Query 047678
Match_columns 136
No_of_seqs 223 out of 1690
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 13:33:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047678.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047678hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.4 1.5E-12 3.2E-17 76.0 9.0 60 6-65 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.3 1.5E-11 3.2E-16 73.8 9.1 67 3-69 2-70 (71)
3 KOG1603 Copper chaperone [Inor 99.3 3.3E-11 7.2E-16 72.7 8.4 67 3-71 5-72 (73)
4 KOG4656 Copper chaperone for s 98.8 4E-08 8.7E-13 69.3 7.5 67 3-71 7-73 (247)
5 PRK10671 copA copper exporting 98.4 1.3E-06 2.7E-11 74.1 8.5 66 1-69 1-66 (834)
6 PLN02957 copper, zinc superoxi 98.2 2E-05 4.3E-10 57.7 9.6 68 3-72 6-73 (238)
7 COG2217 ZntA Cation transport 98.0 2.5E-05 5.4E-10 65.1 8.2 65 3-68 2-69 (713)
8 TIGR00003 copper ion binding p 97.9 0.00031 6.8E-09 38.7 8.9 63 3-65 2-66 (68)
9 KOG0207 Cation transport ATPas 97.5 0.00044 9.6E-09 58.4 7.2 68 3-70 146-215 (951)
10 PRK11033 zntA zinc/cadmium/mer 97.1 0.0033 7.2E-08 53.0 8.8 67 3-69 53-119 (741)
11 PRK10671 copA copper exporting 97.1 0.0032 7E-08 53.7 8.7 66 4-70 100-165 (834)
12 KOG0207 Cation transport ATPas 96.7 0.007 1.5E-07 51.5 6.9 69 5-73 71-141 (951)
13 TIGR02052 MerP mercuric transp 93.3 0.98 2.1E-05 26.6 9.1 65 4-68 24-90 (92)
14 PRK13748 putative mercuric red 89.4 3.9 8.4E-05 33.4 9.0 67 5-71 2-69 (561)
15 PF01206 TusA: Sulfurtransfera 86.8 4.1 8.8E-05 23.5 5.8 55 6-69 2-57 (70)
16 COG1888 Uncharacterized protei 86.4 3.4 7.3E-05 25.8 5.2 52 19-70 22-80 (97)
17 PF02680 DUF211: Uncharacteriz 85.1 4.2 9.1E-05 25.6 5.3 51 19-69 20-77 (95)
18 cd00371 HMA Heavy-metal-associ 82.2 4.2 9.2E-05 19.6 7.7 39 8-46 3-41 (63)
19 PRK11018 hypothetical protein; 81.0 9.5 0.00021 22.8 6.2 55 5-68 9-64 (78)
20 PRK00299 sulfur transfer prote 75.0 16 0.00034 22.0 6.4 56 4-68 9-65 (81)
21 cd03420 SirA_RHOD_Pry_redox Si 73.3 15 0.00033 21.2 5.1 54 7-69 2-56 (69)
22 cd03421 SirA_like_N SirA_like_ 72.3 15 0.00033 20.9 4.8 52 7-68 2-54 (67)
23 PRK10553 assembly protein for 68.6 25 0.00054 21.7 5.9 47 15-61 16-62 (87)
24 cd03423 SirA SirA (also known 64.3 26 0.00055 20.2 5.5 53 8-69 3-56 (69)
25 cd03422 YedF YedF is a bacteri 62.8 28 0.0006 20.1 5.0 52 8-68 3-55 (69)
26 cd00291 SirA_YedF_YeeD SirA, Y 59.2 31 0.00066 19.5 5.0 54 8-70 3-57 (69)
27 PF01883 DUF59: Domain of unkn 59.0 25 0.00054 20.3 4.0 19 18-36 54-72 (72)
28 PF14437 MafB19-deam: MafB19-l 58.7 37 0.0008 23.1 5.1 39 4-43 101-140 (146)
29 PRK14054 methionine sulfoxide 56.0 45 0.00097 23.3 5.3 47 15-61 10-77 (172)
30 PF13216 DUF4024: Protein of u 51.1 4.9 0.00011 19.7 -0.0 12 121-132 8-19 (35)
31 PF03927 NapD: NapD protein; 48.7 58 0.0012 19.5 6.5 45 17-62 16-60 (79)
32 TIGR03527 selenium_YedF seleni 41.9 98 0.0021 22.0 5.4 52 9-69 3-55 (194)
33 COG0425 SirA Predicted redox p 41.0 79 0.0017 18.9 6.1 50 5-63 6-56 (78)
34 PRK00058 methionine sulfoxide 40.2 1E+02 0.0022 22.4 5.2 47 15-61 52-119 (213)
35 PRK05528 methionine sulfoxide 39.5 1.3E+02 0.0027 20.7 5.6 47 15-61 8-70 (156)
36 PF09122 DUF1930: Domain of un 37.7 58 0.0012 18.9 3.0 42 5-46 21-62 (68)
37 PRK13014 methionine sulfoxide 35.9 95 0.002 22.0 4.5 46 15-60 15-81 (186)
38 PF08712 Nfu_N: Scaffold prote 33.5 1.1E+02 0.0025 18.6 5.9 41 20-62 38-79 (87)
39 PHA01634 hypothetical protein 33.5 12 0.00026 25.2 -0.3 16 9-24 95-110 (156)
40 cd08032 LARP_7 La RNA-binding 32.4 15 0.00031 22.5 -0.1 8 122-129 14-21 (82)
41 KOG3411 40S ribosomal protein 28.5 58 0.0013 21.8 2.2 43 15-61 97-140 (143)
42 KOG1796 Vacuolar protein sorti 28.1 20 0.00042 29.5 -0.0 17 119-135 91-108 (609)
43 PF01625 PMSR: Peptide methion 26.5 2.2E+02 0.0047 19.5 6.2 27 15-41 7-33 (155)
44 TIGR03406 FeS_long_SufT probab 26.3 1.1E+02 0.0023 21.5 3.4 20 19-38 134-153 (174)
45 PRK11200 grxA glutaredoxin 1; 25.8 1.5E+02 0.0032 17.4 4.8 27 11-38 8-38 (85)
46 TIGR01617 arsC_related transcr 24.8 1.9E+02 0.0041 18.3 4.4 48 11-67 6-53 (117)
47 PF08777 RRM_3: RNA binding mo 24.3 1.9E+02 0.0042 18.2 6.6 57 6-62 3-60 (105)
48 TIGR02830 spore_III_AG stage I 24.0 75 0.0016 22.5 2.3 20 17-36 62-81 (186)
49 COG2151 PaaD Predicted metal-s 22.7 2.2E+02 0.0048 18.3 4.2 31 7-37 55-88 (111)
50 PF13732 DUF4162: Domain of un 22.6 1.7E+02 0.0037 17.0 4.8 38 25-64 26-65 (84)
51 TIGR02190 GlrX-dom Glutaredoxi 22.5 1.7E+02 0.0037 16.9 4.3 31 4-37 9-39 (79)
52 PF04972 BON: BON domain; Int 21.8 75 0.0016 17.5 1.7 28 20-48 3-33 (64)
53 COG4004 Uncharacterized protei 21.3 1.9E+02 0.0042 18.1 3.5 22 26-47 37-58 (96)
54 PRK11023 outer membrane lipopr 21.3 2.8E+02 0.0061 19.4 4.9 49 12-61 45-96 (191)
55 COG2177 FtsX Cell division pro 20.4 4E+02 0.0086 20.3 5.9 22 15-36 71-92 (297)
