similarity=0.293 Sum_probs=30.2
Q ss_pred CHHHHHHHHhhcCCCcCCCCCcccCChhhhhh-CCCCCCEEEEEecCC
Q 030447 119 TDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYY-GLERGQVVKVTYSGE 165 (177)
Q Consensus 119 s~eEk~~lL~~y~i~~~QLPrI~~sDPvary~-Glk~GdVVKI~R~Se 165 (177)
+-+=-..+++++++....|=+|...|+-++.| .++|||.+.+.-.+.
T Consensus 9 ~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d~~ 56 (85)
T PF04225_consen 9 SGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLDED 56 (85)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-TT
T ss_pred CCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEECCC
Confidence 33445678999999999999999999666554 789999999987763
No 17
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=43.74 E-value=46 Score=26.39 Aligned_cols=34 Identities=18% Similarity=0.309 Sum_probs=27.3
Q ss_pred CcccCChhhhhh-CCCCCCEEEEEecCCCCccceEEEEe
Q 030447 139 RMLKKDAIAQYY-GLERGQVVKVTYSGEITESHVTYRCV 176 (177)
Q Consensus 139 rI~~sDPvary~-Glk~GdVVKI~R~SetaG~~v~YR~V 176 (177)
+|+..-|+++.+ |.+.||.|.+.-++. . ..|+++
T Consensus 114 ~IS~~SPlG~ALlG~~~Gd~v~v~~p~g---~-~~~~I~ 148 (151)
T TIGR01462 114 KISIDSPLGKALIGKKVGDVVEVQTPKG---E-KEYEIL 148 (151)
T ss_pred eecCCCHHHHHHcCCCCCCEEEEEeCCC---c-EEEEEE
Confidence 999999999875 999999999976542 2 566654
No 18
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=42.76 E-value=19 Score=25.48 Aligned_cols=14 Identities=21% Similarity=0.456 Sum_probs=12.0
Q ss_pred hhhCCCCCCEEEEE
Q 030447 148 QYYGLERGQVVKVT 161 (177)
Q Consensus 148 ry~Glk~GdVVKI~ 161 (177)
+--|++.||.|+|-
T Consensus 50 ~~~G~~~GD~V~Ig 63 (69)
T TIGR03595 50 RKAGAKDGDTVRIG 63 (69)
T ss_pred HHcCCCCCCEEEEc
Confidence 55699999999994
No 19
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=42.74 E-value=11 Score=30.91 Aligned_cols=15 Identities=40% Similarity=0.840 Sum_probs=12.6
Q ss_pred HHHHHhcCCCCccCh
Q 030447 48 TVLEMLKDRGYAVAL 62 (177)
Q Consensus 48 Tv~eMl~DRGY~V~~ 62 (177)
.++++|+++||.|+.
T Consensus 244 gvl~lLr~~Gy~V~~ 258 (259)
T PF01963_consen 244 GVLDLLRKKGYTVEP 258 (259)
T ss_pred hHHHHHHhCCceeec
Confidence 478999999999874
No 20
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=42.55 E-value=42 Score=27.17 Aligned_cols=35 Identities=14% Similarity=0.073 Sum_probs=27.6
Q ss_pred CCcccCChhhhhh-CCCCCCEEEEEecCCCCccceEEEEe
Q 030447 138 PRMLKKDAIAQYY-GLERGQVVKVTYSGEITESHVTYRCV 176 (177)
Q Consensus 138 PrI~~sDPvary~-Glk~GdVVKI~R~SetaG~~v~YR~V 176 (177)
-+|+..-|+++.+ |.+.||.|.+.-++.+ ..|+++
T Consensus 117 ~~IS~~SPlG~ALlGk~vGd~v~v~~p~g~----~~~eI~ 152 (157)
T PRK01885 117 GYISIDSPMARALLKKEVGDEVTVNTPAGE----AEWYVN 152 (157)
T ss_pred CeEeccCHHHHHHhCCCCCCEEEEEcCCCc----EEEEEE
Confidence 4899999999875 9999999999876532 456654
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=41.31 E-value=10 Score=24.39 Aligned_cols=24 Identities=29% Similarity=0.440 Sum_probs=17.6
Q ss_pred CceecCHHHHHHHHhhcCCCcCCC
Q 030447 114 KHQVLTDQEKEKLLKKYSIEEKQL 137 (177)
Q Consensus 114 kH~vLs~eEk~~lL~~y~i~~~QL 137 (177)
.|+--|++||++|.+.-+++..|+
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 456679999999999999887764
No 22
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=40.35 E-value=18 Score=28.21 Aligned_cols=17 Identities=29% Similarity=0.344 Sum_probs=14.7
Q ss_pred hhhCCCCCCEEEEEecC
Q 030447 148 QYYGLERGQVVKVTYSG 164 (177)
Q Consensus 148 ry~Glk~GdVVKI~R~S 164 (177)
-..|.++|+.|||-|+.
T Consensus 36 p~ig~~RGskVrIlR~E 52 (101)
T PLN00045 36 PPIGPKRGSKVKILRPE 52 (101)
T ss_pred CCcccCCCCEEEEcccc
Confidence 35799999999999984
No 23
>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=40.26 E-value=31 Score=23.67 Aligned_cols=20 Identities=10% Similarity=0.356 Sum_probs=17.2
Q ss_pred HHHHHHhcCCCCccChhhhc
Q 030447 47 RTVLEMLKDRGYAVALSEIN 66 (177)
Q Consensus 47 rTv~eMl~DRGY~V~~~el~ 66 (177)
.-+++..+..||.++.+|+.
T Consensus 28 e~~~~lA~~~Gf~ft~~el~ 47 (64)
T TIGR03798 28 EDRVAIAKEAGFEFTGEDLK 47 (64)
T ss_pred HHHHHHHHHcCCCCCHHHHH
Confidence 45678899999999999994
No 24
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=40.20 E-value=19 Score=25.45 Aligned_cols=13 Identities=23% Similarity=0.537 Sum_probs=8.3
Q ss_pred hhhCCCCCCEEEE
Q 030447 148 QYYGLERGQVVKV 160 (177)
Q Consensus 148 ry~Glk~GdVVKI 160 (177)
+-.|++.||.|+|
T Consensus 50 ~~~G~~~GD~V~I 62 (69)
T PF09269_consen 50 RKAGAKEGDTVRI 62 (69)
T ss_dssp HTTT--TT-EEEE
T ss_pred HHcCCCCCCEEEE
Confidence 4559999999998
No 25
>KOG4449 consensus Translocase of outer mitochondrial membrane complex, subunit TOM7 [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.60 E-value=23 Score=24.82 Aligned_cols=38 Identities=24% Similarity=0.360 Sum_probs=27.6
Q ss_pred ecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCC
Q 030447 117 VLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQ 156 (177)
Q Consensus 117 vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~Gd 156 (177)
.||+|-|+.|-+-+++...- -=..-=|.+-|+|++.|-
T Consensus 2 klS~esKerl~k~~~is~~v--ih~G~IP~VlyLG~a~~a 39 (53)
T KOG4449|consen 2 KLSEESKERLVKVFNISKFV--IHYGWIPLVLYLGFAFGA 39 (53)
T ss_pred ccCHHHHHHHHHHeechhee--eeechhhHHHHhhhhhcC
Confidence 58999999998888875322 122334899999999873
No 26
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=39.32 E-value=37 Score=27.03 Aligned_cols=31 Identities=23% Similarity=0.363 Sum_probs=24.4
Q ss_pred ecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEec
Q 030447 117 VLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 163 (177)
Q Consensus 117 vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~ 163 (177)
.|+.+|.+.+|+... + ..++++||.|+|+.-
T Consensus 76 ~l~~~Ei~~il~~~~-------------~---~~~~~~G~~V~I~~G 106 (153)
T PRK08559 76 EISFEEVEHFLKPKP-------------I---VEGIKEGDIVELIAG 106 (153)
T ss_pred CCCHHHHHHHHhccC-------------c---ccCCCCCCEEEEecc
Confidence 599999999995422 1 267999999999874
No 27
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=39.28 E-value=54 Score=26.49 Aligned_cols=35 Identities=14% Similarity=0.110 Sum_probs=26.9
Q ss_pred CCcccCChhhhhh-CCCCCCEEEEEecCCCCccceEEEEe
Q 030447 138 PRMLKKDAIAQYY-GLERGQVVKVTYSGEITESHVTYRCV 176 (177)
Q Consensus 138 PrI~~sDPvary~-Glk~GdVVKI~R~SetaG~~v~YR~V 176 (177)
=+|+..-|+++.+ |.+.||.|.+.-++. ...|.++
T Consensus 115 ~~IS~~SPlG~ALlGk~~GD~v~v~~p~g----~~~~eI~ 150 (156)
T TIGR01461 115 NYISIDSPLARALLKKEVGDEVVVNTPAG----EASWYVN 150 (156)
T ss_pred CeECCCCHHHHHHcCCCCCCEEEEEcCCC----cEEEEEE
Confidence 3888999999975 999999999976553 2455543
No 28
>cd06573 PASTA PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.
