Query 034633
Match_columns 88
No_of_seqs 119 out of 1047
Neff 11.0
Searched_HMMs 46136
Date Fri Mar 29 04:53:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034633.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034633hhsearch_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 4.9E-12 1.1E-16 58.6 8.5 58 6-63 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.3 4.9E-11 1.1E-15 56.7 8.8 63 4-66 3-69 (71)
3 KOG4656 Copper chaperone for s 98.7 4.7E-07 1E-11 50.6 8.1 66 4-69 8-73 (247)
4 PRK10671 copA copper exporting 98.6 6E-07 1.3E-11 59.6 9.2 66 1-68 1-67 (834)
5 KOG1603 Copper chaperone [Inor 98.5 4.8E-06 1E-10 39.7 8.5 58 4-61 6-63 (73)
6 COG2217 ZntA Cation transport 98.3 9.5E-06 2.1E-10 53.2 7.7 63 3-66 2-69 (713)
7 PLN02957 copper, zinc superoxi 98.2 0.00013 2.9E-09 42.2 10.2 66 4-69 7-72 (238)
8 TIGR00003 copper ion binding p 97.7 0.00054 1.2E-08 30.3 8.6 59 5-63 4-66 (68)
9 KOG0207 Cation transport ATPas 97.7 0.00034 7.3E-09 46.9 7.0 65 4-68 147-215 (951)
10 KOG0207 Cation transport ATPas 97.3 0.002 4.3E-08 43.5 7.0 66 5-70 71-140 (951)
11 PRK11033 zntA zinc/cadmium/mer 97.2 0.005 1.1E-07 41.1 8.1 62 4-65 54-117 (741)
12 PRK10671 copA copper exporting 97.2 0.0052 1.1E-07 41.5 8.0 61 5-65 101-162 (834)
13 PRK13748 putative mercuric red 84.9 8.7 0.00019 25.2 8.8 61 7-67 4-67 (561)
14 TIGR02052 MerP mercuric transp 81.6 4.1 8.9E-05 19.0 9.3 60 5-64 25-88 (92)
15 PRK11018 hypothetical protein; 75.5 7.5 0.00016 18.6 6.3 53 5-66 9-64 (78)
16 PF01206 TusA: Sulfurtransfera 74.4 7.3 0.00016 17.9 5.6 53 6-67 2-57 (70)
17 PRK00299 sulfur transfer prote 58.6 20 0.00044 17.2 6.6 54 4-66 9-65 (81)
18 cd03423 SirA SirA (also known 52.2 25 0.00053 16.2 5.7 51 8-67 3-56 (69)
19 cd03421 SirA_like_N SirA_like_ 51.2 25 0.00054 16.0 5.6 50 8-67 3-55 (67)
20 cd03420 SirA_RHOD_Pry_redox Si 50.7 26 0.00057 16.2 5.6 52 7-67 2-56 (69)
21 COG0425 SirA Predicted redox p 47.5 34 0.00073 16.5 3.4 53 4-65 5-61 (78)
22 cd03422 YedF YedF is a bacteri 47.4 31 0.00066 16.0 5.3 51 8-67 3-56 (69)
23 PF14599 zinc_ribbon_6: Zinc-r 44.1 9.3 0.0002 17.6 0.3 14 5-18 42-56 (61)
24 cd00371 HMA Heavy-metal-associ 34.6 33 0.00072 12.7 7.5 35 10-44 6-40 (63)
25 KOG3150 Uncharacterized conser 31.5 12 0.00026 20.8 -0.5 22 6-27 107-129 (182)
26 KOG2990 C2C2-type Zn-finger pr 31.1 38 0.00083 20.9 1.5 18 6-23 46-65 (317)
27 PRK14054 methionine sulfoxide 30.2 1.1E+02 0.0024 17.3 3.9 28 14-41 10-37 (172)
28 PRK05528 methionine sulfoxide 28.6 90 0.002 17.3 2.6 27 14-40 8-34 (156)
29 cd00291 SirA_YedF_YeeD SirA, Y 27.7 71 0.0015 14.3 5.8 51 8-67 3-56 (69)
30 PRK10509 bacterioferritin-asso 27.4 42 0.00092 15.5 1.1 18 10-27 36-53 (64)
31 PF12606 RELT: Tumour necrosis 26.6 73 0.0016 14.1 1.8 16 53-68 20-35 (50)
32 PF08394 Arc_trans_TRASH: Arch 26.4 57 0.0012 13.4 1.2 14 10-23 23-36 (37)
33 COG1856 Uncharacterized homolo 24.1 61 0.0013 19.5 1.5 15 10-24 22-36 (275)
34 PF03698 UPF0180: Uncharacteri 23.5 1.1E+02 0.0023 15.0 2.7 22 48-69 8-29 (80)
35 COG4837 Uncharacterized protei 23.4 59 0.0013 16.6 1.2 18 1-18 1-21 (106)
36 PF01625 PMSR: Peptide methion 22.7 1.5E+02 0.0033 16.4 3.0 27 14-40 7-33 (155)