56 COG4545 Glutaredoxin-related p 20.4 1.8E+02 0.004 17.6 3.1 22 1-24 1-22 (85)
57 TIGR00489 aEF-1_beta translati 20.3 1.2E+02 0.0025 18.8 2.4 22 16-37 62-83 (88)
No 1
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.45 E-value=1.5e-12 Score=75.95 Aligned_cols=60 Identities=38% Similarity=0.707 Sum_probs=55.1
Q ss_pred EEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecC--CCHHHHHHHHHHhCcc
Q 047678 6 EVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYA--LDEKKVLKAIKRAGKA 65 (136)
Q Consensus 6 ~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~--~~~~~v~~~l~~~g~~ 65 (136)
+|+|.+|.|++|+++|+++|.+++||.++.+|+..++++|.++. .+.+++.+.|+++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 47899999999999999999999999999999999999999863 5679999999999984
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.35 E-value=1.5e-11 Score=73.83 Aligned_cols=67 Identities=25% Similarity=0.467 Sum_probs=59.4
Q ss_pred eEEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecC--CCHHHHHHHHHHhCcccccC
Q 047678 3 LMVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYA--LDEKKVLKAIKRAGKAAEPW 69 (136)
Q Consensus 3 ~~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~--~~~~~v~~~l~~~g~~~~~~ 69 (136)
++..|++++|.|.+|+..|+++|.+++||..+.+++..+.+.|+.+. ++.+.+.+++..+||.+..+
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 45779999999999999999999999999999999999777776543 78999999999999987654
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.29 E-value=3.3e-11 Score=72.67 Aligned_cols=67 Identities=52% Similarity=0.873 Sum_probs=61.1
Q ss_pred eEEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecCCCHHHHHHHHHHhC-cccccCCC
Q 047678 3 LMVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYALDEKKVLKAIKRAG-KAAEPWPF 71 (136)
Q Consensus 3 ~~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~~~~~~v~~~l~~~g-~~~~~~~~ 71 (136)
+..++++ .|+|++|..+|++.|..++||.++.+|...++++|.|. +++..+++.|++.+ ++.++|..
T Consensus 5 ~~~v~kv-~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~-~~p~~vl~~l~k~~~k~~~~~~~ 72 (73)
T KOG1603|consen 5 KTVVLKV-NMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGN-VDPVKLLKKLKKTGGKRAELWKV 72 (73)
T ss_pred cEEEEEE-CcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEe-cCHHHHHHHHHhcCCCceEEecC
Confidence 4567888 89999999999999999999999999999999999998 99999999999887 77777753
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.77 E-value=4e-08 Score=69.30 Aligned_cols=67 Identities=22% Similarity=0.426 Sum_probs=61.5
Q ss_pred eEEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecCCCHHHHHHHHHHhCcccccCCC
Q 047678 3 LMVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYALDEKKVLKAIKRAGKAAEPWPF 71 (136)
Q Consensus 3 ~~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~~~~~~v~~~l~~~g~~~~~~~~ 71 (136)
-+.+|.| .|.|++|+..|++.|..++||.++++|+..+.+.|.+. ..+.++...|+.+|.++.+...
T Consensus 7 ~~~efaV-~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts-~p~s~i~~~le~tGr~Avl~G~ 73 (247)
T KOG4656|consen 7 YEAEFAV-QMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETS-VPPSEIQNTLENTGRDAVLRGA 73 (247)
T ss_pred eeEEEEE-echhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEcc-CChHHHHHHHHhhChheEEecC
Confidence 3578999 89999999999999999999999999999999999987 8899999999999999887654
No 5
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.41 E-value=1.3e-06 Score=74.10 Aligned_cols=66 Identities=23% Similarity=0.443 Sum_probs=58.2
Q ss_pred CceEEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecCCCHHHHHHHHHHhCcccccC
Q 047678 1 MQLMVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYALDEKKVLKAIKRAGKAAEPW 69 (136)
Q Consensus 1 ~~~~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~~~~~~v~~~l~~~g~~~~~~ 69 (136)
|++++.++|++|+|.+|..+|+++|++++||..+.+++. +.++++. .+.+.+.+.++..|++++..
T Consensus 1 ~~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~-~~~~~i~~~i~~~Gy~~~~~ 66 (834)
T PRK10671 1 MSQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGT-ASAEALIETIKQAGYDASVS 66 (834)
T ss_pred CCeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEec-CCHHHHHHHHHhcCCccccc
Confidence 678899999999999999999999999999999999984 4455554 68889999999999998875
No 6
>PLN02957 copper, zinc superoxide dismutase
Probab=98.20 E-value=2e-05 Score=57.69 Aligned_cols=68 Identities=31% Similarity=0.506 Sum_probs=60.1
Q ss_pred eEEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecCCCHHHHHHHHHHhCcccccCCCC
Q 047678 3 LMVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYALDEKKVLKAIKRAGKAAEPWPFP 72 (136)
Q Consensus 3 ~~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~~~~~~v~~~l~~~g~~~~~~~~~ 72 (136)
.++.+.+ +|.|..|+.++++.|.++.||..+.+++..+++.+... .....+.+.+++.|+.++++...