Probab=38.01 E-value=56 Score=19.68 Aligned_cols=21 Identities=14% Similarity=0.226 Sum_probs=16.6
Q ss_pred cCCceecCHHHHHHHHhhcCCC
Q 030447 112 KPKHQVLTDQEKEKLLKKYSIE 133 (177)
Q Consensus 112 VPkH~vLs~eEk~~lL~~y~i~ 133 (177)
+|.-.-++.+|.++.|+. ++.
T Consensus 2 ~p~~~g~~~~~a~~~l~~-g~~ 22 (53)
T cd06573 2 VPDLVGISKKDLEEQLYD-LLK 22 (53)
T ss_pred CCcccCCcHHHHHHHHHc-CCc
Confidence 566677899999999997 654
No 29
>KOG3259 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=37.64 E-value=34 Score=28.73 Aligned_cols=59 Identities=20% Similarity=0.316 Sum_probs=40.3
Q ss_pred ceecCHHHHHHHHhhcCCCcCCCCC------cccCChhhh---------------------hhCCCCCCEEEEEecCCCC
Q 030447 115 HQVLTDQEKEKLLKKYSIEEKQLPR------MLKKDAIAQ---------------------YYGLERGQVVKVTYSGEIT 167 (177)
Q Consensus 115 H~vLs~eEk~~lL~~y~i~~~QLPr------I~~sDPvar---------------------y~Glk~GdVVKI~R~Seta 167 (177)
|.-.|.||+..+|+-|.-+..+=+. ++.+|+-.. .|-|++|++--|.-.+ +
T Consensus 77 ~it~skeeA~~llk~~~~~l~~g~~~f~elA~q~SdCSSaKRGGDLG~fgrgqMqk~FEdaafaL~~ge~SgiV~t~--S 154 (163)
T KOG3259|consen 77 NITRSKEEALDLLKGYHEDLKSGSGDFEELAKQRSDCSSAKRGGDLGFFGRGQMQKPFEDAAFALKVGEMSGIVDTD--S 154 (163)
T ss_pred cchhhHHHHHHHHHHhHHHhhcCcccHHHHHHhhcChhhhccCCcccccccccccccchhhhhhcccccccCceecC--C
Confidence 4778999999999988654444443 344444322 3567888888887655 7
Q ss_pred ccceEEEE
Q 030447 168 ESHVTYRC 175 (177)
Q Consensus 168 G~~v~YR~ 175 (177)
|-.|-||.
T Consensus 155 G~HiI~R~ 162 (163)
T KOG3259|consen 155 GVHIIYRT 162 (163)
T ss_pred ceEEEEec
Confidence 88888884
No 30
>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=37.58 E-value=29 Score=23.96 Aligned_cols=53 Identities=11% Similarity=0.221 Sum_probs=34.8
Q ss_pred ccccccCCCCCCCcccccccccCCCChhhhHHHHHHHHHHHHHhcCCCCccChh
Q 030447 10 SMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALS 63 (177)
Q Consensus 10 ~~~~~~~~~~~~~p~~~c~~~~m~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~ 63 (177)
++..+|...++...+..-....... ......|..+.+.+-+.++++||..+..
T Consensus 5 ~i~~~G~~~~~~~~l~~~~~~~~g~-~l~~~~l~~~~~~l~~~y~~~GY~~s~v 57 (76)
T PF08479_consen 5 GIRFEGNTLLPEEELQAILAPYIGR-CLTLADLQQLADALTNYYREKGYITSRV 57 (76)
T ss_dssp EEEEES-TSSSCCHHHHHHGGGTTS-BB-HHHHHHHHHHHHHHHHHTT-TT-EE
T ss_pred EEEEECCCcCCHHHHHHHHHHhcCC-CcCHHHHHHHHHHHHHHHHHcCceEEEE
Confidence 4566776667766655555554442 2336778899999999999999998753
No 31
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=37.29 E-value=40 Score=21.59 Aligned_cols=20 Identities=30% Similarity=0.547 Sum_probs=16.9
Q ss_pred hhhhhhCCCCCCEEEEEecC
Q 030447 145 AIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 145 Pvary~Glk~GdVVKI~R~S 164 (177)
.+++.+|+++||.|.|.-..
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEG 33 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEET
T ss_pred HHHHHcCCCCCCEEEEEEeC
Confidence 46788999999999998764
No 32
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=37.08 E-value=26 Score=24.37 Aligned_cols=27 Identities=22% Similarity=0.304 Sum_probs=23.5
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|.+..+..-|+.+|++.||.|.|...-
T Consensus 23 ~~v~~~~~da~~lgl~~Gd~v~v~~~~ 49 (101)
T cd02775 23 PVVEINPEDAAALGIKDGDLVRVESRR 49 (101)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 778888889999999999999988654
No 33
>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=36.95 E-value=16 Score=32.08 Aligned_cols=24 Identities=29% Similarity=0.616 Sum_probs=21.6
Q ss_pred cCHHHHHHHHhhcCCCcCCCCCcc
Q 030447 118 LTDQEKEKLLKKYSIEEKQLPRML 141 (177)
Q Consensus 118 Ls~eEk~~lL~~y~i~~~QLPrI~ 141 (177)
|+++|++++|+.|++++..||||-
T Consensus 244 l~~ee~~~fl~~~gi~es~l~riI 267 (274)
T cd01900 244 LDEEEAAEFLEELGLEESGLDRLI 267 (274)
T ss_pred CCHHHHHHHHHHcCCccccHHHHH
Confidence 578999999999999999998874
No 34
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=35.82 E-value=55 Score=25.06 Aligned_cols=28 Identities=29% Similarity=0.440 Sum_probs=20.0
Q ss_pred hhCCCCCCEEEEEecCC--------CCccceEEEEe
Q 030447 149 YYGLERGQVVKVTYSGE--------ITESHVTYRCV 176 (177)
Q Consensus 149 y~Glk~GdVVKI~R~Se--------taG~~v~YR~V 176 (177)
.+|+-.||+|++..... .+|...|+|++
T Consensus 23 a~glA~gDvV~~~~~~g~~~~~~~v~~sGnsTiRv~ 58 (117)
T PF14085_consen 23 AYGLALGDVVRAEPDDGELWFQKVVESSGNSTIRVI 58 (117)
T ss_pred cCCCCCCCEEEEEeCCCeEEEEEEEecCCCEEEEEE
Confidence 46999999999999862 22445566665
No 35
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=35.57 E-value=33 Score=24.56 Aligned_cols=27 Identities=22% Similarity=0.263 Sum_probs=19.9
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|.|..+-=-|+.+|++-||.|+|.-+.
T Consensus 30 ~~v~inp~dA~~~Gi~~Gd~V~v~s~~ 56 (110)
T PF01568_consen 30 PFVEINPEDAAKLGIKDGDWVRVSSPR 56 (110)
T ss_dssp EEEEEEHHHHHHCT--TTCEEEEEETT
T ss_pred CEEEEcHHHHHHhcCcCCCEEEEEecc
Confidence 566666667889999999999998754
No 36
>COG0782 Uncharacterized conserved protein, YhbC family [Function unknown]
Probab=35.33 E-value=65 Score=25.96 Aligned_cols=27 Identities=15% Similarity=0.246 Sum_probs=23.1
Q ss_pred CCCcccCChhhhhh-CCCCCCEEEEEec
Q 030447 137 LPRMLKKDAIAQYY-GLERGQVVKVTYS 163 (177)
Q Consensus 137 LPrI~~sDPvary~-Glk~GdVVKI~R~ 163 (177)
-=+|+..-|+++.| |.+.||+|.+.=+
T Consensus 110 ~~~IS~~SPig~aLlGk~vGd~v~v~~p 137 (151)
T COG0782 110 KGKISVDSPLGRALLGKKVGDTVEVNTP 137 (151)
T ss_pred cCceeccCHHHHHHhCCCCCCEEEEecC
Confidence 45899999999975 9999999999754
No 37
>PRK06437 hypothetical protein; Provisional
Probab=35.20 E-value=32 Score=23.89 Aligned_cols=41 Identities=7% Similarity=0.195 Sum_probs=32.4
Q ss_pred HHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEec
Q 030447 123 KEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 163 (177)
Q Consensus 123 k~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~ 163 (177)
.++||+++++....+--+....++..-.-++.||-|.|.+.
T Consensus 23 v~dLL~~Lgi~~~~vaV~vNg~iv~~~~~L~dgD~Veiv~~ 63 (67)
T PRK06437 23 VNDIIKDLGLDEEEYVVIVNGSPVLEDHNVKKEDDVLILEV 63 (67)
T ss_pred HHHHHHHcCCCCccEEEEECCEECCCceEcCCCCEEEEEec
Confidence 67889999998777655556666667778899999999874
No 38
>PF04023 FeoA: FeoA domain; InterPro: IPR007167 This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria. This domain also occurs at the C terminus in related proteins. The transporter Feo is composed of three proteins: FeoA a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor [, ]. Feo allows the bacterial cell to acquire iron from its environment. ; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 1G3T_A 1C0W_B 1BI3_A 1QVP_A 1BI1_A 1BYM_A 2QQB_A ....