37 PF04324 Fer2_BFD: BFD-like [2 22.6 38 0.00082 14.7 0.4 16 10-25 37-52 (55)
38 COG0225 MsrA Peptide methionin 21.5 1.8E+02 0.0038 16.7 3.5 27 14-40 13-39 (174)
39 TIGR00401 msrA methionine-S-su 21.2 1.3E+02 0.0029 16.5 2.4 27 14-40 7-33 (149)
40 COG4669 EscJ Type III secretor 20.6 1.7E+02 0.0038 17.7 2.8 21 17-37 111-131 (246)
41 PF01514 YscJ_FliF: Secretory 20.6 1.9E+02 0.0041 16.7 3.3 20 17-36 117-136 (206)
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=99.43 E-value=4.9e-12 Score=58.57 Aligned_cols=58 Identities=34% Similarity=0.717 Sum_probs=52.3
Q ss_pred EEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEEe---cCCHHHHHHHHHhcCCc
Q 034633 6 VLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKG---NVQPDAVLQTVSKTGKK 63 (88)
Q Consensus 6 ~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~~---~~~~~~~~~~i~~~g~~ 63 (88)
.|.+ ||.|.+|...+++.|.+++|+..+.+++..+++.+.. .....++...|...||+
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 3788 9999999999999999999999999999999999982 24569999999999984
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.34 E-value=4.9e-11 Score=56.65 Aligned_cols=63 Identities=35% Similarity=0.662 Sum_probs=55.8
Q ss_pred EEEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--e-cCCHHHHHHHHHhcCCceEe
Q 034633 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--G-NVQPDAVLQTVSKTGKKTAF 66 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~-~~~~~~~~~~i~~~g~~~~~ 66 (88)
+..+++ ||+|.+|...+.+.|.+++|+..+.+++..+...+. . ....+++...+..+||.+..
T Consensus 3 ~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~ 69 (71)
T COG2608 3 KTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEE 69 (71)
T ss_pred eEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeee
Confidence 367899 999999999999999999999999999999777666 3 57889999999999998753
No 3
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.66 E-value=4.7e-07 Score=50.64 Aligned_cols=66 Identities=32% Similarity=0.610 Sum_probs=59.3
Q ss_pred EEEEEecccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEEecCCHHHHHHHHHhcCCceEeecc
Q 034633 4 TVVLKVGMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTGKKTAFWEE 69 (88)
Q Consensus 4 ~~~~~~g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g~~~~~~~~ 69 (88)
...|.+.|+|.+|.+.+.+.|..++|+..+++++..+.+.+.....+..+...++..|-++.+...
T Consensus 8 ~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~ 73 (247)
T KOG4656|consen 8 EAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGA 73 (247)
T ss_pred eEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecC
Confidence 466778999999999999999999999999999999999999878899999999999998876543
No 4
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.63 E-value=6e-07 Score=59.55 Aligned_cols=66 Identities=32% Similarity=0.564 Sum_probs=56.4
Q ss_pred CceEEEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEEecCCHHHHHHHHHhcCCceEeec
Q 034633 1 MSQTVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTGKKTAFWE 68 (88)
Q Consensus 1 m~~~~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g~~~~~~~ 68 (88)
|+.+..+.+ ||+|.+|...+++.+.+++|+..+.+++. +..+........+...+...||.+....