T Consensus 6 ~~~~~~V-gMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~-~~~~~I~~aIe~~Gy~a~~~~~~ 73 (238)
T PLN02957 6 LLTEFMV-DMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS-SPVKAMTAALEQTGRKARLIGQG 73 (238)
T ss_pred EEEEEEE-CccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec-CCHHHHHHHHHHcCCcEEEecCC
Confidence 4567889 79999999999999999999999999999999998875 67888889999999998877654
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.04 E-value=2.5e-05 Score=65.12 Aligned_cols=65 Identities=31% Similarity=0.506 Sum_probs=57.4
Q ss_pred eEEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecC--CC-HHHHHHHHHHhCccccc
Q 047678 3 LMVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYA--LD-EKKVLKAIKRAGKAAEP 68 (136)
Q Consensus 3 ~~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~--~~-~~~v~~~l~~~g~~~~~ 68 (136)
.+..|.++||+|..|.++++ +|++++||..+.+++.++++.+..+. .+ .+.+.+.++..|+.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 45779999999999999999 99999999999999999999988652 34 68899999999997765
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.89 E-value=0.00031 Score=38.73 Aligned_cols=63 Identities=27% Similarity=0.401 Sum_probs=49.8
Q ss_pred eEEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecC--CCHHHHHHHHHHhCcc
Q 047678 3 LMVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYA--LDEKKVLKAIKRAGKA 65 (136)
Q Consensus 3 ~~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~--~~~~~v~~~l~~~g~~ 65 (136)
++..+.+.++.|..|...+++.+....++....+++....+.++... .+...+...+...|+.
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYE 66 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCC
Confidence 45679999999999999999999999999999999999888877531 3555665556666654
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.48 E-value=0.00044 Score=58.45 Aligned_cols=68 Identities=24% Similarity=0.405 Sum_probs=61.0
Q ss_pred eEEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecC--CCHHHHHHHHHHhCcccccCC
Q 047678 3 LMVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYA--LDEKKVLKAIKRAGKAAEPWP 70 (136)
Q Consensus 3 ~~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~--~~~~~v~~~l~~~g~~~~~~~ 70 (136)
.++.|.+.||.|..|..++++.|.++.||.+.+++..++++.|..++ ..+..+.+.+...|+.+...+
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~ 215 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRP 215 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeee
Confidence 36789999999999999999999999999999999999999987653 789999999999998876655
No 10
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.12 E-value=0.0033 Score=53.04 Aligned_cols=67 Identities=25% Similarity=0.383 Sum_probs=53.7
Q ss_pred eEEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecCCCHHHHHHHHHHhCcccccC
Q 047678 3 LMVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYALDEKKVLKAIKRAGKAAEPW 69 (136)
Q Consensus 3 ~~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~~~~~~v~~~l~~~g~~~~~~ 69 (136)
++..+++.+|+|..|..++++.+.++.||..+.+++..+++.+..+....+.+.+.+...|+.+..+
T Consensus 53 ~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 53 TRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 3567889999999999999999999999999999999988877643222256667777888876544
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.11 E-value=0.0032 Score=53.72 Aligned_cols=66 Identities=21% Similarity=0.452 Sum_probs=55.5
Q ss_pred EEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecCCCHHHHHHHHHHhCcccccCC
Q 047678 4 MVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYALDEKKVLKAIKRAGKAAEPWP 70 (136)
Q Consensus 4 ~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~~~~~~v~~~l~~~g~~~~~~~ 70 (136)
++.+.+.+|+|..|...+++.+.+++|+..+.+++..++..+... .+...+.+.+.+.|+.+.++.
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~-~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGS-ASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEcc-CCHHHHHHHHHhcCCCccccc
Confidence 356889999999999999999999999999999999988777644 567777788888888766543
No 12
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.66 E-value=0.007 Score=51.50 Aligned_cols=69 Identities=22% Similarity=0.319 Sum_probs=60.4
Q ss_pred EEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecC--CCHHHHHHHHHHhCcccccCCCCC
Q 047678 5 VEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYA--LDEKKVLKAIKRAGKAAEPWPFPG 73 (136)
Q Consensus 5 v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~--~~~~~v~~~l~~~g~~~~~~~~~~ 73 (136)
-.+++.||.|..|.+.+++.|++.+|+.++.+.+...+..+..++ ..++.+.+.+.+.|+.+++.....
T Consensus 71 ~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~~ 141 (951)
T KOG0207|consen 71 CYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESVN 141 (951)
T ss_pred eEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhccc
Confidence 357899999999999999999999999999999999999887653 678888999999999988776543
No 13
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=93.29 E-value=0.98 Score=26.62 Aligned_cols=65 Identities=25% Similarity=0.387 Sum_probs=45.5
Q ss_pred EEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec--CCCHHHHHHHHHHhCccccc
Q 047678 4 MVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY--ALDEKKVLKAIKRAGKAAEP 68 (136)
Q Consensus 4 ~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~--~~~~~~v~~~l~~~g~~~~~ 68 (136)
.+.+.+.++.|..|...++..+....++.............+... ......+...+...|+..++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 456778899999999999999998888888887777776555421 13445554555566665443
No 14
>PRK13748 putative mercuric reductase; Provisional
Probab=89.36 E-value=3.9 Score=33.38 Aligned_cols=67 Identities=18% Similarity=0.292 Sum_probs=49.6
Q ss_pred EEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCcccccCCC
Q 047678 5 VEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEPWPF 71 (136)
Q Consensus 5 v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~~~~ 71 (136)
+.+.+.++.|..|..+++..+....++....+++......+... ......+...+...++..+++..
T Consensus 2 ~~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~ 69 (561)
T PRK13748 2 TTLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADA 69 (561)
T ss_pred EEEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCc
Confidence 34678899999999999999999999888888888877666532 13455555666677776655554
No 15
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=86.85 E-value=4.1 Score=23.53 Aligned_cols=55 Identities=16% Similarity=0.104 Sum_probs=38.6
Q ss_pred EEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCcccccC
Q 047678 6 EVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEPW 69 (136)
Q Consensus 6 ~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~~ 69 (136)
++.+.|..|+....+++++|.+++. .+.+.|..+ ......+.+.+++.|++...+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~---------G~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPP---------GEVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGT---------T-EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCC---------CCEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 4667799999999999999998732 234444443 245677888899999875444
No 16
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=86.39 E-value=3.4 Score=25.77 Aligned_cols=52 Identities=33% Similarity=0.407 Sum_probs=37.1
Q ss_pred HHHHHHHhCCCCeeEEEEecc-----C--cEEEEEecCCCHHHHHHHHHHhCcccccCC
Q 047678 19 SKCKRALFKLKGVEEVEIEME-----V--QKITVRGYALDEKKVLKAIKRAGKAAEPWP 70 (136)
Q Consensus 19 ~~v~~~l~~~~gv~~v~vd~~-----~--~~v~V~~~~~~~~~v~~~l~~~g~~~~~~~ 70 (136)
..+-+.|+++.||..+++... + -++++.|..++.+++.+.|.+.|.....+.