Probab=35.16 E-value=30 Score=23.37 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=15.8
Q ss_pred hhCCCCCCEEEEEecCCCCcc
Q 030447 149 YYGLERGQVVKVTYSGEITES 169 (177)
Q Consensus 149 y~Glk~GdVVKI~R~SetaG~ 169 (177)
.+|+.+|.-|+|.+.++..|.
T Consensus 30 ~lGl~~G~~i~v~~~~~~~~~ 50 (74)
T PF04023_consen 30 DLGLTPGSEITVIRKNPFGGP 50 (74)
T ss_dssp HCT-STTEEEEEEEEETTSSE
T ss_pred HCCCCCCCEEEEEEeCCCCCC
Confidence 469999999999987665443
No 39
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=35.09 E-value=54 Score=27.24 Aligned_cols=60 Identities=23% Similarity=0.189 Sum_probs=38.6
Q ss_pred hhhhhhcCCccc--ccCCc----eecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCc
Q 030447 99 ITDLLVNITKHV--LKPKH----QVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITE 168 (177)
Q Consensus 99 e~eLlvNIt~H~--LVPkH----~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG 168 (177)
+.-.++.-|.|+ +|.-+ ..++++|...+|....-. .+|..--..+++||.|+|+. ++-||
T Consensus 74 ~~w~~Vr~tpgV~GfVg~~~~~P~pi~~~ei~~~l~~~~~~---------~~~~~~~~~~e~Gd~VrI~~-GpFa~ 139 (178)
T COG0250 74 EAWHLVRNTPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEE---------VAPKKPKVDFEPGDVVRIID-GPFAG 139 (178)
T ss_pred ceEEEEecCCCcEEEeccCCCCCcccCHHHHHHHHhhcccc---------ccCCcccccCCCCCEEEEec-cCCCC
Confidence 444455555553 45433 789999999977766533 33334456789999999985 33444
No 40
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=33.87 E-value=31 Score=23.32 Aligned_cols=19 Identities=21% Similarity=0.485 Sum_probs=13.7
Q ss_pred cccCChhhhhhCCCCCCEEE
Q 030447 140 MLKKDAIAQYYGLERGQVVK 159 (177)
Q Consensus 140 I~~sDPvary~Glk~GdVVK 159 (177)
|....|.++. |+++||+|-
T Consensus 20 v~~~s~a~~~-gl~~GD~I~ 38 (85)
T cd00988 20 VLPGSPAAKA-GIKAGDIIV 38 (85)
T ss_pred ecCCCCHHHc-CCCCCCEEE
Confidence 4445676665 999999984
No 41
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=33.85 E-value=74 Score=25.26 Aligned_cols=34 Identities=26% Similarity=0.421 Sum_probs=26.7
Q ss_pred CcccCChhhhhh-CCCCCCEEEEEecCCCCccceEEEEe
Q 030447 139 RMLKKDAIAQYY-GLERGQVVKVTYSGEITESHVTYRCV 176 (177)
Q Consensus 139 rI~~sDPvary~-Glk~GdVVKI~R~SetaG~~v~YR~V 176 (177)
+|+..-|+++.+ |.+.||.|.+..++. ...|+++
T Consensus 119 ~IS~~SPlG~aLlGk~~Gd~v~~~~p~g----~~~~~I~ 153 (157)
T PRK00226 119 KISIESPIARALIGKKVGDTVEVTTPGG----EYEYEIL 153 (157)
T ss_pred eeccCChHHHHHhCCCCCCEEEEEcCCC----cEEEEEE
Confidence 799999999875 999999999987643 3455543
No 42
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=33.58 E-value=37 Score=24.65 Aligned_cols=27 Identities=30% Similarity=0.350 Sum_probs=20.9
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|-+..+-=-|..+|++.||.|+|..+.
T Consensus 31 ~~v~i~p~dA~~lgi~~Gd~V~v~s~~ 57 (116)
T cd02786 31 PTLLIHPADAAARGIADGDLVVVFNDR 57 (116)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 555555556888999999999998654
No 43
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=33.02 E-value=45 Score=23.85 Aligned_cols=24 Identities=13% Similarity=0.167 Sum_probs=18.6
Q ss_pred cccCChhhhhhCCCCCCEEEE-Eec
Q 030447 140 MLKKDAIAQYYGLERGQVVKV-TYS 163 (177)
Q Consensus 140 I~~sDPvary~Glk~GdVVKI-~R~ 163 (177)
|..+=..+|-|||++||+|.= +|+
T Consensus 29 vyVs~~~Irr~~LR~GD~V~G~vr~ 53 (68)
T cd04459 29 IYVSPSQIRRFNLRTGDTVVGQIRP 53 (68)
T ss_pred EEECHHHHHHhCCCCCCEEEEEEeC
Confidence 455556889999999999986 444
No 44
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=32.36 E-value=70 Score=26.15 Aligned_cols=36 Identities=19% Similarity=0.307 Sum_probs=27.1
Q ss_pred ceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhh-CCCCCCEEEE
Q 030447 115 HQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYY-GLERGQVVKV 160 (177)
Q Consensus 115 H~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~-Glk~GdVVKI 160 (177)
..++.+.|..- .--+|+..-|+++.+ |.+.||+|.|
T Consensus 113 ~~IVg~~Ead~----------~~g~IS~~SPlG~ALlGk~vGD~V~v 149 (160)
T PRK06342 113 YRIVGEDEADP----------KAGSISYVSPVARALMGKAVGDVVSV 149 (160)
T ss_pred EEEEChHHhCc----------CCCcccccCHHHHHHcCCCCCCEEEE
Confidence 45566666532 124788899999875 9999999998
No 45
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=32.03 E-value=45 Score=24.05 Aligned_cols=27 Identities=26% Similarity=0.316 Sum_probs=20.1
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|.+..+-=-|.-+|++.||.|+|..+-
T Consensus 29 ~~v~inp~dA~~lGi~~Gd~V~v~s~~ 55 (96)
T cd02788 29 PYARLSPADAARLGLADGDLVEFSLGD 55 (96)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEECC
Confidence 445444446889999999999997653
No 46
>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=31.90 E-value=54 Score=26.37 Aligned_cols=41 Identities=24% Similarity=0.463 Sum_probs=28.1
Q ss_pred CCCCCCCc-ccccccccCCCChhhhHHHHHHHHHHHHHhcCCCCccCh
Q 030447 16 GNGYNGEP-TESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVAL 62 (177)
Q Consensus 16 ~~~~~~~p-~~~c~~~~m~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~ 62 (177)
||||..-| ++.+.-.. ....||.--.-|++-|..|||.++.
T Consensus 29 g~Gw~~~h~Tv~yVf~~------s~~~L~~yH~lv~~EM~~RGY~~~~ 70 (120)
T TIGR02328 29 GNGWGKKHSTVDYVFCY------SPYKLFAYHLLVMEEMATRGYHVSK 70 (120)
T ss_pred ccccCCCcceehhhhhc------CHHHHHHHHHHHHHHHHHcCCCCCh
Confidence 56666666 44443221 2367787777788888899999998
No 47
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=31.49 E-value=66 Score=24.01 Aligned_cols=36 Identities=11% Similarity=0.039 Sum_probs=24.5
Q ss_pred CCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEe
Q 030447 137 LPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCV 176 (177)
Q Consensus 137 LPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V 176 (177)
--++.+-||-. .++.||+|.|. .+........|+++
T Consensus 39 ~kk~~aHDe~n---~~~~GD~V~I~-e~RPlSKtK~~~v~ 74 (84)
T CHL00142 39 TKKYLVHDEEN---ECNIGDQVLIE-ETRPLSKTKRWILK 74 (84)
T ss_pred eEEEEEeCCCC---CCCCCCEEEEE-EcCCCCCcEEEEEE
Confidence 34667778766 58999999996 33344456666654
No 48
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.44 E-value=54 Score=23.92 Aligned_cols=25 Identities=16% Similarity=0.158 Sum_probs=18.9
Q ss_pred cccCChhhhhhCCCCCCEEEEEecC
Q 030447 140 MLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 140 I~~sDPvary~Glk~GdVVKI~R~S 164 (177)
+.-+---|+.+|++-||.|+|.-+.
T Consensus 33 v~i~p~dA~~lgI~dGd~V~v~s~~ 57 (112)
T cd02787 33 VFMNPDDIARLGLKAGDRVDLESAF 57 (112)
T ss_pred EEECHHHHHHhCCCCCCEEEEEecC
Confidence 4444444888999999999997664
No 49
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=31.33 E-value=25 Score=22.84 Aligned_cols=12 Identities=25% Similarity=0.656 Sum_probs=9.7
Q ss_pred hCCCCCCEEEEE
Q 030447 150 YGLERGQVVKVT 161 (177)
Q Consensus 150 ~Glk~GdVVKI~ 161 (177)
|.+++||+|.|+
T Consensus 16 Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 16 LSFKKGDVIEVL 27 (55)
T ss_dssp -EB-TTEEEEEE
T ss_pred eEEecCCEEEEE
Confidence 889999999999
No 50
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=30.50 E-value=45 Score=23.98 Aligned_cols=28 Identities=21% Similarity=0.207 Sum_probs=21.6
Q ss_pred CCCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 137 LPRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 137 LPrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
.|.+..+---|+.+|++.||.|+|....
