Query 032155
Match_columns 146
No_of_seqs 204 out of 1659
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 10:19:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032155.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032155hhsearch_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 6.3E-12 1.4E-16 76.7 8.5 58 27-84 1-62 (62)
2 KOG4656 Copper chaperone for s 99.3 1.7E-12 3.8E-17 95.7 6.0 74 24-97 7-80 (247)
3 KOG1603 Copper chaperone [Inor 99.3 1.2E-11 2.6E-16 78.3 8.9 68 22-89 3-71 (73)
4 COG2608 CopZ Copper chaperone 99.2 1.1E-10 2.4E-15 73.5 9.0 65 24-88 2-70 (71)
5 PLN02957 copper, zinc superoxi 98.4 6E-06 1.3E-10 63.3 10.7 72 23-94 5-76 (238)
6 PRK10671 copA copper exporting 98.1 9.6E-06 2.1E-10 72.0 8.3 64 24-89 3-67 (834)
7 COG2217 ZntA Cation transport 97.7 0.00013 2.8E-09 63.8 7.9 63 24-87 2-69 (713)
8 TIGR00003 copper ion binding p 97.6 0.0011 2.4E-08 37.8 8.5 60 25-84 3-66 (68)
9 KOG0207 Cation transport ATPas 97.4 0.00072 1.6E-08 59.9 8.2 68 24-91 146-217 (951)
10 PRK10671 copA copper exporting 96.7 0.007 1.5E-07 54.1 8.1 63 25-87 100-163 (834)
11 KOG0207 Cation transport ATPas 96.6 0.0078 1.7E-07 53.6 7.0 66 25-90 70-139 (951)
12 PRK11033 zntA zinc/cadmium/mer 96.0 0.032 7E-07 49.4 7.9 65 23-87 52-118 (741)
13 TIGR02052 MerP mercuric transp 91.5 2.1 4.5E-05 26.2 9.2 63 25-87 24-90 (92)
14 PRK13748 putative mercuric red 82.7 11 0.00023 32.1 8.7 63 27-89 3-68 (561)
15 COG1888 Uncharacterized protei 82.6 11 0.00024 24.7 7.5 65 23-87 5-78 (97)
16 PF01206 TusA: Sulfurtransfera 75.1 15 0.00033 22.0 6.1 53 27-88 2-57 (70)
17 cd00371 HMA Heavy-metal-associ 74.4 8.9 0.00019 19.0 7.3 38 29-66 3-41 (63)
18 PF02680 DUF211: Uncharacteriz 70.5 28 0.0006 23.0 7.7 65 22-87 3-76 (95)
19 PF01883 DUF59: Domain of unkn 63.4 17 0.00038 21.9 4.0 20 37-56 53-72 (72)
20 PRK10553 assembly protein for 62.0 40 0.00087 21.8 6.2 45 35-79 16-61 (87)
21 PRK11198 LysM domain/BON super 56.6 49 0.0011 23.3 5.8 66 1-80 1-71 (147)
22 PRK11018 hypothetical protein; 50.1 61 0.0013 20.2 6.4 53 26-87 9-64 (78)
23 PF03927 NapD: NapD protein; 49.6 63 0.0014 20.2 6.4 43 37-80 16-59 (79)
24 cd03421 SirA_like_N SirA_like_ 46.9 60 0.0013 19.2 5.4 52 28-89 2-56 (67)
25 PF14437 MafB19-deam: MafB19-l 44.6 76 0.0016 22.7 5.1 40 23-63 99-140 (146)
26 cd03420 SirA_RHOD_Pry_redox Si 42.0 77 0.0017 19.0 5.6 52 28-88 2-56 (69)
27 PF04805 Pox_E10: E10-like pro 39.8 25 0.00053 21.7 1.8 25 31-55 15-39 (70)
28 KOG3411 40S ribosomal protein 38.5 31 0.00068 24.2 2.3 49 33-81 92-141 (143)
29 PRK14054 methionine sulfoxide 34.3 1.7E+02 0.0038 21.3 5.8 27 35-61 10-36 (172)
30 cd04888 ACT_PheB-BS C-terminal 32.5 1.1E+02 0.0024 18.0 5.1 33 24-56 41-74 (76)
31 PF04972 BON: BON domain; Int 32.0 39 0.00085 19.6 1.8 31 40-71 3-36 (64)
32 cd03422 YedF YedF is a bacteri 30.7 1.2E+02 0.0027 18.1 5.5 51 29-88 3-56 (69)
33 PHA03005 sulfhydryl oxidase; P 29.0 46 0.00099 21.9 1.8 25 31-55 40-64 (96)
34 PF09580 Spore_YhcN_YlaJ: Spor 28.5 2.2E+02 0.0047 20.2 5.7 33 34-66 73-105 (177)
35 TIGR03406 FeS_long_SufT probab 28.2 90 0.0019 22.8 3.5 21 39-59 134-154 (174)
36 PF08712 Nfu_N: Scaffold prote 28.1 1.6E+02 0.0036 18.7 5.8 41 39-81 37-79 (87)
37 PF13732 DUF4162: Domain of un 27.7 1.5E+02 0.0032 18.0 5.5 42 45-88 26-69 (84)
38 PF02672 CP12: CP12 domain; I 27.6 12 0.00027 23.2 -1.0 15 131-145 52-68 (71)
39 cd00291 SirA_YedF_YeeD SirA, Y 26.6 1.4E+02 0.003 17.4 6.0 52 28-88 2-56 (69)
40 PF11047 SopD: Salmonella oute 26.1 21 0.00045 28.4 -0.2 21 1-21 34-54 (319)
41 cd03423 SirA SirA (also known 26.1 1.5E+02 0.0033 17.6 6.0 52 29-89 3-57 (69)
42 COG0425 SirA Predicted redox p 25.6 1.4E+02 0.003 18.6 3.6 49 25-82 5-56 (78)
43 PF13291 ACT_4: ACT domain; PD 24.9 1.7E+02 0.0036 17.6 4.6 35 21-55 45-79 (80)
44 TIGR00489 aEF-1_beta translati 24.0 93 0.002 20.1 2.6 23 35-57 61-83 (88)
45 cd04877 ACT_TyrR N-terminal AC 23.4 1.8E+02 0.0038 17.4 3.8 18 38-55 51-68 (74)
46 COG2092 EFB1 Translation elong 21.4 1.8E+02 0.004 18.9 3.5 32 26-57 51-83 (88)
47 PRK05528 methionine sulfoxide 20.4 1.4E+02 0.0031 21.4 3.2 26 35-60 8-33 (156)