T Consensus 22 ve~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSiD 80 (97)
T COG1888 22 VELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSID 80 (97)
T ss_pred HHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeehh
Confidence 345667788888887766443 2 345666766899999999999997665544
No 17
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=85.14 E-value=4.2 Score=25.56 Aligned_cols=51 Identities=29% Similarity=0.441 Sum_probs=35.9
Q ss_pred HHHHHHHhCCCCeeEEEEecc-----Cc--EEEEEecCCCHHHHHHHHHHhCcccccC
Q 047678 19 SKCKRALFKLKGVEEVEIEME-----VQ--KITVRGYALDEKKVLKAIKRAGKAAEPW 69 (136)
Q Consensus 19 ~~v~~~l~~~~gv~~v~vd~~-----~~--~v~V~~~~~~~~~v~~~l~~~g~~~~~~ 69 (136)
-.+-+.|.+++||..+++... +. ++++.|..++.+++.+.|.+.|.....+
T Consensus 20 ~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSI 77 (95)
T PF02680_consen 20 VELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSI 77 (95)
T ss_dssp HHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEE
T ss_pred HHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEee
Confidence 356678899999988876543 33 4455676689999999999999765544
No 18
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=82.20 E-value=4.2 Score=19.56 Aligned_cols=39 Identities=49% Similarity=0.800 Sum_probs=29.4
Q ss_pred EecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEE
Q 047678 8 RVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVR 46 (136)
Q Consensus 8 ~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~ 46 (136)
.+.++.|..|...++..+....++......+......+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVE 41 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEE
Confidence 356788999999999888888887777666666655544
No 19
>PRK11018 hypothetical protein; Provisional
Probab=80.99 E-value=9.5 Score=22.80 Aligned_cols=55 Identities=15% Similarity=0.051 Sum_probs=39.2
Q ss_pred EEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCccccc
Q 047678 5 VEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEP 68 (136)
Q Consensus 5 v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~ 68 (136)
..+.+.|..|+...-+.+++|.++.. .+.+.|..+ ......+...+++.|+.+..
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~---------G~~L~V~~d~~~a~~di~~~~~~~G~~v~~ 64 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKK---------GEILEVVSDCPQSINNIPLDARNHGYTVLD 64 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCC---------CCEEEEEeCCccHHHHHHHHHHHcCCEEEE
Confidence 56778899999999999999998742 233344332 24556777788888987643
No 20
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=74.99 E-value=16 Score=22.02 Aligned_cols=56 Identities=4% Similarity=0.030 Sum_probs=39.2
Q ss_pred EEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCccccc
Q 047678 4 MVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEP 68 (136)
Q Consensus 4 ~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~ 68 (136)
..++.+.|..|+.-.-+++++|.+++. .+.+.|..+ ......+....+..|.+...
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~---------G~~l~V~~dd~~~~~di~~~~~~~G~~~~~ 65 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQP---------GETLLIIADDPATTRDIPSFCRFMDHELLA 65 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCC---------CCEEEEEeCCccHHHHHHHHHHHcCCEEEE
Confidence 456778899999999999999998732 233344332 24566777777888887643
No 21
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=73.35 E-value=15 Score=21.20 Aligned_cols=54 Identities=20% Similarity=0.214 Sum_probs=37.7
Q ss_pred EEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCcccccC
Q 047678 7 VRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEPW 69 (136)
Q Consensus 7 ~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~~ 69 (136)
+.+.|+.|+.-..+.+++|.++.. .+.+.|..+ ......+....+..|+.....
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~---------G~~l~V~~d~~~a~~di~~~~~~~G~~~~~~ 56 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQD---------GEQLEVKASDPGFARDAQAWCKSTGNTLISL 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEEEEE
Confidence 345689999999999999998742 233444332 255677888888889876533
No 22
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=72.34 E-value=15 Score=20.93 Aligned_cols=52 Identities=21% Similarity=0.246 Sum_probs=35.1
Q ss_pred EEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCccccc
Q 047678 7 VRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEP 68 (136)
Q Consensus 7 ~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~ 68 (136)
+.+.|+.|+....+++++| ++.. .+.+.|..+ ....+.+...+++.|+..+.
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~~~~ 54 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYEVSV 54 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCEEEE
Confidence 3456899999999999999 5532 223333332 14456788888899988743
No 23
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=68.65 E-value=25 Score=21.68 Aligned_cols=47 Identities=19% Similarity=0.155 Sum_probs=33.5
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecCCCHHHHHHHHHH
Q 047678 15 EGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYALDEKKVLKAIKR 61 (136)
Q Consensus 15 ~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~~~~~~v~~~l~~ 61 (136)
+.-...|.+.|..++|+.-...+...+|+.|+-+..+...+++.+..
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~ 62 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIES 62 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHH
Confidence 34467789999999999877777777888877543455656555554
No 24
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=64.25 E-value=26 Score=20.22 Aligned_cols=53 Identities=13% Similarity=0.080 Sum_probs=37.2
Q ss_pred EecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCcccccC
Q 047678 8 RVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEPW 69 (136)
Q Consensus 8 ~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~~ 69 (136)
.+.|..|+.-.-+++++|.++.- .+.+.|..+ ......+...+++.|+++...