T Consensus 34 ~~~v~in~~dA~~lgi~~Gd~V~v~~~~ 61 (116)
T cd02790 34 EEYVEINPEDAKRLGIEDGEKVRVSSRR 61 (116)
T ss_pred CcEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 3555555566889999999999998754
No 51
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=30.26 E-value=40 Score=22.37 Aligned_cols=17 Identities=24% Similarity=0.268 Sum_probs=12.6
Q ss_pred hhhhhhCCCCCCEEEEE
Q 030447 145 AIAQYYGLERGQVVKVT 161 (177)
Q Consensus 145 Pvary~Glk~GdVVKI~ 161 (177)
..|...|+++||+|.=+
T Consensus 23 s~a~~~gl~~GD~I~~i 39 (79)
T cd00989 23 SPAAKAGLKAGDRILAI 39 (79)
T ss_pred CHHHHcCCCCCCEEEEE
Confidence 34667899999988543
No 52
>COG4624 Iron only hydrogenase large subunit, C-terminal domain [General function prediction only]
Probab=29.43 E-value=43 Score=31.84 Aligned_cols=37 Identities=30% Similarity=0.289 Sum_probs=33.4
Q ss_pred ceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhC
Q 030447 115 HQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYG 151 (177)
Q Consensus 115 H~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~G 151 (177)
-.+||.+|-.++|+..+|+..+||...-.+|.-.+-|
T Consensus 220 D~vLTtrEL~~ml~~l~id~~~lp~~~~~s~~g~~sg 256 (411)
T COG4624 220 DFVLTTRELVKMLKELRIDFARLPDGHYDSPAGFSSG 256 (411)
T ss_pred eEEecHHHHHHHHHHhCCCHhHCCCCCcccccccccc
Confidence 4689999999999999999999999998888877766
No 53
>PF07957 DUF3294: Protein of unknown function (DUF3294); InterPro: IPR012917 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of mitochondrial ribosomal proteins, which appears to be fungal specific [].
Probab=29.14 E-value=16 Score=31.94 Aligned_cols=34 Identities=44% Similarity=0.657 Sum_probs=27.2
Q ss_pred eecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCC
Q 030447 116 QVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLE 153 (177)
Q Consensus 116 ~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk 153 (177)
...++++..+.++.|. .+||=-| .|=+|||||++
T Consensus 175 ~~~~d~~i~~~~k~~s--~~eld~i--fdelARylGlr 208 (216)
T PF07957_consen 175 NEESDEEIEKELKKYS--KEELDEI--FDELARYLGLR 208 (216)
T ss_pred CCCChHHHHHHHHhcC--HHHHHHH--HHHHHHHhCch
Confidence 5567888888888776 6677777 78899999984
No 54
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=28.78 E-value=42 Score=24.44 Aligned_cols=28 Identities=18% Similarity=0.127 Sum_probs=22.1
Q ss_pred CCCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 137 LPRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 137 LPrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
-|.+..+---|+-+|++.||.|+|..+.
T Consensus 34 ~~~v~i~p~dA~~lgi~~Gd~V~v~s~~ 61 (122)
T cd02792 34 EMFVEISPELAAERGIKNGDMVWVSSPR 61 (122)
T ss_pred CcEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 3556666667999999999999998654
No 55
>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=28.65 E-value=31 Score=22.27 Aligned_cols=20 Identities=20% Similarity=0.524 Sum_probs=16.1
Q ss_pred HHHHHHhcCCCCccChhhhc
Q 030447 47 RTVLEMLKDRGYAVALSEIN 66 (177)
Q Consensus 47 rTv~eMl~DRGY~V~~~el~ 66 (177)
.-+..+.++.||.++.+||.
T Consensus 30 ~e~~~lA~~~Gy~ft~~el~ 49 (49)
T PF07862_consen 30 EEVVALAREAGYDFTEEELE 49 (49)
T ss_pred HHHHHHHHHcCCCCCHHHhC
Confidence 34667889999999998873
No 56
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=28.42 E-value=44 Score=23.67 Aligned_cols=19 Identities=16% Similarity=0.342 Sum_probs=16.3
Q ss_pred hhhhhhCCCCCCEEEEEec
Q 030447 145 AIAQYYGLERGQVVKVTYS 163 (177)
Q Consensus 145 Pvary~Glk~GdVVKI~R~ 163 (177)
|+...+.|++||||.+.++
T Consensus 22 tl~ell~L~~Gdvi~L~~~ 40 (77)
T TIGR02480 22 TLGDLLKLGEGSVIELDKL 40 (77)
T ss_pred EHHHHhcCCCCCEEEcCCC
Confidence 6778899999999999764
No 57
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=28.24 E-value=48 Score=23.85 Aligned_cols=27 Identities=22% Similarity=0.311 Sum_probs=21.0
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|.+..+---|+-+|++.||.|+|....
T Consensus 35 ~~v~inp~dA~~lgi~~Gd~V~v~~~~ 61 (120)
T cd00508 35 PFVEIHPEDAARLGIKDGDLVRVSSRR 61 (120)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEeCC
Confidence 555555556889999999999998654
No 58
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=27.81 E-value=40 Score=24.53 Aligned_cols=28 Identities=29% Similarity=0.318 Sum_probs=23.2
Q ss_pred CCCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 137 LPRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 137 LPrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
.|.+..+.--|+-+|++.||.|+|....
T Consensus 34 ~~~v~in~~dA~~lgi~~Gd~V~v~~~~ 61 (122)
T cd02791 34 EPYVEIHPEDAARLGLKEGDLVRVTSRR 61 (122)
T ss_pred CCEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 4667777777999999999999998765
No 59
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=27.80 E-value=78 Score=26.07 Aligned_cols=28 Identities=18% Similarity=0.321 Sum_probs=20.6
Q ss_pred hhhhhCCCCCCEEEEEecCCCCccceEEEEe
Q 030447 146 IAQYYGLERGQVVKVTYSGEITESHVTYRCV 176 (177)
Q Consensus 146 vary~Glk~GdVVKI~R~SetaG~~v~YR~V 176 (177)
....-.+++||.|.|++.. |.+..||+.
T Consensus 103 F~~L~~L~~GD~I~v~~~~---g~~~~Y~V~ 130 (174)
T TIGR03784 103 FAFLQELRPGDVIRLQTPD---GQWQSYQVT 130 (174)
T ss_pred CCChhhCCCCCEEEEEECC---CeEEEEEEe
Confidence 4444578999999999864 566778763
No 60
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=27.80 E-value=75 Score=22.32 Aligned_cols=23 Identities=26% Similarity=0.293 Sum_probs=16.5
Q ss_pred CCCCCEEEEE--ecCCCCccceEEEE
Q 030447 152 LERGQVVKVT--YSGEITESHVTYRC 175 (177)
Q Consensus 152 lk~GdVVKI~--R~SetaG~~v~YR~ 175 (177)
..+||.|.+. -.+.+-| .|.||+
T Consensus 47 i~vGD~V~ve~~~~~~~~g-~Iv~r~ 71 (72)
T PRK00276 47 ILPGDKVTVELSPYDLTKG-RITYRH 71 (72)
T ss_pred cCCCCEEEEEEcccCCCeE-EEEEEe
Confidence 4789999998 4444444 788885
No 61
>PRK06033 hypothetical protein; Validated
Probab=27.74 E-value=46 Score=24.42 Aligned_cols=19 Identities=26% Similarity=0.426 Sum_probs=16.3
Q ss_pred hhhhhhCCCCCCEEEEEec
Q 030447 145 AIAQYYGLERGQVVKVTYS 163 (177)
Q Consensus 145 Pvary~Glk~GdVVKI~R~ 163 (177)
|+...++|++||||.+.++
T Consensus 21 ~l~dlL~L~~GDVI~L~~~ 39 (83)
T PRK06033 21 PIHQVLRMGRGAVIPLDAT 39 (83)
T ss_pred cHHHHhCCCCCCEEEeCCC
Confidence 5778899999999999764
No 62
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=27.54 E-value=49 Score=24.48 Aligned_cols=29 Identities=21% Similarity=0.118 Sum_probs=23.5
Q ss_pred CCCCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 136 QLPRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 136 QLPrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
+.|.+..+---|+-+|++.||.|+|...-
T Consensus 31 ~~~~v~inp~dA~~~gi~~Gd~V~v~s~~ 59 (130)
T cd02781 31 PDPVAEINPETAAKLGIADGDWVWVETPR 59 (130)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEECCC
Confidence 34667777778999999999999998654
No 63
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=27.29 E-value=39 Score=24.93 Aligned_cols=32 Identities=19% Similarity=0.337 Sum_probs=22.5
Q ss_pred cCCCcCCCCCcccCChhhhhhCCCCCCEEEEE
Q 030447 130 YSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 161 (177)
Q Consensus 130 y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~ 161 (177)
|+++..+==.++.--.-.+.+||+|||-.+|.