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=99.37 E-value=6.3e-12 Score=76.69 Aligned_cols=58 Identities=33% Similarity=0.620 Sum_probs=53.6
Q ss_pred EEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEec---CCHHHHHHHHHhcCCc
Q 032155 27 EIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGY---VEPNKVLKRVKSTGKR 84 (146)
Q Consensus 27 ~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~---~d~~~i~~~i~~~G~~ 84 (146)
+|+| +|+|++|..+|+++|.+++||.++.+|+..++++|.+. .+.++|.++|+++||+
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 5789 99999999999999999999999999999999999965 4569999999999984
No 2
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.35 E-value=1.7e-12 Score=95.75 Aligned_cols=74 Identities=28% Similarity=0.451 Sum_probs=69.1
Q ss_pred eEEEEEEcCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEecCCHHHHHHHHHhcCCceEEecCCCCcccc
Q 032155 24 QTVEIKVKMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGYVEPNKVLKRVKSTGKRAEFWPYIPQHLVH 97 (146)
Q Consensus 24 ~~v~l~V~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~~d~~~i~~~i~~~G~~a~~~~~~~~~~~~ 97 (146)
-+.+|.|.|+|++|+..|++.|..++||.++++|++++.+.|.+...+.+|...|+.+|.+|.+.+.+..+.+.
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~psava 80 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKPSAVA 80 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCchhHHH
Confidence 46799999999999999999999999999999999999999999999999999999999999999987766543
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.34 E-value=1.2e-11 Score=78.26 Aligned_cols=68 Identities=50% Similarity=0.946 Sum_probs=62.5
Q ss_pred CceEEEEEEcCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEecCCHHHHHHHHHhcC-CceEEec
Q 032155 22 AMQTVEIKVKMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGYVEPNKVLKRVKSTG-KRAEFWP 89 (146)
Q Consensus 22 ~~~~v~l~V~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~~d~~~i~~~i~~~G-~~a~~~~ 89 (146)
..+..++++.|+|++|..+|++.|..++||.++.+|...++++|.|.+++..|++.+++.+ +++++|.
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 3466788899999999999999999999999999999999999999999999999999888 7777764
No 4
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.24 E-value=1.1e-10 Score=73.46 Aligned_cols=65 Identities=26% Similarity=0.502 Sum_probs=57.8
Q ss_pred eEEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEE--e-cCCHHHHHHHHHhcCCceEEe
Q 032155 24 QTVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVS--G-YVEPNKVLKRVKSTGKRAEFW 88 (146)
Q Consensus 24 ~~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~--g-~~d~~~i~~~i~~~G~~a~~~ 88 (146)
.+..|++ +|+|.+|+.+|+++|.+++||.++++++..+.+.|. + .++.++|.+++..+||.+..+
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 4678999 999999999999999999999999999999666665 4 489999999999999987653
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.37 E-value=6e-06 Score=63.32 Aligned_cols=72 Identities=29% Similarity=0.446 Sum_probs=63.5
Q ss_pred ceEEEEEEcCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEecCCHHHHHHHHHhcCCceEEecCCCCc
Q 032155 23 MQTVEIKVKMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGYVEPNKVLKRVKSTGKRAEFWPYIPQH 94 (146)
Q Consensus 23 ~~~v~l~V~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~~d~~~i~~~i~~~G~~a~~~~~~~~~ 94 (146)
.+++++.++|.|+.|..++++.|.+++||..+.+++..+++.|........+.+.+++.|+.+++++....+
T Consensus 5 ~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 5 ELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred cEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 356778889999999999999999999999999999999999987778889999999999999888765443
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.14 E-value=9.6e-06 Score=72.05 Aligned_cols=64 Identities=22% Similarity=0.470 Sum_probs=56.8
Q ss_pred eEEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEecCCHHHHHHHHHhcCCceEEec
Q 032155 24 QTVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGYVEPNKVLKRVKSTGKRAEFWP 89 (146)
Q Consensus 24 ~~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~~d~~~i~~~i~~~G~~a~~~~ 89 (146)
+++.+.| +|+|.+|..+|+++|.+++||.++++++. +..+.+..+.+.+.+.+++.|+.++...