T Consensus 3 D~~G~~CP~P~i~~k~~l~~l~~---------G~~l~V~~dd~~s~~di~~~~~~~g~~~~~~ 56 (69)
T cd03423 3 DTRGLRCPEPVMMLHKKVRKMKP---------GDTLLVLATDPSTTRDIPKFCTFLGHELLAQ 56 (69)
T ss_pred cccCCcCCHHHHHHHHHHHcCCC---------CCEEEEEeCCCchHHHHHHHHHHcCCEEEEE
Confidence 34589999999999999988732 223344332 256677888888999876543
No 25
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=62.82 E-value=28 Score=20.12 Aligned_cols=52 Identities=15% Similarity=0.034 Sum_probs=36.4
Q ss_pred EecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCccccc
Q 047678 8 RVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEP 68 (136)
Q Consensus 8 ~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~ 68 (136)
.+.|..|+.-.-+.+++|+++.. .+.+.|..+ ......+.+.++..|+++..
T Consensus 3 D~rG~~CP~Pvi~~kkal~~l~~---------G~~l~V~~d~~~s~~ni~~~~~~~g~~v~~ 55 (69)
T cd03422 3 DLRGEPCPYPAIATLEALPSLKP---------GEILEVISDCPQSINNIPIDARNHGYKVLA 55 (69)
T ss_pred ccCCCcCCHHHHHHHHHHHcCCC---------CCEEEEEecCchHHHHHHHHHHHcCCEEEE
Confidence 34589999999999999998742 233333332 25567778888888987754
No 26
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=59.22 E-value=31 Score=19.48 Aligned_cols=54 Identities=22% Similarity=0.111 Sum_probs=37.2
Q ss_pred EecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCcccccCC
Q 047678 8 RVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEPWP 70 (136)
Q Consensus 8 ~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~~~ 70 (136)
.+.|+.|+.-..+++++|.++.. .+.+.+..+ ......+.+.++..|++...+.
T Consensus 3 D~rg~~CP~Pl~~~~~~l~~l~~---------g~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~~ 57 (69)
T cd00291 3 DLRGLPCPLPVLKTKKALEKLKS---------GEVLEVLLDDPGAVEDIPAWAKETGHEVLEVE 57 (69)
T ss_pred cccCCcCCHHHHHHHHHHhcCCC---------CCEEEEEecCCcHHHHHHHHHHHcCCEEEEEE
Confidence 34589999999999999988632 233444433 2456778888889998865443
No 27
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=59.03 E-value=25 Score=20.25 Aligned_cols=19 Identities=32% Similarity=0.492 Sum_probs=14.2
Q ss_pred HHHHHHHHhCCCCeeEEEE
Q 047678 18 ASKCKRALFKLKGVEEVEI 36 (136)
Q Consensus 18 ~~~v~~~l~~~~gv~~v~v 36 (136)
...++++|..++|+.++++
T Consensus 54 ~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 54 REEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHhCCCCceEeC
Confidence 4567888899999988875
No 28
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=58.67 E-value=37 Score=23.12 Aligned_cols=39 Identities=21% Similarity=0.282 Sum_probs=29.2
Q ss_pred EEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEecc-CcEE
Q 047678 4 MVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEME-VQKI 43 (136)
Q Consensus 4 ~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~-~~~v 43 (136)
..++.|..--|..|..-|.....++ |+.++.|... ++++
T Consensus 101 ~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~ 140 (146)
T PF14437_consen 101 SMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKV 140 (146)
T ss_pred eEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcE
Confidence 4677887778999998887776665 8888888766 4543
No 29
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=56.01 E-value=45 Score=23.31 Aligned_cols=47 Identities=13% Similarity=0.221 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeccCcE-------------------EEEEecC--CCHHHHHHHHHH
Q 047678 15 EGCASKCKRALFKLKGVEEVEIEMEVQK-------------------ITVRGYA--LDEKKVLKAIKR 61 (136)
Q Consensus 15 ~~C~~~v~~~l~~~~gv~~v~vd~~~~~-------------------v~V~~~~--~~~~~v~~~l~~ 61 (136)
.+|=+.++..+..++||.++.+-...+. |.|+.++ ++.++|++..-+
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~~ 77 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFFQ 77 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHHH
Confidence 5799999999999999999998877664 3445443 677777776543
No 30
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=51.07 E-value=4.9 Score=19.68 Aligned_cols=12 Identities=25% Similarity=0.348 Sum_probs=9.5
Q ss_pred cCCCCCCCCCCc
Q 047678 121 VASLFSDDNPHA 132 (136)
Q Consensus 121 ~~~~fsdenp~a 132 (136)
..++|.|||.|-
T Consensus 8 ~lhlfrde~vnf 19 (35)
T PF13216_consen 8 NLHLFRDEKVNF 19 (35)
T ss_pred EEEEeecCCccE
Confidence 347999999983
No 31
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=48.72 E-value=58 Score=19.50 Aligned_cols=45 Identities=22% Similarity=0.204 Sum_probs=31.9
Q ss_pred HHHHHHHHHhCCCCeeEEEEeccCcEEEEEecCCCHHHHHHHHHHh
Q 047678 17 CASKCKRALFKLKGVEEVEIEMEVQKITVRGYALDEKKVLKAIKRA 62 (136)
Q Consensus 17 C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~~~~~~v~~~l~~~ 62 (136)
=...+.++|..++|+.-...+.. +|+.|+-+..+...+.+.+...
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i 60 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAI 60 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHH
Confidence 45678999999999965566544 8887775435667777666654
No 32
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=41.93 E-value=98 Score=21.97 Aligned_cols=52 Identities=23% Similarity=0.108 Sum_probs=36.7
Q ss_pred ecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhCcccccC
Q 047678 9 VPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAGKAAEPW 69 (136)
Q Consensus 9 v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g~~~~~~ 69 (136)
..|+.|+....+.+++|.++.. .+.+.|..+ ....+.+.+.+++.|++++..