T Consensus 31 yr~~Vq~NGnLLIG~AYT~~m~L~PGdEFeI~ 62 (71)
T PF14250_consen 31 YRVSVQGNGNLLIGSAYTKQMGLKPGDEFEIK 62 (71)
T ss_pred EEEEEecCCCEEEcHHHHHHhCCCCCCEEEEE
Confidence 34444444455666667788999999999985
No 64
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=27.24 E-value=55 Score=24.21 Aligned_cols=25 Identities=20% Similarity=0.116 Sum_probs=18.7
Q ss_pred cccCChhhhhhCCCCCCEEEEEecC
Q 030447 140 MLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 140 I~~sDPvary~Glk~GdVVKI~R~S 164 (177)
+..+---|+.+|++-||.|+|..+.
T Consensus 32 v~i~p~~A~~~gi~~Gd~V~v~s~~ 56 (121)
T cd02794 32 VWINPLDAAARGIKDGDRVLVFNDR 56 (121)
T ss_pred EEECHHHHHHcCCCCCCEEEEEcCC
Confidence 3334444888999999999998654
No 65
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=27.20 E-value=37 Score=23.42 Aligned_cols=19 Identities=16% Similarity=0.399 Sum_probs=14.1
Q ss_pred hhhhhhCCCCCCEEEEEec
Q 030447 145 AIAQYYGLERGQVVKVTYS 163 (177)
Q Consensus 145 Pvary~Glk~GdVVKI~R~ 163 (177)
|+...+.|++||||.+..+
T Consensus 22 ~l~el~~L~~Gdvi~l~~~ 40 (77)
T PF01052_consen 22 TLGELLNLKVGDVIPLDKP 40 (77)
T ss_dssp EHHHHHC--TT-EEEECCE
T ss_pred EHHHHhcCCCCCEEEeCCC
Confidence 6788899999999999887
No 66
>PF08045 CDC14: Cell division control protein 14, SIN component; InterPro: IPR012535 Cdc14 is a component of the septation initiation network (SIN) and is required for the localisation and activity of Sid1. Sid1 is a protein kinase that localises asymmetrically to one spindle pole body (SPB) in anaphase disappears prior to cell separation [], [].
Probab=27.15 E-value=1.5e+02 Score=26.25 Aligned_cols=71 Identities=24% Similarity=0.313 Sum_probs=48.0
Q ss_pred hhhHHHHHHH---HHHHHHhcCCCCccChhhhccCHHHHHHHhCC--CCCCCceeEeecCCCCCchhhhhhhhcCCcccc
Q 030447 37 RDSLRYYLSR---RTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ--DPDVDRLRISISHQSDPSKRITDLLVNITKHVL 111 (177)
Q Consensus 37 ~e~~rl~r~r---rTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~--~~~r~~L~~~~~~~~dp~~ke~eLlvNIt~H~L 111 (177)
.+-.|.|... .||..+++++. ++.++.+..-||.--|-. .|... ..... .-
T Consensus 166 p~N~r~FE~~~Gl~~v~~llk~~~---~~~~~r~K~~EFL~fyl~~E~~~~~-----~~~~~----------------~~ 221 (257)
T PF08045_consen 166 PENQRDFEELNGLSTVCSLLKSKS---TDRELRLKCIEFLYFYLMPETPSIP-----PGSSS----------------SG 221 (257)
T ss_pred hHHHHHHHHhCCHHHHHHHHcccc---ccHHHhHHHHHHHHHHHcccCCCCC-----ccccc----------------cc
Confidence 4456677665 58888999998 689999999999998832 22222 00000 11
Q ss_pred cCCceecCHHHHHHHHhhcC
Q 030447 112 KPKHQVLTDQEKEKLLKKYS 131 (177)
Q Consensus 112 VPkH~vLs~eEk~~lL~~y~ 131 (177)
-++...+|.+||+++|.+|-
T Consensus 222 ~~~~~~~t~~eKq~ll~~~~ 241 (257)
T PF08045_consen 222 SEGRATKTTEEKQELLGRYL 241 (257)
T ss_pred CCCcCcccHHHHHHHHHHhc
Confidence 12233889999999999984
No 67
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=26.91 E-value=47 Score=24.55 Aligned_cols=26 Identities=23% Similarity=0.051 Sum_probs=19.7
Q ss_pred CcccCChhhhhhCCCCCCEEEEEecC
Q 030447 139 RMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 139 rI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
-+..+.--|+-+|++.||.|+|...-
T Consensus 32 ~v~i~p~dA~~lgi~~Gd~V~v~~~~ 57 (106)
T cd02789 32 YCEINPEDYKLLGKPEGDKVKVTSEF 57 (106)
T ss_pred EEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 35555556899999999999997543
No 68
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=26.72 E-value=54 Score=27.39 Aligned_cols=31 Identities=26% Similarity=0.420 Sum_probs=21.3
Q ss_pred ChhhhhhCCCCCCEEEEEecCCCCccceEEE
Q 030447 144 DAIAQYYGLERGQVVKVTYSGEITESHVTYR 174 (177)
Q Consensus 144 DPvary~Glk~GdVVKI~R~SetaG~~v~YR 174 (177)
.-+.+.+|++.||.|.|.-.+-.-|.+|..|
T Consensus 78 ~wmm~~L~l~~g~~V~v~~~~LPkgt~vkLq 108 (176)
T PF03152_consen 78 PWMMQNLGLQEGDIVRVEYVSLPKGTFVKLQ 108 (176)
T ss_dssp CHHHHHHT--TTEEEEEEEEE----SEEEEE
T ss_pred ccHHhhcCCCCCCEEEEEEeECCCCCEEEEe
Confidence 3489999999999999998888888888765
No 69
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=25.92 E-value=60 Score=17.85 Aligned_cols=17 Identities=24% Similarity=0.335 Sum_probs=12.7
Q ss_pred CCCCCEEEEEecCCCCcc
Q 030447 152 LERGQVVKVTYSGEITES 169 (177)
Q Consensus 152 lk~GdVVKI~R~SetaG~ 169 (177)
+++||.|+|+.-+ -+|.
T Consensus 2 ~~~G~~V~I~~G~-~~g~ 18 (28)
T smart00739 2 FEVGDTVRVIAGP-FKGK 18 (28)
T ss_pred CCCCCEEEEeECC-CCCc
Confidence 5799999999844 4444
No 70
>cd03735 SOCS_SOCS1 SOCS (suppressors of cytokine signaling) box of SOCS1-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS1, like CIS1 and SOCS3, is involved in the down-regulation of the JAK/STAT pathway. SOCS1 has a dual function as a direct potent JAK kinase inhibitor and as a component of an E3 ubiquitin-ligase complex recruiting substrates to the protein degradation machinery.
Probab=25.83 E-value=63 Score=21.40 Aligned_cols=33 Identities=15% Similarity=0.271 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhC
Q 030447 43 YLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYG 77 (177)
Q Consensus 43 ~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~ 77 (177)
.+||+||..-+. |..+..-.|..++-+|...|.
T Consensus 8 hLCR~tI~~~~~--~~~i~~lpLP~~LKdyL~~y~ 40 (43)
T cd03735 8 ELCRKSIVATFG--RENLARIPLNPVLKDYLKSFP 40 (43)
T ss_pred HHHHHHHHHhcC--ccccccCcCCHHHHHHHHhCC
Confidence 578999998863 445555567788999999883
No 71
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=25.77 E-value=53 Score=24.51 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=21.1
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|-+..+.--|+.+|++.||.|+|..+.
T Consensus 34 ~~v~i~p~dA~~lgi~~Gd~V~v~s~~ 60 (127)
T cd02777 34 EPVWINPLDAAARGIKDGDIVRVFNDR 60 (127)
T ss_pred CeEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 336666667889999999999998654
No 72
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=25.53 E-value=70 Score=20.82 Aligned_cols=35 Identities=14% Similarity=0.187 Sum_probs=29.7
Q ss_pred cCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 118 LTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 118 Ls~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
.|+|+|++|++. .+|-+++.+|..+.+|.-++..-
T Consensus 12 rs~eqk~~l~~~------------it~~l~~~~~~p~~~v~V~i~e~ 46 (61)
T PRK02220 12 RTEEQLKALVKD------------VTAAVSKNTGAPAEHIHVIINEM 46 (61)
T ss_pred CCHHHHHHHHHH------------HHHHHHHHhCcChhhEEEEEEEe
Confidence 599999999985 46889999999999998887654
No 73
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=25.09 E-value=73 Score=23.25 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=21.1
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|.+..+---|..+|++.||.|+|....