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 5689999 99999999999999999999999999984 5566666789999999999999988753
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.73 E-value=0.00013 Score=63.84 Aligned_cols=63 Identities=30% Similarity=0.557 Sum_probs=55.7
Q ss_pred eEEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEec---CC-HHHHHHHHHhcCCceEE
Q 032155 24 QTVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGY---VE-PNKVLKRVKSTGKRAEF 87 (146)
Q Consensus 24 ~~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~---~d-~~~i~~~i~~~G~~a~~ 87 (146)
.+..|.+ ||+|..|..+|+ +|.+++||....+++..+++.|... .+ .+.+...++..|+.+..
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 3568999 999999999999 9999999999999999999998833 45 78999999999997765
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=97.61 E-value=0.0011 Score=37.80 Aligned_cols=60 Identities=20% Similarity=0.395 Sum_probs=48.4
Q ss_pred EEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEe---cCCHHHHHHHHHhcCCc
Q 032155 25 TVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSG---YVEPNKVLKRVKSTGKR 84 (146)
Q Consensus 25 ~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g---~~d~~~i~~~i~~~G~~ 84 (146)
+..+.+ ++.|..|...+++.+....++....+++....+.+.. ..+...+...+...|+.
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYE 66 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCC
Confidence 457899 9999999999999999999999999998888877763 24666676666666653
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.42 E-value=0.00072 Score=59.94 Aligned_cols=68 Identities=26% Similarity=0.505 Sum_probs=61.9
Q ss_pred eEEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEe---cCCHHHHHHHHHhcCCceEEecCC
Q 032155 24 QTVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSG---YVEPNKVLKRVKSTGKRAEFWPYI 91 (146)
Q Consensus 24 ~~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g---~~d~~~i~~~i~~~G~~a~~~~~~ 91 (146)
.+++|.| +|.|..|+.++++.|.+++||.++++++..+++.|.- ...+.++.+.++.+|+.+...++.
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~ 217 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYG 217 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeecc
Confidence 6789999 9999999999999999999999999999999999873 389999999999999998877643
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.74 E-value=0.007 Score=54.08 Aligned_cols=63 Identities=30% Similarity=0.523 Sum_probs=54.7
Q ss_pred EEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEecCCHHHHHHHHHhcCCceEE
Q 032155 25 TVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGYVEPNKVLKRVKSTGKRAEF 87 (146)
Q Consensus 25 ~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~~d~~~i~~~i~~~G~~a~~ 87 (146)
++.+.+ +|+|..|...+++.+.+++||..+.+++..++..+.+..+...+.+.+++.|+.+.+
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~ 163 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEA 163 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccc
Confidence 567889 999999999999999999999999999988888777556778888888888887654
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.58 E-value=0.0078 Score=53.64 Aligned_cols=66 Identities=21% Similarity=0.391 Sum_probs=59.0
Q ss_pred EEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEE--e-cCCHHHHHHHHHhcCCceEEecC
Q 032155 25 TVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVS--G-YVEPNKVLKRVKSTGKRAEFWPY 90 (146)
Q Consensus 25 ~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~--g-~~d~~~i~~~i~~~G~~a~~~~~ 90 (146)
+-.+.+ ||+|..|+..+++.|++++|+.++.+.+...+..+. + ...++.+.+.+++.|+.+++...
T Consensus 70 ~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~ 139 (951)
T KOG0207|consen 70 KCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIES 139 (951)
T ss_pred eeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhc
Confidence 568999 999999999999999999999999999999888887 2 37889999999999999887653
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.01 E-value=0.032 Score=49.39 Aligned_cols=65 Identities=29% Similarity=0.374 Sum_probs=51.3
Q ss_pred ceEEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEec-CCHHHHHHHHHhcCCceEE
Q 032155 23 MQTVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGY-VEPNKVLKRVKSTGKRAEF 87 (146)
Q Consensus 23 ~~~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~-~d~~~i~~~i~~~G~~a~~ 87 (146)
..+..+.+ +|+|..|..++++.+...+||..+.++....++.+... .....+.+.++..|+.+..
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~ 118 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRD 118 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhccccccc
Confidence 34677889 99999999999999999999999999998888777622 1225666777777876543
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=91.55 E-value=2.1 Score=26.23 Aligned_cols=63 Identities=24% Similarity=0.390 Sum_probs=44.6
Q ss_pred EEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEE--e-cCCHHHHHHHHHhcCCceEE
Q 032155 25 TVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVS--G-YVEPNKVLKRVKSTGKRAEF 87 (146)
Q Consensus 25 ~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~--g-~~d~~~i~~~i~~~G~~a~~ 87 (146)
++.+.+ ++.|..|...++..+....++.....+.......+. . ..+...+...+.+.|+.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 346778 999999999999999999998877777666665443 1 23555555555666666544
No 14
>PRK13748 putative mercuric reductase; Provisional
Probab=82.73 E-value=11 Score=32.11 Aligned_cols=63 Identities=27% Similarity=0.479 Sum_probs=46.5
Q ss_pred EEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEe--cCCHHHHHHHHHhcCCceEEec
Q 032155 27 EIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSG--YVEPNKVLKRVKSTGKRAEFWP 89 (146)
Q Consensus 27 ~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g--~~d~~~i~~~i~~~G~~a~~~~ 89 (146)
.+.+ ++.|..|..+++..+...+++....++.......+.. ..+...+...+...|+..+...