T Consensus 3 ~rGl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~~~a~~nV~~~~~~~G~~v~~~ 55 (194)
T TIGR03527 3 ARGLACPQPVILTKKALDELGE---------EGVLTVIVDNEAAKENVSKFATSLGYEVEVE 55 (194)
T ss_pred CCCCCCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHHHcCCEEEEE
Confidence 3488999999999999998742 223333332 255677888888999887543
No 33
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=40.97 E-value=79 Score=18.88 Aligned_cols=50 Identities=24% Similarity=0.294 Sum_probs=34.1
Q ss_pred EEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEec-CCCHHHHHHHHHHhC
Q 047678 5 VEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGY-ALDEKKVLKAIKRAG 63 (136)
Q Consensus 5 v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~-~~~~~~v~~~l~~~g 63 (136)
.++.+.|..|+.-...++++|+++.- ...+.|..+ +.....+...+++.|
T Consensus 6 ~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~~dIp~~~~~~~ 56 (78)
T COG0425 6 KVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAKEDIPAWAKKEG 56 (78)
T ss_pred eEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchHHHHHHHHHHcC
Confidence 46788899999999999999998732 334444432 244456666666455
No 34
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=40.22 E-value=1e+02 Score=22.40 Aligned_cols=47 Identities=17% Similarity=0.248 Sum_probs=35.2
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeccCcE-------------------EEEEecC--CCHHHHHHHHHH
Q 047678 15 EGCASKCKRALFKLKGVEEVEIEMEVQK-------------------ITVRGYA--LDEKKVLKAIKR 61 (136)
Q Consensus 15 ~~C~~~v~~~l~~~~gv~~v~vd~~~~~-------------------v~V~~~~--~~~~~v~~~l~~ 61 (136)
.+|-+.++..+.+++||.++.+-...+. |.|+.++ ++.++|++..-+
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff~ 119 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFWE 119 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHHH
Confidence 6899999999999999999999877442 3444443 677777776543
No 35
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=39.49 E-value=1.3e+02 Score=20.74 Aligned_cols=47 Identities=13% Similarity=0.126 Sum_probs=34.2
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeccCcE--------------EEEEecC--CCHHHHHHHHHH
Q 047678 15 EGCASKCKRALFKLKGVEEVEIEMEVQK--------------ITVRGYA--LDEKKVLKAIKR 61 (136)
Q Consensus 15 ~~C~~~v~~~l~~~~gv~~v~vd~~~~~--------------v~V~~~~--~~~~~v~~~l~~ 61 (136)
.+|=+.++..+.+++||.++.+-...+. |.|+.++ ++.++|++..-+
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~~ 70 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLFE 70 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHHH
Confidence 5799999999999999999998766543 3344443 677777766543
No 36
>PF09122 DUF1930: Domain of unknown function (DUF1930); InterPro: IPR015206 This entry represents a domain found in 3-mercaptopyruvate sulphurtransferase which has no known function. This domain adopts a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase []. ; PDB: 1OKG_A.
Probab=37.73 E-value=58 Score=18.90 Aligned_cols=42 Identities=21% Similarity=0.176 Sum_probs=27.9
Q ss_pred EEEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEE
Q 047678 5 VEVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVR 46 (136)
Q Consensus 5 v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~ 46 (136)
.++.+.|--|..--..+..++..+.--+...+.++.+++.+.
T Consensus 21 ~tl~vDg~~v~~PD~El~sA~~HlH~GEkA~V~FkS~Rv~~i 62 (68)
T PF09122_consen 21 ATLIVDGEIVENPDAELKSALVHLHIGEKAQVFFKSQRVAVI 62 (68)
T ss_dssp --EEETTEEESS--HHHHHHHTT-BTT-EEEEEETTS-EEEE
T ss_pred eEEEEcCeEcCCCCHHHHHHHHHhhcCceeEEEEecCcEEEE
Confidence 567888888888888888888888666678888888877653
No 37
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=35.86 E-value=95 Score=22.02 Aligned_cols=46 Identities=13% Similarity=0.153 Sum_probs=34.2
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeccCcE-------------------EEEEecC--CCHHHHHHHHH
Q 047678 15 EGCASKCKRALFKLKGVEEVEIEMEVQK-------------------ITVRGYA--LDEKKVLKAIK 60 (136)
Q Consensus 15 ~~C~~~v~~~l~~~~gv~~v~vd~~~~~-------------------v~V~~~~--~~~~~v~~~l~ 60 (136)
.+|=+.++..+.+++||.++.+-...+. |.|+.++ ++.++|++..-
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff 81 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFF 81 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHH
Confidence 5788899999999999999998877653 3444443 67777776553
No 38
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=33.54 E-value=1.1e+02 Score=18.55 Aligned_cols=41 Identities=29% Similarity=0.308 Sum_probs=28.5
Q ss_pred HHHHHHhCCCCeeEEEEeccCcEEEEEecC-CCHHHHHHHHHHh
Q 047678 20 KCKRALFKLKGVEEVEIEMEVQKITVRGYA-LDEKKVLKAIKRA 62 (136)
Q Consensus 20 ~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~-~~~~~v~~~l~~~ 62 (136)
-+-+.|-.++||.+|-+ ...-++|+-.. .+++.|...|...
T Consensus 38 pLA~~Lf~i~gV~~Vf~--~~dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 38 PLAQALFAIPGVKSVFI--GDDFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp HHHHHHHTSTTEEEEEE--ETTEEEEEE-TTS-HHHHHHHHHHH
T ss_pred HHHHHhcCCCCEeEEEE--ECCEEEEeeCCCCCHHHHHHHHHHH
Confidence 34445558999999887 46677777532 8999998888754
No 39
>PHA01634 hypothetical protein
Probab=33.51 E-value=12 Score=25.18 Aligned_cols=16 Identities=38% Similarity=0.825 Sum_probs=11.9
Q ss_pred ecCCCChhHHHHHHHH
Q 047678 9 VPNLDCEGCASKCKRA 24 (136)
Q Consensus 9 v~~m~C~~C~~~v~~~ 24 (136)
+--|+|++|+.++.-.
T Consensus 95 i~~iDCeGCE~~l~v~ 110 (156)
T PHA01634 95 IFVMDCEGCEEKLNVS 110 (156)
T ss_pred eEEEEccchHHhcCHH
Confidence 3358999999987543
No 40
>cd08032 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.
Probab=32.40 E-value=15 Score=22.49 Aligned_cols=8 Identities=38% Similarity=0.385 Sum_probs=6.2
Q ss_pred CCCCCCCC
Q 047678 122 ASLFSDDN 129 (136)
Q Consensus 122 ~~~fsden 129 (136)
--+|||+|
T Consensus 14 EfYFSd~N 21 (82)
T cd08032 14 DFWFGDVN 21 (82)
T ss_pred Hhhcchhh
Confidence 34899998
No 41
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=28.48 E-value=58 Score=21.82 Aligned_cols=43 Identities=26% Similarity=0.249 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeccCc-EEEEEecCCCHHHHHHHHHH
Q 047678 15 EGCASKCKRALFKLKGVEEVEIEMEVQ-KITVRGYALDEKKVLKAIKR 61 (136)
Q Consensus 15 ~~C~~~v~~~l~~~~gv~~v~vd~~~~-~v~V~~~~~~~~~v~~~l~~ 61 (136)
.+|.+++-++|+ .+.-++.+...+ +++-.|. .+.+.|...|+.