T Consensus 30 ~~v~i~p~dA~~~gi~~Gd~V~v~s~~ 56 (123)
T cd02778 30 NTLWINPETAARLGIKDGDRVEVSSAR 56 (123)
T ss_pred CeEEECHHHHHHcCCCCCCEEEEEeCC
Confidence 555555556889999999999997654
No 74
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=25.05 E-value=54 Score=22.56 Aligned_cols=17 Identities=24% Similarity=0.216 Sum_probs=12.7
Q ss_pred ChhhhhhCCCCCCEEEE
Q 030447 144 DAIAQYYGLERGQVVKV 160 (177)
Q Consensus 144 DPvary~Glk~GdVVKI 160 (177)
+..|...|+++||+|-=
T Consensus 20 ~spa~~aGL~~GDiI~~ 36 (79)
T cd00991 20 GSPAENAVLHTGDVIYS 36 (79)
T ss_pred CChHHhcCCCCCCEEEE
Confidence 44566789999998753
No 75
>KOG2776 consensus Metallopeptidase [General function prediction only]
Probab=24.94 E-value=48 Score=31.34 Aligned_cols=14 Identities=43% Similarity=0.717 Sum_probs=12.0
Q ss_pred hhCCCCCCEEEEEe
Q 030447 149 YYGLERGQVVKVTY 162 (177)
Q Consensus 149 y~Glk~GdVVKI~R 162 (177)
-|-||.||||||.=
T Consensus 100 ~~~Lk~GDvVKIdL 113 (398)
T KOG2776|consen 100 DYTLKEGDVVKIDL 113 (398)
T ss_pred cccccCCCEEEEEe
Confidence 67899999999963
No 76
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=24.06 E-value=30 Score=20.96 Aligned_cols=37 Identities=19% Similarity=0.221 Sum_probs=21.2
Q ss_pred HHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEE
Q 030447 121 QEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160 (177)
Q Consensus 121 eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI 160 (177)
+=-..+-++|++..++|=+.- |-..--.+.+||.+.|
T Consensus 7 Dtl~~IA~~~~~~~~~l~~~N---~~~~~~~l~~G~~l~i 43 (44)
T PF01476_consen 7 DTLWSIAKRYGISVDELMELN---PNIDSDNLQPGQKLCI 43 (44)
T ss_dssp --HHHHHHHTTS-HHHHHHHC---CTTHGGCGGTTEEEEE
T ss_pred CcHHHHHhhhhhhHhHHHHhc---CCCCcccCCCCCEEEe
Confidence 334556677777766654444 3333333889999887
No 77
>PRK13622 psbV cytochrome c-550; Provisional
Probab=23.54 E-value=1e+02 Score=26.16 Aligned_cols=82 Identities=15% Similarity=0.233 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceeEeecCCCCCc-----hhhhhhhhcCCcccccCCc
Q 030447 41 RYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPS-----KRITDLLVNITKHVLKPKH 115 (177)
Q Consensus 41 rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~-----~ke~eLlvNIt~H~LVPkH 115 (177)
++| ..-+-.||-+|+.+......+++.+. ++..|.++.+.=++....+|. ....|+.-|+-.....|+.
T Consensus 67 ~lF---~~~Ca~CH~~G~ni~~P~~tLk~~aL---~~a~p~rdnv~AIv~yLk~p~tYdg~~~~~e~~p~~~~~~~~p~~ 140 (180)
T PRK13622 67 KLF---NRACAQCHVGGQTYPNPDVSLKLSDL---EGATPPRDNVLAIVDYIKNPVTYDGVESLLEYHPNTQLLSEYPRL 140 (180)
T ss_pred HHH---HhhhHHhccCCCCCcCCCcccCHHHH---cCCCCCcccHHHHHHHHhcccccCCccchhhccccchhccccccc
Confidence 455 44477899999999998888877644 344455544322221111222 1245666677777779999
Q ss_pred eecCHHHHHHHHh
Q 030447 116 QVLTDQEKEKLLK 128 (177)
Q Consensus 116 ~vLs~eEk~~lL~ 128 (177)
..||++|.+.+..
T Consensus 141 ~~LsdeEI~~VA~ 153 (180)
T PRK13622 141 RNLTDEDLKLIAG 153 (180)
T ss_pred cCCCHHHHHHHHH
Confidence 9999999998744
No 78
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=23.49 E-value=1.5e+02 Score=23.38 Aligned_cols=44 Identities=23% Similarity=0.391 Sum_probs=27.5
Q ss_pred eecCH-HHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCcc
Q 030447 116 QVLTD-QEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITES 169 (177)
Q Consensus 116 ~vLs~-eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~ 169 (177)
..+++ +|.+.|+....- ....|. .+ .++++||.|+|+. .+-+|-
T Consensus 92 ~~I~~~~ei~~l~~~~~~-~~~~~~------~~--~~~~~G~~V~I~~-Gpf~G~ 136 (172)
T TIGR00922 92 KALSEDEEVKNILNALEE-GKDKPK------PK--IDFEVGEQVRVND-GPFANF 136 (172)
T ss_pred eccCCHHHHHHHHHHhhc-ccccCc------cc--cCCCCCCEEEEee-cCCCCc
Confidence 35888 999998865431 112221 11 5689999999984 445553
No 79
>TIGR01312 XylB D-xylulose kinase. D-xylulose kinase (XylB) generally is found with xylose isomerase (XylA) and acts in xylose utilization.
Probab=23.44 E-value=79 Score=28.48 Aligned_cols=21 Identities=29% Similarity=0.621 Sum_probs=15.5
Q ss_pred HHHHhhcCCCcCCCCCcccCC
Q 030447 124 EKLLKKYSIEEKQLPRMLKKD 144 (177)
Q Consensus 124 ~~lL~~y~i~~~QLPrI~~sD 144 (177)
.++|+.+++..++||.|....
T Consensus 188 ~~~l~~~gi~~~~Lp~iv~~~ 208 (481)
T TIGR01312 188 KELLDALDLPESQLPELIESS 208 (481)
T ss_pred HHHHHHhCCCHHHCCCccCCC
Confidence 356778888888888887654
No 80
>PRK11649 putative peptidase; Provisional
Probab=23.40 E-value=71 Score=30.00 Aligned_cols=58 Identities=19% Similarity=0.289 Sum_probs=39.7
Q ss_pred CceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEE
Q 030447 114 KHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTY 173 (177)
Q Consensus 114 kH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~Y 173 (177)
+|.+=+-+=-..+|++++|....+=.|...|.- .-.+++||.++|.....-.-..+.|
T Consensus 97 ~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~--L~~Lr~Gq~l~~~~d~dG~L~~l~~ 154 (439)
T PRK11649 97 EYVVSTGDTLSSILNQYGIDMSDISQLAAQDKE--LRNLKIGQQLSWTLTADGDLQRLTW 154 (439)
T ss_pred EEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChH--hhcCCCCCEEEEEECCCCCeEEEEE
Confidence 444555555778899999988887777666643 3479999999998665323334444
No 81
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=23.33 E-value=59 Score=23.96 Aligned_cols=32 Identities=16% Similarity=0.197 Sum_probs=19.2
Q ss_pred CcccCChhhhhhCCCCCCEEEE-EecCCCCccc
Q 030447 139 RMLKKDAIAQYYGLERGQVVKV-TYSGEITESH 170 (177)
Q Consensus 139 rI~~sDPvary~Glk~GdVVKI-~R~SetaG~~ 170 (177)
-|..+-..+|-|||+.||+|.= +|+.....+|
T Consensus 30 DvYVs~~qIrrf~LR~GD~V~G~vr~p~~~ek~ 62 (78)
T PF07497_consen 30 DVYVSPSQIRRFGLRTGDLVEGQVRPPREGEKY 62 (78)
T ss_dssp SEEE-CCCCCCTT--TTEEEEEEEE--STTSSS
T ss_pred CEEECHHHHHHcCCCCCCEEEEEEeCCCCCCcc
Confidence 3667778889999999999984 5554444443
No 82
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=23.17 E-value=96 Score=18.61 Aligned_cols=17 Identities=12% Similarity=0.358 Sum_probs=14.3
Q ss_pred hhhCCCCCCEEEEEecC
Q 030447 148 QYYGLERGQVVKVTYSG 164 (177)
Q Consensus 148 ry~Glk~GdVVKI~R~S 164 (177)
..+-+++||+|.|+..+
T Consensus 17 ~~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 17 DELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCCEEEEEEcC
Confidence 44678999999999886
No 83
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.10 E-value=71 Score=23.74 Aligned_cols=27 Identities=26% Similarity=0.234 Sum_probs=20.7
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|.+..+-=-|..+|++-||.|+|....
T Consensus 33 ~~v~i~p~dA~~~gi~~Gd~V~v~s~~ 59 (129)
T cd02782 33 CTLRIHPDDAAALGLADGDKVRVTSAA 59 (129)
T ss_pred ceEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 445555556888999999999998764
No 84
>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=22.95 E-value=47 Score=26.90 Aligned_cols=17 Identities=29% Similarity=0.444 Sum_probs=12.9
Q ss_pred HHHHHHHHhcCCCCccC
Q 030447 45 SRRTVLEMLKDRGYAVA 61 (177)
Q Consensus 45 ~rrTv~eMl~DRGY~V~ 61 (177)
+|..+.+||+|+||.-.