T Consensus 1 ~~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 1 MSQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred CCeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 778899999 99999999999999999999999999984 3444444577889999999999988653
No 5
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.53 E-value=4.8e-06 Score=39.70 Aligned_cols=58 Identities=66% Similarity=1.007 Sum_probs=51.5
Q ss_pred EEEEEecccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEEecCCHHHHHHHHHhcC
Q 034633 4 TVVLKVGMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTG 61 (88)
Q Consensus 4 ~~~~~~g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g 61 (88)
...+.+.|+|.+|...+...+..+.|+.....+...+.+++.+..++..+...+.+.+
T Consensus 6 ~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~ 63 (73)
T KOG1603|consen 6 TVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTG 63 (73)
T ss_pred EEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcC
Confidence 3455669999999999999999999999999999999999996688889998888866
No 6
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.26 E-value=9.5e-06 Score=53.16 Aligned_cols=63 Identities=30% Similarity=0.624 Sum_probs=54.4
Q ss_pred eEEEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE-e--cCC-HHHHHHHHHhcCCceEe
Q 034633 3 QTVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK-G--NVQ-PDAVLQTVSKTGKKTAF 66 (88)
Q Consensus 3 ~~~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~-~--~~~-~~~~~~~i~~~g~~~~~ 66 (88)
.+..+.+ ||+|..|...++ .+.+++|+...++++.++++.+. . ... .+.+...+...||....
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 3467899 999999999999 99999999999999999999887 2 233 67889999999998764
No 7
>PLN02957 copper, zinc superoxide dismutase
Probab=98.15 E-value=0.00013 Score=42.20 Aligned_cols=66 Identities=35% Similarity=0.604 Sum_probs=54.7
Q ss_pred EEEEEecccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEEecCCHHHHHHHHHhcCCceEeecc
Q 034633 4 TVVLKVGMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTGKKTAFWEE 69 (88)
Q Consensus 4 ~~~~~~g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g~~~~~~~~ 69 (88)
++.|.++|.|..|...+++.+.++.++....+++....+.+........+...+...||.+.+...
T Consensus 7 ~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~ 72 (238)
T PLN02957 7 LTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQ 72 (238)
T ss_pred EEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecC
Confidence 344555999999999999999999999999999999988877545677788889999999866543
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=97.74 E-value=0.00054 Score=30.28 Aligned_cols=59 Identities=20% Similarity=0.536 Sum_probs=44.9
Q ss_pred EEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEEe---cCCHHHHHHHHHhcCCc
Q 034633 5 VVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKG---NVQPDAVLQTVSKTGKK 63 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~~---~~~~~~~~~~i~~~g~~ 63 (88)
..+.+ ++.|..|...++..+....++....+++......+.. ......+...+...||.
T Consensus 4 ~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 66 (68)
T TIGR00003 4 FTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYE 66 (68)
T ss_pred EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCC
Confidence 45788 9999999999999999988988888888888776652 23455555556666664
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.67 E-value=0.00034 Score=46.95 Aligned_cols=65 Identities=25% Similarity=0.595 Sum_probs=57.6
Q ss_pred EEEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE---ecCCHHHHHHHHHhcCCceEeec
Q 034633 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK---GNVQPDAVLQTVSKTGKKTAFWE 68 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~---~~~~~~~~~~~i~~~g~~~~~~~ 68 (88)
+..+.+ ||.|..|...+++.+.++.|+...+++...+++.+. ....+.++.+.+...|+......
T Consensus 147 ~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~ 215 (951)
T KOG0207|consen 147 KIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRP 215 (951)
T ss_pred cEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeee
Confidence 567889 999999999999999999999999999999988876 45788899999999999876543
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.32 E-value=0.002 Score=43.54 Aligned_cols=66 Identities=30% Similarity=0.566 Sum_probs=56.8
Q ss_pred EEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE---ecCCHHHHHHHHHhcCCceEeeccC
Q 034633 5 VVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK---GNVQPDAVLQTVSKTGKKTAFWEEE 70 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~---~~~~~~~~~~~i~~~g~~~~~~~~~ 70 (88)
-.+++ ||.|..|...++..+.+..|+...-+.+......+. .....+.+...+...|+....++..