T Consensus 97 ~~i~rkvlQ~Le---~~~~ve~hp~gGR~lt~~Gq-rdldrIa~~i~~ 140 (143)
T KOG3411|consen 97 GGIARKVLQALE---KMGIVEKHPKGGRRLTEQGQ-RDLDRIAGQIRE 140 (143)
T ss_pred cHHHHHHHHHHH---hCCceeeCCCCcceeCcccc-hhHHHHHHHHHh
Confidence 345555555554 455566666664 4444455 677777766654
No 42
>KOG1796 consensus Vacuolar protein sorting-associated protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.10 E-value=20 Score=29.51 Aligned_cols=17 Identities=35% Similarity=0.712 Sum_probs=13.5
Q ss_pred cccCCCCCCCC-CCcccc
Q 047678 119 EAVASLFSDDN-PHACTI 135 (136)
Q Consensus 119 ~~~~~~fsden-p~aCsi 135 (136)
..++.-|+||| |++|+.
T Consensus 91 ~plmf~fad~~qP~~c~~ 108 (609)
T KOG1796|consen 91 HPLMFSFADENQPKACRS 108 (609)
T ss_pred CceeeeeecccCcchhhh
Confidence 34677899999 899974
No 43
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=26.48 E-value=2.2e+02 Score=19.48 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=23.6
Q ss_pred hhHHHHHHHHHhCCCCeeEEEEeccCc
Q 047678 15 EGCASKCKRALFKLKGVEEVEIEMEVQ 41 (136)
Q Consensus 15 ~~C~~~v~~~l~~~~gv~~v~vd~~~~ 41 (136)
.||=+.++..+.+++||.++.+-...+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG 33 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGG 33 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESS
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCC
Confidence 479999999999999999999877655
No 44
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=26.26 E-value=1.1e+02 Score=21.48 Aligned_cols=20 Identities=25% Similarity=0.541 Sum_probs=15.5
Q ss_pred HHHHHHHhCCCCeeEEEEec
Q 047678 19 SKCKRALFKLKGVEEVEIEM 38 (136)
Q Consensus 19 ~~v~~~l~~~~gv~~v~vd~ 38 (136)
..++.+|..++||.++++++
T Consensus 134 ~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 134 EDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred HHHHHHHHhCCCceeEEEEE
Confidence 44788888889998887754
No 45
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=25.78 E-value=1.5e+02 Score=17.36 Aligned_cols=27 Identities=19% Similarity=0.356 Sum_probs=16.7
Q ss_pred CCCChhHHHHHHHHHhCC----CCeeEEEEec
Q 047678 11 NLDCEGCASKCKRALFKL----KGVEEVEIEM 38 (136)
Q Consensus 11 ~m~C~~C~~~v~~~l~~~----~gv~~v~vd~ 38 (136)
.-.|+.|. ++++.|..+ .|+.-..+|.
T Consensus 8 ~~~C~~C~-~a~~~L~~l~~~~~~i~~~~idi 38 (85)
T PRK11200 8 RPGCPYCV-RAKELAEKLSEERDDFDYRYVDI 38 (85)
T ss_pred CCCChhHH-HHHHHHHhhcccccCCcEEEEEC
Confidence 35699995 677777765 3554444443
No 46
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=24.78 E-value=1.9e+02 Score=18.28 Aligned_cols=48 Identities=19% Similarity=0.355 Sum_probs=28.1
Q ss_pred CCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecCCCHHHHHHHHHHhCcccc
Q 047678 11 NLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYALDEKKVLKAIKRAGKAAE 67 (136)
Q Consensus 11 ~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~~~~~~v~~~l~~~g~~~~ 67 (136)
.-.|+.|. ++++.|.+ .|+.-..+|.... +.+.+++.+.+...|...+
T Consensus 6 ~~~C~~c~-ka~~~L~~-~~i~~~~idi~~~-------~~~~~el~~l~~~~~~~~~ 53 (117)
T TIGR01617 6 SPNCTTCK-KARRWLEA-NGIEYQFIDIGED-------GPTREELLDILSLLEDGID 53 (117)
T ss_pred CCCCHHHH-HHHHHHHH-cCCceEEEecCCC-------hhhHHHHHHHHHHcCCCHH
Confidence 35799996 55566655 3555444443221 2456677777777775443
No 47
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=24.28 E-value=1.9e+02 Score=18.18 Aligned_cols=57 Identities=19% Similarity=0.132 Sum_probs=33.0
Q ss_pred EEEecCCCChhHHHHHHHHHhCCCCeeEEEEeccCcEEEEEecC-CCHHHHHHHHHHh
Q 047678 6 EVRVPNLDCEGCASKCKRALFKLKGVEEVEIEMEVQKITVRGYA-LDEKKVLKAIKRA 62 (136)
Q Consensus 6 ~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd~~~~~v~V~~~~-~~~~~v~~~l~~~ 62 (136)
.+++.|+.-+.+...++..++....|..|.+..-.....|.... .....++..+...
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 35666655566677899999998899999888777777787652 3466677776655
No 48
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=24.00 E-value=75 Score=22.52 Aligned_cols=20 Identities=30% Similarity=0.476 Sum_probs=16.2
Q ss_pred HHHHHHHHHhCCCCeeEEEE
Q 047678 17 CASKCKRALFKLKGVEEVEI 36 (136)
Q Consensus 17 C~~~v~~~l~~~~gv~~v~v 36 (136)
-+.+++..|+++.||..+.+
T Consensus 62 lE~~L~~iL~~I~GvG~V~V 81 (186)
T TIGR02830 62 YENELKEILEKIEGVGDVTV 81 (186)
T ss_pred HHHHHHHHHHhccCcceeEE
Confidence 46778889999999888665
No 49
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=22.74 E-value=2.2e+02 Score=18.35 Aligned_cols=31 Identities=32% Similarity=0.521 Sum_probs=21.1
Q ss_pred EEecCCCChh---HHHHHHHHHhCCCCeeEEEEe
Q 047678 7 VRVPNLDCEG---CASKCKRALFKLKGVEEVEIE 37 (136)
Q Consensus 7 ~~v~~m~C~~---C~~~v~~~l~~~~gv~~v~vd 37 (136)
+....+-|+. -...++.++..+.||..+++.