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~ 68 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLAD 68 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccC
Confidence 4667 9999999999999999999988888887777765552 2355556566666776655444
No 15
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=82.64 E-value=11 Score=24.69 Aligned_cols=65 Identities=12% Similarity=0.264 Sum_probs=43.0
Q ss_pred ceEEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEec-------CCCEEEEEec-CCHHHHHHHHHhcCCceEE
Q 032155 23 MQTVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNR-------KQSRVTVSGY-VEPNKVLKRVKSTGKRAEF 87 (146)
Q Consensus 23 ~~~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~-------~~~~v~V~g~-~d~~~i~~~i~~~G~~a~~ 87 (146)
..++.|.+ --+-.--.--+-+.|++++||..|++.. .+-+++|.|. ++.+++.+.|++.|....-
T Consensus 5 iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHS 78 (97)
T COG1888 5 IRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHS 78 (97)
T ss_pred ceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeee
Confidence 45566666 3333333334556688888887776643 2234556675 9999999999999976543
No 16
>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=75.10 E-value=15 Score=22.00 Aligned_cols=53 Identities=9% Similarity=0.085 Sum_probs=38.0
Q ss_pred EEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEec--CCHHHHHHHHHhcCCceEEe
Q 032155 27 EIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGY--VEPNKVLKRVKSTGKRAEFW 88 (146)
Q Consensus 27 ~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~--~d~~~i~~~i~~~G~~a~~~ 88 (146)
++.+ |..|+...-+++++|.+++. .+.+.|..+ .....|..-++..|+....+
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 5677 99999999999999998733 345555533 45577888889999875544
No 17
>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=74.38 E-value=8.9 Score=18.95 Aligned_cols=38 Identities=37% Similarity=0.732 Sum_probs=28.3
Q ss_pred EE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEE
Q 032155 29 KV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVS 66 (146)
Q Consensus 29 ~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~ 66 (146)
.+ ++.|..|...++..+....++.............+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVE 41 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEE
Confidence 45 788999999999888888887766666655554443
No 18
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=70.51 E-value=28 Score=22.98 Aligned_cols=65 Identities=14% Similarity=0.310 Sum_probs=41.9
Q ss_pred CceEEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEec-----CCC--EEEEEec-CCHHHHHHHHHhcCCceEE
Q 032155 22 AMQTVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNR-----KQS--RVTVSGY-VEPNKVLKRVKSTGKRAEF 87 (146)
Q Consensus 22 ~~~~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~-----~~~--~v~V~g~-~d~~~i~~~i~~~G~~a~~ 87 (146)
...++.|.| -.+-+. .-.+-+.|.+++||..+++.. ... +++|+|. ++.+.+.+.|++.|....-
T Consensus 3 ~irRlVLDVlKP~~p~-i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHS 76 (95)
T PF02680_consen 3 GIRRLVLDVLKPHEPS-IVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHS 76 (95)
T ss_dssp SEEEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEE
T ss_pred ceeEEEEEeecCCCCC-HHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEe
Confidence 345667777 333333 335566789999998887754 222 2345576 8999999999999976543
No 19
>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=63.40 E-value=17 Score=21.92 Aligned_cols=20 Identities=35% Similarity=0.635 Sum_probs=15.2
Q ss_pred HHHHHHHHHhCCCCceEEEE
Q 032155 37 CERRVKNAVNSMKGVKSVEV 56 (146)
Q Consensus 37 C~~~v~~~l~~~~GV~~v~v 56 (146)
=...++++|..++|+.+++|
T Consensus 53 l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 53 LREEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHHhCCCCceEeC
Confidence 34677888999999988875
No 20
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=62.03 E-value=40 Score=21.75 Aligned_cols=45 Identities=9% Similarity=0.182 Sum_probs=31.8
Q ss_pred HhHHHHHHHHHhCCCCceEEEEecCCCEEEEEe-cCCHHHHHHHHH
Q 032155 35 DGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSG-YVEPNKVLKRVK 79 (146)
Q Consensus 35 ~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g-~~d~~~i~~~i~ 79 (146)
+.=...|.+.|..++|+.-...|.+.+|+.|+- ..+...+.+.+.
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 334668899999999998777776778888773 345555555554
No 21
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=56.61 E-value=49 Score=23.28 Aligned_cols=66 Identities=17% Similarity=0.316 Sum_probs=39.9
Q ss_pred Ccchhhhhcc----cccCcchhccCCceEEEEEEcCcCHhHHHHHHHHHhCC-CCceEEEEecCCCEEEEEecCCHHHHH
Q 032155 1 MGALDYLSNF----CTVTSTRSKRKAMQTVEIKVKMDCDGCERRVKNAVNSM-KGVKSVEVNRKQSRVTVSGYVEPNKVL 75 (146)
Q Consensus 1 ~~~~~~~~~~----~~~~~~~~~~~~~~~v~l~V~m~C~~C~~~v~~~l~~~-~GV~~v~vd~~~~~v~V~g~~d~~~i~ 75 (146)
||+++|+-++ |.....+ . .-+.-...|.+.|.+. -+...+++....+.|++.|.+......