T Consensus 71 ~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~ 140 (951)
T KOG0207|consen 71 CYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESV 140 (951)
T ss_pred eEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhcc
Confidence 34788 999999999999999999999999999888888776 4577888999999999998876553
No 11
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.20 E-value=0.005 Score=41.15 Aligned_cols=62 Identities=26% Similarity=0.418 Sum_probs=48.8
Q ss_pred EEEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE-ecCCHHHHHHHHHhcCCceE
Q 034633 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK-GNVQPDAVLQTVSKTGKKTA 65 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~-~~~~~~~~~~~i~~~g~~~~ 65 (88)
+..+.+ ||+|.+|...++..+.+.+|+....+++...+..+. .......+...+...||.+.
T Consensus 54 r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~ 117 (741)
T PRK11033 54 RYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLR 117 (741)
T ss_pred eEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccc
Confidence 456789 999999999999999999999999999888887665 22222556667778888754
No 12
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.17 E-value=0.0052 Score=41.55 Aligned_cols=61 Identities=33% Similarity=0.581 Sum_probs=50.3
Q ss_pred EEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEEecCCHHHHHHHHHhcCCceE
Q 034633 5 VVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVKGNVQPDAVLQTVSKTGKKTA 65 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~~~~~~~~~~~~i~~~g~~~~ 65 (88)
..+.+ ||+|..|...+++.+.+.+|+....+++......+........+...+...||.+.
T Consensus 101 ~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~ 162 (834)
T PRK10671 101 QQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAE 162 (834)
T ss_pred EEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCcc
Confidence 45789 99999999999999999999999999988887666533456667777888898765
No 13
>PRK13748 putative mercuric reductase; Provisional
Probab=84.93 E-value=8.7 Score=25.23 Aligned_cols=61 Identities=30% Similarity=0.572 Sum_probs=42.7
Q ss_pred EEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcCCceEee
Q 034633 7 LKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 7 ~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~ 67 (88)
+.+ ++.|.+|...++..+...+++.....++......+. .......+...+...++.....
T Consensus 4 i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~ 67 (561)
T PRK13748 4 LKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLA 67 (561)
T ss_pred EEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeecc
Confidence 557 999999999999988888887777777777764444 1224444555566677765443
No 14
>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=81.64 E-value=4.1 Score=19.05 Aligned_cols=60 Identities=28% Similarity=0.516 Sum_probs=39.1
Q ss_pred EEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE-e--cCCHHHHHHHHHhcCCce
Q 034633 5 VVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK-G--NVQPDAVLQTVSKTGKKT 64 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~-~--~~~~~~~~~~i~~~g~~~ 64 (88)
..+.+ ++.|..|...++..+....++.....++......+. . ......+...+...|+..
T Consensus 25 ~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 88 (92)
T TIGR02052 25 VTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPS 88 (92)
T ss_pred EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCe
Confidence 34667 999999999999888888887767766666654443 1 123444444455566653
No 15
>PRK11018 hypothetical protein; Provisional
Probab=75.49 E-value=7.5 Score=18.61 Aligned_cols=53 Identities=15% Similarity=0.070 Sum_probs=38.3
Q ss_pred EEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcCCceEe
Q 034633 5 VVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAF 66 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~ 66 (88)
..+.. |..|+...-...+.|.++.... .+.+. ......++.......||.+..
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G~---------~L~V~~d~~~a~~di~~~~~~~G~~v~~ 64 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKKGE---------ILEVVSDCPQSINNIPLDARNHGYTVLD 64 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCCCC---------EEEEEeCCccHHHHHHHHHHHcCCEEEE
Confidence 56778 9999999999999998874322 22332 344566778888899998754
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=74.37 E-value=7.3 Score=17.91 Aligned_cols=53 Identities=17% Similarity=0.199 Sum_probs=36.9
Q ss_pred EEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcCCceEee
Q 034633 6 VLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 6 ~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~ 67 (88)
.+.. |..|+.....+.+.+.+++... .+.+. ......++.......||....+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G~---------~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPGE---------VLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCCC---------EEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 4567 9999999999999999874322 33333 3455677888889999985544
No 17
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=58.56 E-value=20 Score=17.24 Aligned_cols=54 Identities=13% Similarity=0.154 Sum_probs=37.4
Q ss_pred EEEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcCCceEe
Q 034633 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAF 66 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~ 66 (88)
...+.. |..|+...-...+.+.++.... .+.+. ......++..-....|+.+..