T Consensus 55 mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~ 88 (111)
T COG2151 55 MTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVE 88 (111)
T ss_pred EecCCCCCCccHHHHHHHHHHHHhcCCcceEEEE
Confidence 3333444543 256689999999998888774
No 50
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=22.60 E-value=1.7e+02 Score=16.96 Aligned_cols=38 Identities=26% Similarity=0.349 Sum_probs=26.8
Q ss_pred HhCCCCeeEEEEeccCcEEEEE--ecCCCHHHHHHHHHHhCc
Q 047678 25 LFKLKGVEEVEIEMEVQKITVR--GYALDEKKVLKAIKRAGK 64 (136)
Q Consensus 25 l~~~~gv~~v~vd~~~~~v~V~--~~~~~~~~v~~~l~~~g~ 64 (136)
|..++||..+...- .+.+.+. .. .....+++.+...|.
T Consensus 26 l~~~~~v~~v~~~~-~~~~~i~l~~~-~~~~~ll~~l~~~g~ 65 (84)
T PF13732_consen 26 LEELPGVESVEQDG-DGKLRIKLEDE-ETANELLQELIEKGI 65 (84)
T ss_pred HhhCCCeEEEEEeC-CcEEEEEECCc-ccHHHHHHHHHhCCC
Confidence 77779999988643 4434444 33 567888999988886
No 51
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=22.48 E-value=1.7e+02 Score=16.90 Aligned_cols=31 Identities=35% Similarity=0.375 Sum_probs=19.6
Q ss_pred EEEEEecCCCChhHHHHHHHHHhCCCCeeEEEEe
Q 047678 4 MVEVRVPNLDCEGCASKCKRALFKLKGVEEVEIE 37 (136)
Q Consensus 4 ~v~~~v~~m~C~~C~~~v~~~l~~~~gv~~v~vd 37 (136)
.+++-. .-.|+.|. ++++.|... |+....++
T Consensus 9 ~V~ly~-~~~Cp~C~-~ak~~L~~~-gi~y~~id 39 (79)
T TIGR02190 9 SVVVFT-KPGCPFCA-KAKATLKEK-GYDFEEIP 39 (79)
T ss_pred CEEEEE-CCCCHhHH-HHHHHHHHc-CCCcEEEE
Confidence 344555 56899995 677777653 66554444
No 52
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=21.76 E-value=75 Score=17.50 Aligned_cols=28 Identities=25% Similarity=0.353 Sum_probs=14.4
Q ss_pred HHHHHHhC---CCCeeEEEEeccCcEEEEEec
Q 047678 20 KCKRALFK---LKGVEEVEIEMEVQKITVRGY 48 (136)
Q Consensus 20 ~v~~~l~~---~~gv~~v~vd~~~~~v~V~~~ 48 (136)
+|+..|.. +++. .+.+....+.+.++|.
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~ 33 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGE 33 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEE
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEee
Confidence 45555555 3333 5777778999999986
No 53
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.32 E-value=1.9e+02 Score=18.07 Aligned_cols=22 Identities=27% Similarity=0.381 Sum_probs=18.7
Q ss_pred hCCCCeeEEEEeccCcEEEEEe
Q 047678 26 FKLKGVEEVEIEMEVQKITVRG 47 (136)
Q Consensus 26 ~~~~gv~~v~vd~~~~~v~V~~ 47 (136)
...+|+..+++.++.+++.|++
T Consensus 37 as~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 37 ASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EecCCceEEEEecccceEEEec
Confidence 4568899999999999998876
No 54
>PRK11023 outer membrane lipoprotein; Provisional
Probab=21.31 E-value=2.8e+02 Score=19.42 Aligned_cols=49 Identities=14% Similarity=0.172 Sum_probs=32.1
Q ss_pred CCChhHHHHHHHHHhCCCCee---EEEEeccCcEEEEEecCCCHHHHHHHHHH
Q 047678 12 LDCEGCASKCKRALFKLKGVE---EVEIEMEVQKITVRGYALDEKKVLKAIKR 61 (136)
Q Consensus 12 m~C~~C~~~v~~~l~~~~gv~---~v~vd~~~~~v~V~~~~~~~~~v~~~l~~ 61 (136)
++...-..+|+.+|...+... .+++....+.++++|. +..+.......+
T Consensus 45 ~dD~~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~-V~~~~~k~~A~~ 96 (191)
T PRK11023 45 VDDGTLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQ-SPNAELSERAKQ 96 (191)
T ss_pred ehhHHHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEEE-eCCHHHHHHHHH
Confidence 344556778888887655553 5777778899999997 444443333333
No 55
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=20.40 E-value=4e+02 Score=20.34 Aligned_cols=22 Identities=18% Similarity=0.288 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHhCCCCeeEEEE
Q 047678 15 EGCASKCKRALFKLKGVEEVEI 36 (136)
Q Consensus 15 ~~C~~~v~~~l~~~~gv~~v~v 36 (136)
+.|...+++.+.+.+||.++++
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~ 92 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRF 92 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEE
Confidence 8899999999999999998886
No 56
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.38 E-value=1.8e+02 Score=17.59 Aligned_cols=22 Identities=18% Similarity=0.164 Sum_probs=14.6
Q ss_pred CceEEEEEecCCCChhHHHHHHHH
Q 047678 1 MQLMVEVRVPNLDCEGCASKCKRA 24 (136)
Q Consensus 1 ~~~~v~~~v~~m~C~~C~~~v~~~ 24 (136)
|++.+ +-- .+.|+.|+..++..
T Consensus 1 mskp~-lfg-sn~Cpdca~a~eyl 22 (85)
T COG4545 1 MSKPK-LFG-SNLCPDCAPAVEYL 22 (85)
T ss_pred CCCce-eec-cccCcchHHHHHHH
Confidence 44543 333 68999999877664
No 57
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=20.35 E-value=1.2e+02 Score=18.78 Aligned_cols=22 Identities=32% Similarity=0.548 Sum_probs=18.7
Q ss_pred hHHHHHHHHHhCCCCeeEEEEe
Q 047678 16 GCASKCKRALFKLKGVEEVEIE 37 (136)
Q Consensus 16 ~C~~~v~~~l~~~~gv~~v~vd 37 (136)
+-...++.++++++||.++++-
T Consensus 62 g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEE
Confidence 4457899999999999999874
Done!