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~-~-------------~~~~~~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~ 66 (147)
T PRK11198 1 MGLFSFVKEAGEKLFDAVTAQ-A-------------DNEDAADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAK 66 (147)
T ss_pred CcHHHHHHHHHHHhcCCCCcc-c-------------chHHHHHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHH
Confidence 8999999864 3322111 0 1144556677777542 234456666678999999986665555
Q ss_pred HHHHh
Q 032155 76 KRVKS 80 (146)
Q Consensus 76 ~~i~~ 80 (146)
.++..
T Consensus 67 ~~~~~ 71 (147)
T PRK11198 67 EKILL 71 (147)
T ss_pred HHHHH
Confidence 55543
No 22
>PRK11018 hypothetical protein; Provisional
Probab=50.13 E-value=61 Score=20.15 Aligned_cols=53 Identities=11% Similarity=0.045 Sum_probs=39.2
Q ss_pred EEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEec--CCHHHHHHHHHhcCCceEE
Q 032155 26 VEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGY--VEPNKVLKRVKSTGKRAEF 87 (146)
Q Consensus 26 v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~--~d~~~i~~~i~~~G~~a~~ 87 (146)
.++.+ |..|+.-.-+.+++|.+++. .+.+.|..+ .....|..-++..|+.+..
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 57888 99999999999999988743 234444432 4556788888889988654
No 23
>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=49.61 E-value=63 Score=20.24 Aligned_cols=43 Identities=14% Similarity=0.258 Sum_probs=30.8
Q ss_pred HHHHHHHHHhCCCCceEEEEecCCCEEEEE-ecCCHHHHHHHHHh
Q 032155 37 CERRVKNAVNSMKGVKSVEVNRKQSRVTVS-GYVEPNKVLKRVKS 80 (146)
Q Consensus 37 C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~-g~~d~~~i~~~i~~ 80 (146)
=...+...|.+++|+.-...+.. +++.|+ ...+...+.+.+..
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHH
Confidence 34578899999999976666644 888776 33566777776664
No 24
>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=46.91 E-value=60 Score=19.20 Aligned_cols=52 Identities=17% Similarity=0.201 Sum_probs=35.7
Q ss_pred EEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEec--CCHHHHHHHHHhcCCceEEec
Q 032155 28 IKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGY--VEPNKVLKRVKSTGKRAEFWP 89 (146)
Q Consensus 28 l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~--~d~~~i~~~i~~~G~~a~~~~ 89 (146)
+.+ |+.|+.-.-+++++| ++.. .+.+.|..+ .....|..-+++.|+..+...
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~~~~~~ 56 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYEVSVEE 56 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCEEEEEe
Confidence 456 889999999999998 5422 234444433 445678888889999875443
No 25
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=44.64 E-value=76 Score=22.65 Aligned_cols=40 Identities=18% Similarity=0.430 Sum_probs=29.8
Q ss_pred ceEEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecC-CCEE
Q 032155 23 MQTVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRK-QSRV 63 (146)
Q Consensus 23 ~~~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~-~~~v 63 (146)
-..+++.| .-.|..|..-|.....++ |+.++.|... .+++
T Consensus 99 g~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~ 140 (146)
T PF14437_consen 99 GRSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKV 140 (146)
T ss_pred CCeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcE
Confidence 34678888 778999998888877764 8887877755 4433
No 26
>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=42.00 E-value=77 Score=19.03 Aligned_cols=52 Identities=15% Similarity=0.236 Sum_probs=37.1
Q ss_pred EEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEec--CCHHHHHHHHHhcCCceEEe
Q 032155 28 IKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGY--VEPNKVLKRVKSTGKRAEFW 88 (146)
Q Consensus 28 l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~--~d~~~i~~~i~~~G~~a~~~ 88 (146)
+.+ |+.|+.=.-+++++|.+++. .+.+.|... .....|..-.+..|+.....
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 456 88999999999999988742 334444432 45577888888899887643
No 27
>PF04805 Pox_E10: E10-like protein conserved region; InterPro: IPR006890 This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process
Probab=39.79 E-value=25 Score=21.73 Aligned_cols=25 Identities=20% Similarity=0.418 Sum_probs=19.4
Q ss_pred cCcCHhHHHHHHHHHhCCCCceEEE
Q 032155 31 KMDCDGCERRVKNAVNSMKGVKSVE 55 (146)
Q Consensus 31 ~m~C~~C~~~v~~~l~~~~GV~~v~ 55 (146)
.+.|..|..+..+++.+-.=+++-+
T Consensus 15 tLPC~~Cr~HA~~ai~kNNiMSs~D 39 (70)
T PF04805_consen 15 TLPCPECRIHAKEAIQKNNIMSSND 39 (70)
T ss_pred cCCCHHHHHHHHHHHHhcCccccCC
Confidence 5789999999999998765554433
No 28
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=38.49 E-value=31 Score=24.19 Aligned_cols=49 Identities=16% Similarity=0.334 Sum_probs=29.5
Q ss_pred cCHhHHHHHHHHHhCCCCceEEEEecCCC-EEEEEecCCHHHHHHHHHhc
Q 032155 33 DCDGCERRVKNAVNSMKGVKSVEVNRKQS-RVTVSGYVEPNKVLKRVKST 81 (146)
Q Consensus 33 ~C~~C~~~v~~~l~~~~GV~~v~vd~~~~-~v~V~g~~d~~~i~~~i~~~ 81 (146)
.|.+.....+++|+.++.+.-|+.+...+ +++-.|.-|.+.|...++..