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~G~---------~l~V~~dd~~~~~di~~~~~~~G~~~~~ 65 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQPGE---------TLLIIADDPATTRDIPSFCRFMDHELLA 65 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCCCC---------EEEEEeCCccHHHHHHHHHHHcCCEEEE
Confidence 356778 9999999999999998874322 22332 344556677777888888754
No 18
>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=52.17 E-value=25 Score=16.24 Aligned_cols=51 Identities=14% Similarity=0.144 Sum_probs=36.1
Q ss_pred Ee-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcCCceEee
Q 034633 8 KV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 8 ~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~ 67 (88)
.. |..|+...-...+.+.++... ..+.+. ......++..-....||.+...
T Consensus 3 D~~G~~CP~P~i~~k~~l~~l~~G---------~~l~V~~dd~~s~~di~~~~~~~g~~~~~~ 56 (69)
T cd03423 3 DTRGLRCPEPVMMLHKKVRKMKPG---------DTLLVLATDPSTTRDIPKFCTFLGHELLAQ 56 (69)
T ss_pred cccCCcCCHHHHHHHHHHHcCCCC---------CEEEEEeCCCchHHHHHHHHHHcCCEEEEE
Confidence 45 889999999999999877422 223333 3456677888888999987643
No 19
>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=51.23 E-value=25 Score=15.99 Aligned_cols=50 Identities=18% Similarity=0.299 Sum_probs=33.4
Q ss_pred Ee-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcCCceEee
Q 034633 8 KV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 8 ~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~ 67 (88)
.. |+.|+.......+++ ++... +.+.+. .......+..-....||.+...
T Consensus 3 D~rG~~CP~P~l~~k~al-~~~~g---------~~l~v~~d~~~s~~~i~~~~~~~G~~~~~~ 55 (67)
T cd03421 3 DARGLACPQPVIKTKKAL-ELEAG---------GEIEVLVDNEVAKENVSRFAESRGYEVSVE 55 (67)
T ss_pred ccCCCCCCHHHHHHHHHH-hcCCC---------CEEEEEEcChhHHHHHHHHHHHcCCEEEEE
Confidence 45 889999988888888 54322 223332 3345567888888999988543
No 20
>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=50.74 E-value=26 Score=16.16 Aligned_cols=52 Identities=17% Similarity=0.265 Sum_probs=36.7
Q ss_pred EEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcCCceEee
Q 034633 7 LKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 7 ~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~ 67 (88)
+.. |+.|+.......+.+.++... ..+.+. ......++..-....||.+...
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~G---------~~l~V~~d~~~a~~di~~~~~~~G~~~~~~ 56 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQDG---------EQLEVKASDPGFARDAQAWCKSTGNTLISL 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEECCccHHHHHHHHHHHcCCEEEEE
Confidence 346 899999999999999887422 233333 3456677888888999987643
No 21
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=47.51 E-value=34 Score=16.47 Aligned_cols=53 Identities=25% Similarity=0.351 Sum_probs=34.0
Q ss_pred EEEEEe-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcC-CceE
Q 034633 4 TVVLKV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTG-KKTA 65 (88)
Q Consensus 4 ~~~~~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g-~~~~ 65 (88)
...+.+ |..|+.......+.+.++.... .+.|. .+....++..-....| |...
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~Ge---------~LeV~~ddp~~~~dIp~~~~~~~~~~ll 61 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKPGE---------ILEVIADDPAAKEDIPAWAKKEGGHELL 61 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCCCC---------EEEEEecCcchHHHHHHHHHHcCCcEEE
Confidence 346788 9999999999999998874322 33333 3344456666666344 5543
No 22
>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=47.41 E-value=31 Score=15.96 Aligned_cols=51 Identities=16% Similarity=0.066 Sum_probs=36.0
Q ss_pred Ee-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcCCceEee
Q 034633 8 KV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 8 ~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~ 67 (88)
.. |..|+...-...+.+.++.... .+.+. .......+.......||.+...