T Consensus 14 ir~~l~~~L~~~~~t~~ 30 (180)
T PF11985_consen 14 IREWLDQMLRDGGFTQY 30 (180)
T ss_pred HHHHHHHHHHhCCCChH
Confidence 67788888888887543
No 85
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=22.86 E-value=32 Score=25.33 Aligned_cols=44 Identities=16% Similarity=0.262 Sum_probs=32.9
Q ss_pred HHHHHhhcCCCcCCCCCcc--c--------CChhhhhhCCCCCCEEEEEecCCC
Q 030447 123 KEKLLKKYSIEEKQLPRML--K--------KDAIAQYYGLERGQVVKVTYSGEI 166 (177)
Q Consensus 123 k~~lL~~y~i~~~QLPrI~--~--------sDPvary~Glk~GdVVKI~R~Set 166 (177)
+.+|-+.-+|.+.+|-+|. . =+-+++++.-+|||++.+..++.+
T Consensus 18 ~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDiley~~d~~~ 71 (73)
T COG3655 18 LKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDILEYVPDSDD 71 (73)
T ss_pred HHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHcCCChhheeEEecCCcc
Confidence 4556666777777777776 2 245789999999999999877644
No 86
>PF06130 PduL: Propanediol utilisation protein PduL; InterPro: IPR008300 Salmonella enterica subsp. enterica serovar Typhimurium degrades 1,2-propanediol by a pathway that requires coenzyme B12, adenosylcobalamin (AdoCbl). Proteins required for 1,2-propanediol degradation are encoded by the pdu operon []. PduL functions in this pathway, but its exact role is not yet determined. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilization of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilization (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and coregulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR010254 from INTERPRO and IPR009204 from INTERPRO for more details on the propanediol utilization pathway and the pdu operon.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups
Probab=22.76 E-value=1.7e+02 Score=21.14 Aligned_cols=16 Identities=31% Similarity=0.187 Sum_probs=12.1
Q ss_pred hhhhCCCCCCEEEEEe
Q 030447 147 AQYYGLERGQVVKVTY 162 (177)
Q Consensus 147 ary~Glk~GdVVKI~R 162 (177)
|..||.++||.+.+..
T Consensus 18 a~~l~~~dg~~v~ve~ 33 (71)
T PF06130_consen 18 AEKLFGQDGQFVSVEV 33 (71)
T ss_pred HHHhCCCCCCEEEEEE
Confidence 3345569999999988
No 87
>PF00370 FGGY_N: FGGY family of carbohydrate kinases, N-terminal domain; InterPro: IPR018484 It has been shown [] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (2.7.1.51 from EC) (gene fucK); gluconokinase (2.7.1.12 from EC) (gene gntK); glycerol kinase (2.7.1.30 from EC) (gene glpK); xylulokinase (2.7.1.17 from EC) (gene xylB); and L-xylulose kinase (2.7.1.53 from EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues. This entry represents the N-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain [, ].; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3G25_D 3GE1_D 2NLX_A 2ITM_A 2ZF5_Y 3L0Q_B 3GG4_B 3I8B_A 3H3O_C 3FLC_X ....
Probab=22.33 E-value=52 Score=26.95 Aligned_cols=46 Identities=30% Similarity=0.407 Sum_probs=32.6
Q ss_pred hhhcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCC--------hhhhhhCCCCCCEE
Q 030447 102 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKD--------AIAQYYGLERGQVV 158 (177)
Q Consensus 102 LlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sD--------Pvary~Glk~GdVV 158 (177)
-++|+.+... + .++|+.+++...+||.|..+. -+|+.+|+..|=.|
T Consensus 179 gl~d~~~~~w-------~----~~~l~~~gi~~~~lP~i~~~g~~~G~~~~~~a~~~Gl~~~~pV 232 (245)
T PF00370_consen 179 GLYDIRTGQW-------D----EELLEALGIPEELLPEIVPPGEIIGTLTPEAAKELGLPEGTPV 232 (245)
T ss_dssp SSEETTTTEE------------HHHHHHTTSGGGGSCEEE-TTSEEEEEEHHHHHHHTSTTTEEE
T ss_pred cccccccccc-------C----HHHHHhhCCChhhCCcEecCCCeeEEECHHHHHHhCCCCCCEE
Confidence 4567766654 2 458899999999999996543 34678899888444
No 88
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=22.31 E-value=1.9e+02 Score=22.83 Aligned_cols=43 Identities=28% Similarity=0.391 Sum_probs=26.9
Q ss_pred ecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCcc
Q 030447 117 VLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITES 169 (177)
Q Consensus 117 vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~ 169 (177)
.++++|.+.|+.... ..+. +.-...++++||.|+|+ ..+-+|.
T Consensus 101 ~i~~~ei~~l~~~~~--~~~~-------~~~~~~~~~~Gd~VrI~-~GPf~G~ 143 (181)
T PRK05609 101 PLSEKEVEKILKQLQ--EGVE-------KPKPKVDFEVGEMVRVI-DGPFADF 143 (181)
T ss_pred cCCHHHHHHHHHHhh--cccc-------cCccccCCCCCCEEEEe-ccCCCCC
Confidence 479999999876432 1111 11122689999999998 4455554
No 89
>COG5429 Uncharacterized secreted protein [Function unknown]
Probab=22.30 E-value=37 Score=30.42 Aligned_cols=108 Identities=20% Similarity=0.135 Sum_probs=57.0
Q ss_pred HHHHHHHhCCCCCCCceeEeecCCCCCc-----hh----hhhhh-hcCCccccc--CCcee--------cCHHHHHHHHh
Q 030447 69 VQDFRAIYGQDPDVDRLRISISHQSDPS-----KR----ITDLL-VNITKHVLK--PKHQV--------LTDQEKEKLLK 128 (177)
Q Consensus 69 l~~F~~~y~~~~~r~~L~~~~~~~~dp~-----~k----e~eLl-vNIt~H~LV--PkH~v--------Ls~eEk~~lL~ 128 (177)
-+++.+++.+.|+--.|++.+.-++=+- -+ |.+-- -+-..|.-| |+..+ -.+.+....|+
T Consensus 59 Ad~~l~k~a~~~~vlALsyhVdYWdYlGWkDtlar~enTeRQ~aY~~a~g~~~vyTPQavvnGr~~~~Gad~~~i~~~i~ 138 (261)
T COG5429 59 ADANLAKLADDPGVLALSYHVDYWDYLGWKDTLARKENTERQRAYARAFGARGVYTPQAVVNGRVHANGADPGAIEDAIA 138 (261)
T ss_pred HHHHHHHhccCCCEEEEEEeecccccCCccccccchhhhHHHHHHHHhhccCCCCCchheeechhhhcCCCHHHHHHHHH
Confidence 3556666666677667777766554221 11 11111 122222222 22211 24566677777
Q ss_pred hcCCCcCCC---CCcc-cCChhhhhhCC-------------CCCCEEEEEecCCCCccceEEEEeC
Q 030447 129 KYSIEEKQL---PRML-KKDAIAQYYGL-------------ERGQVVKVTYSGEITESHVTYRCVW 177 (177)
Q Consensus 129 ~y~i~~~QL---PrI~-~sDPvary~Gl-------------k~GdVVKI~R~SetaG~~v~YR~V~ 177 (177)
..+-+..+| +.++ ..|-|+--.|+ .+|++|+|.| .|++|+.++||-||
T Consensus 139 a~~~~g~gl~vPv~~~~~gdrvaI~~GAg~G~~a~Vvlvyf~~~~~v~i~~-GEN~Gk~l~y~nvV 203 (261)
T COG5429 139 AMARRGAGLEVPVDAQFGGDRVAIDIGAGKGPPADVVLVYFDPGQVVPIAR-GENSGKELTYWNVV 203 (261)
T ss_pred HhhcccccccCCcchhhcCceEEEecCCCCCCCceEEEEEecCCceecccc-cccCCcEeehhhhh
Confidence 666444332 1222 23445555555 4558888876 57999999998764
No 90
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=21.96 E-value=57 Score=23.62 Aligned_cols=13 Identities=23% Similarity=0.468 Sum_probs=11.2
Q ss_pred CCCCCEEEEEecC
Q 030447 152 LERGQVVKVTYSG 164 (177)
Q Consensus 152 lk~GdVVKI~R~S 164 (177)
.++|+.|||-|+.
T Consensus 2 i~rGskVrIlR~E 14 (64)
T CHL00125 2 VKRGSKVRILRKE 14 (64)
T ss_pred cccCCEEEEcccc
Confidence 4799999999984
No 91
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=21.69 E-value=57 Score=24.05 Aligned_cols=13 Identities=23% Similarity=0.493 Sum_probs=11.5
Q ss_pred CCCCCEEEEEecC
Q 030447 152 LERGQVVKVTYSG 164 (177)
Q Consensus 152 lk~GdVVKI~R~S 164 (177)
.++|+.|||-|+.