T Consensus 92 ~~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~~ 141 (143)
T KOG3411|consen 92 FCDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRIAGQIREE 141 (143)
T ss_pred hhccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHHHHHHHhc
Confidence 34443334444444445555567776554 44455888999998888753
No 29
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=34.26 E-value=1.7e+02 Score=21.31 Aligned_cols=27 Identities=26% Similarity=0.414 Sum_probs=21.8
Q ss_pred HhHHHHHHHHHhCCCCceEEEEecCCC
Q 032155 35 DGCERRVKNAVNSMKGVKSVEVNRKQS 61 (146)
Q Consensus 35 ~~C~~~v~~~l~~~~GV~~v~vd~~~~ 61 (146)
.+|-.-++..+.+++||.++.+-...+
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG 36 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGG 36 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCC
Confidence 567777888899999999998876554
No 30
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=32.50 E-value=1.1e+02 Score=18.00 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=24.1
Q ss_pred eEEEEEEcCcCHh-HHHHHHHHHhCCCCceEEEE
Q 032155 24 QTVEIKVKMDCDG-CERRVKNAVNSMKGVKSVEV 56 (146)
Q Consensus 24 ~~v~l~V~m~C~~-C~~~v~~~l~~~~GV~~v~v 56 (146)
..+.|.+...-.. --..+.+.|++++||.+|.+
T Consensus 41 ~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 41 ANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 4455666444444 77888999999999998875
No 31
>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=32.03 E-value=39 Score=19.61 Aligned_cols=31 Identities=26% Similarity=0.424 Sum_probs=15.0
Q ss_pred HHHHHHhC---CCCceEEEEecCCCEEEEEecCCH
Q 032155 40 RVKNAVNS---MKGVKSVEVNRKQSRVTVSGYVEP 71 (146)
Q Consensus 40 ~v~~~l~~---~~GV~~v~vd~~~~~v~V~g~~d~ 71 (146)
+|+..|.. +++. ++.+....+.+.+.|.++.
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~s 36 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGEVPS 36 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEEESS
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEeeCcH
Confidence 45555555 3333 5677777888888887533
No 32
>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=30.73 E-value=1.2e+02 Score=18.11 Aligned_cols=51 Identities=14% Similarity=0.056 Sum_probs=36.1
Q ss_pred EE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEe--cCCHHHHHHHHHhcCCceEEe
Q 032155 29 KV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSG--YVEPNKVLKRVKSTGKRAEFW 88 (146)
Q Consensus 29 ~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g--~~d~~~i~~~i~~~G~~a~~~ 88 (146)
.+ |..|+.=.-+.+++|+++.. .+.+.|.. ......|..-++..|+.+...
T Consensus 3 D~rG~~CP~Pvi~~kkal~~l~~---------G~~l~V~~d~~~s~~ni~~~~~~~g~~v~~~ 56 (69)
T cd03422 3 DLRGEPCPYPAIATLEALPSLKP---------GEILEVISDCPQSINNIPIDARNHGYKVLAI 56 (69)
T ss_pred ccCCCcCCHHHHHHHHHHHcCCC---------CCEEEEEecCchHHHHHHHHHHHcCCEEEEE
Confidence 45 78899999999999988742 33444442 356677888888899887543
No 33
>PHA03005 sulfhydryl oxidase; Provisional
Probab=28.96 E-value=46 Score=21.91 Aligned_cols=25 Identities=24% Similarity=0.533 Sum_probs=19.3
Q ss_pred cCcCHhHHHHHHHHHhCCCCceEEE
Q 032155 31 KMDCDGCERRVKNAVNSMKGVKSVE 55 (146)
Q Consensus 31 ~m~C~~C~~~v~~~l~~~~GV~~v~ 55 (146)
-+.|..|..+..+++.+-.=+++-+
T Consensus 40 tLPC~~Cr~HA~~ai~knnimSs~d 64 (96)
T PHA03005 40 TLPCPACRRHAKEAIEKNNIMSSND 64 (96)
T ss_pred cCCCHHHHHHHHHHHhhcCccccCC
Confidence 6899999999999998754444333
No 34
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=28.52 E-value=2.2e+02 Score=20.21 Aligned_cols=33 Identities=21% Similarity=0.276 Sum_probs=27.7
Q ss_pred CHhHHHHHHHHHhCCCCceEEEEecCCCEEEEE
Q 032155 34 CDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVS 66 (146)
Q Consensus 34 C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~ 66 (146)
-..=...|.+.+.+++||.++.+-.....+.|.