T Consensus 3 D~rG~~CP~Pvi~~kkal~~l~~G~---------~l~V~~d~~~s~~ni~~~~~~~g~~v~~~ 56 (69)
T cd03422 3 DLRGEPCPYPAIATLEALPSLKPGE---------ILEVISDCPQSINNIPIDARNHGYKVLAI 56 (69)
T ss_pred ccCCCcCCHHHHHHHHHHHcCCCCC---------EEEEEecCchHHHHHHHHHHHcCCEEEEE
Confidence 45 8899999999999998874322 22322 4456677888888999988643
No 23
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=44.14 E-value=9.3 Score=17.62 Aligned_cols=14 Identities=29% Similarity=0.681 Sum_probs=5.3
Q ss_pred EEEEe-cccChhhHH
Q 034633 5 VVLKV-GMSCEGCVG 18 (88)
Q Consensus 5 ~~~~~-g~~c~~c~~ 18 (88)
+.|.+ |+.|.+|..
T Consensus 42 v~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 42 VPFHFLGHKCSHCGS 56 (61)
T ss_dssp EE--TT----TTTS-
T ss_pred eeeeHhhhcCCCCCC
Confidence 56888 999999853
No 24
>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=34.61 E-value=33 Score=12.67 Aligned_cols=35 Identities=46% Similarity=0.952 Sum_probs=24.2
Q ss_pred cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEE
Q 034633 10 GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTV 44 (88)
Q Consensus 10 g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v 44 (88)
++.|..|...+...+....++......+......+
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 40 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATV 40 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEE
Confidence 77899999888887777777665555555444333
No 25
>KOG3150 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.54 E-value=12 Score=20.85 Aligned_cols=22 Identities=23% Similarity=0.572 Sum_probs=17.8
Q ss_pred EEEe-cccChhhHHHHHHHhcCC
Q 034633 6 VLKV-GMSCEGCVGAVKRVLGKM 27 (88)
Q Consensus 6 ~~~~-g~~c~~c~~~i~~~l~~~ 27 (88)
.-++ .+.|.+|...+...|+.+
T Consensus 107 ~hr~hNi~cdNCHShVA~aLn~m 129 (182)
T KOG3150|consen 107 KHRTHNIFCDNCHSHVANALNRM 129 (182)
T ss_pred hhcccceeeccHHHHHHHHHHHh
Confidence 3456 788999999999998876
No 26
>KOG2990 consensus C2C2-type Zn-finger protein [Function unknown]
Probab=31.12 E-value=38 Score=20.86 Aligned_cols=18 Identities=17% Similarity=0.549 Sum_probs=13.6
Q ss_pred EEEe--cccChhhHHHHHHH
Q 034633 6 VLKV--GMSCEGCVGAVKRV 23 (88)
Q Consensus 6 ~~~~--g~~c~~c~~~i~~~ 23 (88)
.|.+ .++|.+|.++|...
T Consensus 46 RFEMPynIWC~gC~nhIgmG 65 (317)
T KOG2990|consen 46 RFEMPYNIWCDGCKNHIGMG 65 (317)
T ss_pred EEecccchhhccHHHhhhcc
Confidence 3444 78999999988664
No 27
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=30.16 E-value=1.1e+02 Score=17.31 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=22.7
Q ss_pred hhhHHHHHHHhcCCCCeeEEEEEccCCE
Q 034633 14 EGCVGAVKRVLGKMDGVETFDIDLKEQK 41 (88)
Q Consensus 14 ~~c~~~i~~~l~~~~g~~~~~~~~~~~~ 41 (88)
.+|-+.++..+.+++||....+-...+.