T Consensus 3 i~rGskVrIlR~E 15 (71)
T PRK02749 3 ISRGDKVRILRPE 15 (71)
T ss_pred cccCCEEEEcccc
Confidence 5899999999984
No 92
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=21.55 E-value=1.3e+02 Score=23.54 Aligned_cols=28 Identities=25% Similarity=0.366 Sum_probs=20.5
Q ss_pred hhhhhhCCCCCCEEEEEecCCCCccceEEEE
Q 030447 145 AIAQYYGLERGQVVKVTYSGEITESHVTYRC 175 (177)
Q Consensus 145 Pvary~Glk~GdVVKI~R~SetaG~~v~YR~ 175 (177)
+..+..-+++||.|.|+.. .|....||+
T Consensus 66 ~F~~L~~l~~GD~I~v~~~---~g~~~~Y~V 93 (144)
T cd05829 66 VFFRLGDLRKGDKVEVTRA---DGQTATFRV 93 (144)
T ss_pred hhcchhcCCCCCEEEEEEC---CCCEEEEEE
Confidence 4455556899999999874 456677776
No 93
>KOG0790 consensus Protein tyrosine phosphatase Corkscrew and related SH2 domain enzymes [Signal transduction mechanisms]
Probab=21.45 E-value=67 Score=31.56 Aligned_cols=48 Identities=25% Similarity=0.268 Sum_probs=42.4
Q ss_pred ceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEe
Q 030447 115 HQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTY 162 (177)
Q Consensus 115 H~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R 162 (177)
|.-|+-.|+++||+.+++.-+-|-+-..+.|.+--+-.++||-|.=++
T Consensus 8 h~~~~g~~ae~Ll~~~g~dgsfl~r~s~sNp~~fsl~~r~~~~v~hik 55 (600)
T KOG0790|consen 8 HPDLSGVEAETLLKERGVDGSFLARPSESNPGDFSLSVRRGDKVTHIK 55 (600)
T ss_pred CCCccchhHHHHHHHhccccchhhccccCCCcceeEEEEeCCceEEEE
Confidence 677899999999999999999999999999999888888888765444
No 94
>PRK14560 putative RNA-binding protein; Provisional
Probab=21.31 E-value=1.1e+02 Score=24.34 Aligned_cols=30 Identities=13% Similarity=0.305 Sum_probs=23.7
Q ss_pred cCCCCCcccCChhhhhh----------------CCCCCCEEEEEec
Q 030447 134 EKQLPRMLKKDAIAQYY----------------GLERGQVVKVTYS 163 (177)
Q Consensus 134 ~~QLPrI~~sDPvary~----------------Glk~GdVVKI~R~ 163 (177)
+..+|+|...+++++++ ++++||+|-|.-.
T Consensus 73 ~~~~~~v~Vd~~a~~~i~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~ 118 (160)
T PRK14560 73 KPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEE 118 (160)
T ss_pred CccCCEEEEeccHHHHHHCCCceecCeeeeCCCCCCCCCEEEEEEC
Confidence 45578888888888877 6789999999754
No 95
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=21.14 E-value=81 Score=20.58 Aligned_cols=21 Identities=19% Similarity=0.259 Sum_probs=17.4
Q ss_pred cCCceecCHHHHHHHHhhcCC
Q 030447 112 KPKHQVLTDQEKEKLLKKYSI 132 (177)
Q Consensus 112 VPkH~vLs~eEk~~lL~~y~i 132 (177)
||...=++.+|+++.|+.+++
T Consensus 3 vPd~~g~~~~~a~~~l~~~g~ 23 (63)
T PF03793_consen 3 VPDLVGMTYDEAKSILEAAGL 23 (63)
T ss_dssp E-TTTTSBHHHHHHHHHHTT-
T ss_pred CCCcCCCcHHHHHHHHHHCCC
Confidence 677788999999999999998
No 96
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=21.12 E-value=75 Score=24.31 Aligned_cols=27 Identities=22% Similarity=0.297 Sum_probs=22.3
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|.+..+---|+.+|++.||.|+|....
T Consensus 30 ~~v~inp~dA~~lgI~~Gd~V~v~s~~ 56 (143)
T cd02780 30 NPVWINPEDAAKLGIKTGDRVRVVTPG 56 (143)
T ss_pred CEEEECHHHHHHcCCCCCCEEEEEeCC
Confidence 566677778999999999999998754
No 97
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.86 E-value=87 Score=23.21 Aligned_cols=27 Identities=26% Similarity=0.334 Sum_probs=21.8
Q ss_pred CCcccCChhhhhhCCCCCCEEEEEecC
Q 030447 138 PRMLKKDAIAQYYGLERGQVVKVTYSG 164 (177)
Q Consensus 138 PrI~~sDPvary~Glk~GdVVKI~R~S 164 (177)
|.+..+---|.-+|++-||.|+|....
T Consensus 32 ~~v~i~p~dA~~~gi~~Gd~V~v~s~~ 58 (124)
T cd02785 32 PRVKINPIDAAARGIAHGDLVEVYNDR 58 (124)
T ss_pred CeEEECHHHHHHcCCCCCCEEEEEeCC
Confidence 556666667889999999999998764
No 98
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=20.77 E-value=1.1e+02 Score=20.61 Aligned_cols=41 Identities=12% Similarity=0.315 Sum_probs=27.8
Q ss_pred HHHHHhhcCCCcCCCCCcccCChhhhh----hCCCCCCEEEEEec
Q 030447 123 KEKLLKKYSIEEKQLPRMLKKDAIAQY----YGLERGQVVKVTYS 163 (177)
Q Consensus 123 k~~lL~~y~i~~~QLPrI~~sDPvary----~Glk~GdVVKI~R~ 163 (177)
.++||+++++....+--....-.+.+. .-++.||.|.|+..
T Consensus 17 v~~ll~~l~~~~~~i~V~vNg~~v~~~~~~~~~L~~gD~V~ii~~ 61 (65)
T cd00565 17 LAELLEELGLDPRGVAVALNGEIVPRSEWASTPLQDGDRIEIVTA 61 (65)
T ss_pred HHHHHHHcCCCCCcEEEEECCEEcCHHHcCceecCCCCEEEEEEe
Confidence 567888888776555322333444555 57899999999875
No 99
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=20.46 E-value=1e+02 Score=21.98 Aligned_cols=25 Identities=12% Similarity=0.247 Sum_probs=19.0
Q ss_pred hhCCCCCCEEEEEecCCCCccceEEE
Q 030447 149 YYGLERGQVVKVTYSGEITESHVTYR 174 (177)
Q Consensus 149 y~Glk~GdVVKI~R~SetaG~~v~YR 174 (177)
.+|+.||.-|++.|+++.-|. +.||
T Consensus 28 ~mGl~pG~~V~v~~~aP~gdP-i~i~ 52 (74)
T PRK09555 28 SLGMLPGSSFNVVRVAPLGDP-IHIE 52 (74)
T ss_pred HcCCCCCCEEEEEEECCCCCC-EEEE
Confidence 369999999999999876543 4443
No 100
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=20.32 E-value=1.5e+02 Score=22.04 Aligned_cols=37 Identities=16% Similarity=0.195 Sum_probs=23.9
Q ss_pred CCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEE
Q 030447 135 KQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRC 175 (177)
Q Consensus 135 ~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~ 175 (177)
..--++.+-||-. -++.||+|+|.-- ........|++
T Consensus 40 ~r~kk~~aHD~~n---~~k~GD~V~I~e~-rPlSK~K~~~v 76 (84)
T PRK05610 40 KRSKKYHAHDENN---EAKIGDVVRIMET-RPLSKTKRWRL 76 (84)
T ss_pred EcceEEEEECCCC---CCCCCCEEEEEEc-ccCCCCEEEEE
Confidence 3345778889954 5999999999632 22334455554
No 101
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=20.21 E-value=79 Score=20.92 Aligned_cols=21 Identities=14% Similarity=0.126 Sum_probs=14.2
Q ss_pred cccCChhhhhhCCCCCCEEEEE
Q 030447 140 MLKKDAIAQYYGLERGQVVKVT 161 (177)
Q Consensus 140 I~~sDPvary~Glk~GdVVKI~ 161 (177)
|....|.++ -|+++||+|-=+
T Consensus 33 v~~~s~a~~-~gl~~GD~I~~i 53 (82)
T cd00992 33 VEPGGPAER-GGLRVGDRILEV 53 (82)
T ss_pred ECCCChHHh-CCCCCCCEEEEE
Confidence 344456555 899999987544
No 102
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=20.05 E-value=58 Score=22.65 Aligned_cols=44 Identities=23% Similarity=0.178 Sum_probs=31.0
Q ss_pred eecCHHHHHHHHhhcCCCcC--CCCCcccCChhhhhhCCCCCCEEEE
Q 030447 116 QVLTDQEKEKLLKKYSIEEK--QLPRMLKKDAIAQYYGLERGQVVKV 160 (177)
Q Consensus 116 ~vLs~eEk~~lL~~y~i~~~--QLPrI~~sDPvary~Glk~GdVVKI 160 (177)
..+|++.+++|.+.+.-... |=|....-+-+|..+|+.+ .||||
T Consensus 6 T~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~-~vvKV 51 (58)
T TIGR01565 6 TKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTR-KVFKV 51 (58)
T ss_pred CCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCH-HHeee
Confidence 46788888888877765444 2255666677899999987 45554
Done!