T Consensus 73 ~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 73 RQQLADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 355778889999999999999998888887765
No 35
>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=28.20 E-value=90 Score=22.81 Aligned_cols=21 Identities=29% Similarity=0.333 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCCceEEEEecC
Q 032155 39 RRVKNAVNSMKGVKSVEVNRK 59 (146)
Q Consensus 39 ~~v~~~l~~~~GV~~v~vd~~ 59 (146)
..++.+|.+++||.++++++.
T Consensus 134 ~dV~~aL~~l~gV~~V~V~l~ 154 (174)
T TIGR03406 134 EDVEDKVLAVPNVDEVEVELV 154 (174)
T ss_pred HHHHHHHHhCCCceeEEEEEE
Confidence 457888999999988887743
No 36
>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=28.15 E-value=1.6e+02 Score=18.69 Aligned_cols=41 Identities=20% Similarity=0.266 Sum_probs=29.1
Q ss_pred HHHHHHHhCCCCceEEEEecCCCEEEEE--ecCCHHHHHHHHHhc
Q 032155 39 RRVKNAVNSMKGVKSVEVNRKQSRVTVS--GYVEPNKVLKRVKST 81 (146)
Q Consensus 39 ~~v~~~l~~~~GV~~v~vd~~~~~v~V~--g~~d~~~i~~~i~~~ 81 (146)
.-+-+.|-.++||.+|-+. .+=++|+ ...+++.|...|...
T Consensus 37 spLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHHHH
Confidence 3444556699999988876 6677777 458999998888753
No 37
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=27.69 E-value=1.5e+02 Score=18.03 Aligned_cols=42 Identities=19% Similarity=0.367 Sum_probs=29.5
Q ss_pred HhCCCCceEEEEecCCCEEE--EEecCCHHHHHHHHHhcCCceEEe
Q 032155 45 VNSMKGVKSVEVNRKQSRVT--VSGYVEPNKVLKRVKSTGKRAEFW 88 (146)
Q Consensus 45 l~~~~GV~~v~vd~~~~~v~--V~g~~d~~~i~~~i~~~G~~a~~~ 88 (146)
|..++||..+.... .+.+. +.......+|+..+...|. ..-.
T Consensus 26 l~~~~~v~~v~~~~-~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f 69 (84)
T PF13732_consen 26 LEELPGVESVEQDG-DGKLRIKLEDEETANELLQELIEKGI-IRSF 69 (84)
T ss_pred HhhCCCeEEEEEeC-CcEEEEEECCcccHHHHHHHHHhCCC-eeEE
Confidence 77789999888653 44344 4445677889999998887 4433
No 38
>PF02672 CP12: CP12 domain; InterPro: IPR003823 This entry represents an uncharacterised domain in proteins of unknown function. This domain is found associated with CBS domains in some proteins IPR000644 from INTERPRO.; PDB: 3B1K_I 3B1J_D 3RVD_N 3QV1_I 2LJ9_A.
Probab=27.57 E-value=12 Score=23.23 Aligned_cols=15 Identities=27% Similarity=0.773 Sum_probs=12.0
Q ss_pred CCCCCcCCCCCC--ccc
Q 032155 131 LVSIFSDDNVNA--CSI 145 (146)
Q Consensus 131 ~~~~fsd~np~~--Csi 145 (146)
....|+++||.| |.|
T Consensus 52 ~lE~yC~~nPea~Ecrv 68 (71)
T PF02672_consen 52 PLELYCDENPEADECRV 68 (71)
T ss_dssp CHHHHHHHSTTSTTTTT
T ss_pred HHHHHHHHCCCcHHhhh
Confidence 357899999998 765
No 39
>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=26.63 E-value=1.4e+02 Score=17.38 Aligned_cols=52 Identities=15% Similarity=0.105 Sum_probs=36.2
Q ss_pred EEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEec--CCHHHHHHHHHhcCCceEEe
Q 032155 28 IKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGY--VEPNKVLKRVKSTGKRAEFW 88 (146)
Q Consensus 28 l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~--~d~~~i~~~i~~~G~~a~~~ 88 (146)
+.+ |+.|+.=.-+++++|.++.. .+.+.|... .....|..-++..|+.....
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~---------g~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~ 56 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKS---------GEVLEVLLDDPGAVEDIPAWAKETGHEVLEV 56 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCC---------CCEEEEEecCCcHHHHHHHHHHHcCCEEEEE
Confidence 345 78899888889999887632 344444433 45777888888999886543
No 40
>PF11047 SopD: Salmonella outer protein D; InterPro: IPR022747 The proteins in this entry are also known as secreted effector proteins. Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. They contribute to the formation of Salmonella-induced filaments (Sifs) in infected epithelial cells and to replication in macrophages []. SopD is a type III virulence effector protein whose structure consists of 38% alpha-helix and 26% beta-strand [].; GO: 0009405 pathogenesis, 0033644 host cell membrane
Probab=26.15 E-value=21 Score=28.36 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=18.0
Q ss_pred CcchhhhhcccccCcchhccC
Q 032155 1 MGALDYLSNFCTVTSTRSKRK 21 (146)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~ 21 (146)
||+||.+-|+|-+++|++..+
T Consensus 34 MGlWDKfKD~FRseKK~EALe 54 (319)
T PF11047_consen 34 MGLWDKFKDWFRSEKKQEALE 54 (319)
T ss_pred hhhHHHHHHHHhcccHHHHHH
Confidence 899999999999988877543
No 41
>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=26.10 E-value=1.5e+02 Score=17.64 Aligned_cols=52 Identities=13% Similarity=0.061 Sum_probs=36.5
Q ss_pred EE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEe--cCCHHHHHHHHHhcCCceEEec
Q 032155 29 KV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSG--YVEPNKVLKRVKSTGKRAEFWP 89 (146)
Q Consensus 29 ~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g--~~d~~~i~~~i~~~G~~a~~~~ 89 (146)
.+ |..|+.=.-+++++|.+++- .+.+.|.. ......|..-++..|+.+....