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~ 37 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGH 37 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCC
Confidence 4588889999999999998888765553
No 28
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=28.65 E-value=90 Score=17.35 Aligned_cols=27 Identities=19% Similarity=0.337 Sum_probs=21.9
Q ss_pred hhhHHHHHHHhcCCCCeeEEEEEccCC
Q 034633 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~i~~~l~~~~g~~~~~~~~~~~ 40 (88)
.+|-+.++..+.+++||....+-...+
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG 34 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANG 34 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCC
Confidence 458888999999999999888865553
No 29
>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=27.65 E-value=71 Score=14.32 Aligned_cols=51 Identities=20% Similarity=0.197 Sum_probs=34.8
Q ss_pred Ee-cccChhhHHHHHHHhcCCCCeeEEEEEccCCEEEEE--ecCCHHHHHHHHHhcCCceEee
Q 034633 8 KV-GMSCEGCVGAVKRVLGKMDGVETFDIDLKEQKVTVK--GNVQPDAVLQTVSKTGKKTAFW 67 (88)
Q Consensus 8 ~~-g~~c~~c~~~i~~~l~~~~g~~~~~~~~~~~~~~v~--~~~~~~~~~~~i~~~g~~~~~~ 67 (88)
.. |+.|+.....+.+.+.++.... .+.+. .......+...+...||.+...
T Consensus 3 D~rg~~CP~Pl~~~~~~l~~l~~g~---------~l~v~~d~~~~~~~i~~~~~~~g~~~~~~ 56 (69)
T cd00291 3 DLRGLPCPLPVLKTKKALEKLKSGE---------VLEVLLDDPGAVEDIPAWAKETGHEVLEV 56 (69)
T ss_pred cccCCcCCHHHHHHHHHHhcCCCCC---------EEEEEecCCcHHHHHHHHHHHcCCEEEEE
Confidence 45 8899998888888888764322 23333 3345677888888999986543
No 30
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=27.42 E-value=42 Score=15.47 Aligned_cols=18 Identities=28% Similarity=0.687 Sum_probs=13.9
Q ss_pred cccChhhHHHHHHHhcCC
Q 034633 10 GMSCEGCVGAVKRVLGKM 27 (88)
Q Consensus 10 g~~c~~c~~~i~~~l~~~ 27 (88)
|-.|..|...+...|.+.
T Consensus 36 g~~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 36 GNQCGKCIRAAREVMQDE 53 (64)
T ss_pred CCCccchHHHHHHHHHHH
Confidence 667999999888877543
No 31
>PF12606 RELT: Tumour necrosis factor receptor superfamily member 19; InterPro: IPR022248 The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 []. RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues [].
Probab=26.57 E-value=73 Score=14.08 Aligned_cols=16 Identities=19% Similarity=0.129 Sum_probs=10.3
Q ss_pred HHHHHHhcCCceEeec
Q 034633 53 VLQTVSKTGKKTAFWE 68 (88)
Q Consensus 53 ~~~~i~~~g~~~~~~~ 68 (88)
+...++..||+++...
T Consensus 20 I~~~~K~ygYkht~d~ 35 (50)
T PF12606_consen 20 ICTTLKAYGYKHTVDP 35 (50)
T ss_pred HHHHhhccccccccCC
Confidence 3445677888887544
No 32
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=26.36 E-value=57 Score=13.42 Aligned_cols=14 Identities=21% Similarity=0.605 Sum_probs=9.8
Q ss_pred cccChhhHHHHHHH
Q 034633 10 GMSCEGCVGAVKRV 23 (88)
Q Consensus 10 g~~c~~c~~~i~~~ 23 (88)
-++|..|.....+.
T Consensus 23 ~fCC~tC~~~fk~k 36 (37)
T PF08394_consen 23 YFCCPTCLSQFKKK 36 (37)
T ss_pred EEECHHHHHHHHhh
Confidence 35688998876654
No 33
>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]
Probab=24.05 E-value=61 Score=19.51 Aligned_cols=15 Identities=13% Similarity=0.403 Sum_probs=11.2
Q ss_pred cccChhhHHHHHHHh
Q 034633 10 GMSCEGCVGAVKRVL 24 (88)
Q Consensus 10 g~~c~~c~~~i~~~l 24 (88)
.++|+||.+++...+
T Consensus 22 ~lnC~HCg~~~L~~M 36 (275)
T COG1856 22 SLNCPHCGRHYLEHM 36 (275)
T ss_pred EecChHHHHHHHHHh
Confidence 567999998876553
No 34
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=23.53 E-value=1.1e+02 Score=15.00 Aligned_cols=22 Identities=14% Similarity=0.102 Sum_probs=17.5
Q ss_pred CCHHHHHHHHHhcCCceEeecc
Q 034633 48 VQPDAVLQTVSKTGKKTAFWEE 69 (88)
Q Consensus 48 ~~~~~~~~~i~~~g~~~~~~~~ 69 (88)
..+..+.+.+...||.+..+..