T Consensus 3 D~~G~~CP~P~i~~k~~l~~l~~---------G~~l~V~~dd~~s~~di~~~~~~~g~~~~~~~ 57 (69)
T cd03423 3 DTRGLRCPEPVMMLHKKVRKMKP---------GDTLLVLATDPSTTRDIPKFCTFLGHELLAQE 57 (69)
T ss_pred cccCCcCCHHHHHHHHHHHcCCC---------CCEEEEEeCCCchHHHHHHHHHHcCCEEEEEE
Confidence 45 78899988999999988732 23444442 3566778888889998876443
No 42
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=25.64 E-value=1.4e+02 Score=18.65 Aligned_cols=49 Identities=16% Similarity=0.230 Sum_probs=33.8
Q ss_pred EEEEEE-cCcCHhHHHHHHHHHhCCCCceEEEEecCCCEEEEEec--CCHHHHHHHHHhcC
Q 032155 25 TVEIKV-KMDCDGCERRVKNAVNSMKGVKSVEVNRKQSRVTVSGY--VEPNKVLKRVKSTG 82 (146)
Q Consensus 25 ~v~l~V-~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~V~g~--~d~~~i~~~i~~~G 82 (146)
..+|.+ |+.|+.=.-.++++|++++- .+.+.|..+ .....|..-.++.|
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~~dIp~~~~~~~ 56 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAKEDIPAWAKKEG 56 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchHHHHHHHHHHcC
Confidence 467889 99999999999999998733 345555533 33455655556455
No 43
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=24.88 E-value=1.7e+02 Score=17.64 Aligned_cols=35 Identities=17% Similarity=0.235 Sum_probs=24.9
Q ss_pred CCceEEEEEEcCcCHhHHHHHHHHHhCCCCceEEE
Q 032155 21 KAMQTVEIKVKMDCDGCERRVKNAVNSMKGVKSVE 55 (146)
Q Consensus 21 ~~~~~v~l~V~m~C~~C~~~v~~~l~~~~GV~~v~ 55 (146)
.....+.|.+......=-..+.+.|++++||.+|.
T Consensus 45 ~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 45 DGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp TTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred CCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 34455666665556666678888899999998774
No 44
>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=24.02 E-value=93 Score=20.13 Aligned_cols=23 Identities=30% Similarity=0.601 Sum_probs=20.0
Q ss_pred HhHHHHHHHHHhCCCCceEEEEe
Q 032155 35 DGCERRVKNAVNSMKGVKSVEVN 57 (146)
Q Consensus 35 ~~C~~~v~~~l~~~~GV~~v~vd 57 (146)
.+-...++.++++++||+++++.
T Consensus 61 ~g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 61 EGGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred CcChHHHHHHHhcCCCccEEEEE
Confidence 46678999999999999999875
No 45
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=23.41 E-value=1.8e+02 Score=17.37 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=10.3
Q ss_pred HHHHHHHHhCCCCceEEE
Q 032155 38 ERRVKNAVNSMKGVKSVE 55 (146)
Q Consensus 38 ~~~v~~~l~~~~GV~~v~ 55 (146)
-..+.+.|++++||.++.
T Consensus 51 L~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 51 LQTLMPEIRRIDGVEDVK 68 (74)
T ss_pred HHHHHHHHhCCCCceEEE
Confidence 345555566666665554
No 46
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=21.38 E-value=1.8e+02 Score=18.87 Aligned_cols=32 Identities=31% Similarity=0.504 Sum_probs=23.7
Q ss_pred EEEEEc-CcCHhHHHHHHHHHhCCCCceEEEEe
Q 032155 26 VEIKVK-MDCDGCERRVKNAVNSMKGVKSVEVN 57 (146)
Q Consensus 26 v~l~V~-m~C~~C~~~v~~~l~~~~GV~~v~vd 57 (146)
+.+.+- -+-++-...++.+|+.+.||+++++-
T Consensus 51 l~l~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 51 LKLYVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred EEEEEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 344442 33466788999999999999988875
No 47
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=20.37 E-value=1.4e+02 Score=21.41 Aligned_cols=26 Identities=27% Similarity=0.469 Sum_probs=20.9
Q ss_pred HhHHHHHHHHHhCCCCceEEEEecCC
Q 032155 35 DGCERRVKNAVNSMKGVKSVEVNRKQ 60 (146)
Q Consensus 35 ~~C~~~v~~~l~~~~GV~~v~vd~~~ 60 (146)
.+|-.-++..+.+++||.++.+-...
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYag 33 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRAN 33 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCC
Confidence 56777778889999999999886544
Done!