T Consensus 8 ~~Ls~v~~~L~~~GyeVv~l~~ 29 (80)
T PF03698_consen 8 EGLSNVKEALREKGYEVVDLEN 29 (80)
T ss_pred CCchHHHHHHHHCCCEEEecCC
Confidence 3567889999999999876654
No 35
>COG4837 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.38 E-value=59 Score=16.55 Aligned_cols=18 Identities=39% Similarity=0.728 Sum_probs=11.4
Q ss_pred CceEEEEEe-cc--cChhhHH
Q 034633 1 MSQTVVLKV-GM--SCEGCVG 18 (88)
Q Consensus 1 m~~~~~~~~-g~--~c~~c~~ 18 (88)
|.+.+.+.+ |- .|.+|.+
T Consensus 1 M~~~~~l~VyGae~iCASCV~ 21 (106)
T COG4837 1 MVNEAKLVVYGAEVICASCVN 21 (106)
T ss_pred CCceeEEEEecchhhhHHhcC
Confidence 555556666 54 3888865
No 36
>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=22.66 E-value=1.5e+02 Score=16.39 Aligned_cols=27 Identities=19% Similarity=0.385 Sum_probs=22.1
Q ss_pred hhhHHHHHHHhcCCCCeeEEEEEccCC
Q 034633 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~i~~~l~~~~g~~~~~~~~~~~ 40 (88)
.+|-+.++..+.+++||....+-...+
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 358888999999999999888875554
No 37
>PF04324 Fer2_BFD: BFD-like [2Fe-2S] binding domain; InterPro: IPR007419 The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as bacterioferritin-associated ferredoxin (BFD, P13655 from SWISSPROT). The function of BFD is not known, but it may be a general redox and/or regulatory component involved in the iron storage or mobilisation functions of bacterioferritin in bacteria []. This domain is also found in nitrate reductase proteins in association with the nitrite and sulphite reductase 4Fe-4S domain (IPR006067 from INTERPRO), nitrite/sulphite reductase ferredoxin-like half domain (IPR005117 from INTERPRO) and pyridine nucleotide-disulphide oxidoreductase (IPR001327 from INTERPRO). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N-terminal domain (IPR002871 from INTERPRO) and C-terminal domain (IPR001075 from INTERPRO).; PDB: 2HU9_A.
Probab=22.58 E-value=38 Score=14.74 Aligned_cols=16 Identities=44% Similarity=0.904 Sum_probs=2.7
Q ss_pred cccChhhHHHHHHHhc
Q 034633 10 GMSCEGCVGAVKRVLG 25 (88)
Q Consensus 10 g~~c~~c~~~i~~~l~ 25 (88)
|..|..|...+...|.
T Consensus 37 g~~Cg~C~~~v~~ll~ 52 (55)
T PF04324_consen 37 GTGCGSCVPEVKDLLA 52 (55)
T ss_dssp SS-TH-----------
T ss_pred CCCCCCcccccccccc
Confidence 5567778776665554
No 38
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=21.48 E-value=1.8e+02 Score=16.68 Aligned_cols=27 Identities=19% Similarity=0.261 Sum_probs=21.3
Q ss_pred hhhHHHHHHHhcCCCCeeEEEEEccCC
Q 034633 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~i~~~l~~~~g~~~~~~~~~~~ 40 (88)
.+|-+-++..+.+++||....+-...+
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG 39 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGG 39 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCC
Confidence 457888899999999999888765444
No 39
>TIGR00401 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens.
Probab=21.17 E-value=1.3e+02 Score=16.51 Aligned_cols=27 Identities=19% Similarity=0.317 Sum_probs=21.2
Q ss_pred hhhHHHHHHHhcCCCCeeEEEEEccCC
Q 034633 14 EGCVGAVKRVLGKMDGVETFDIDLKEQ 40 (88)
Q Consensus 14 ~~c~~~i~~~l~~~~g~~~~~~~~~~~ 40 (88)
.+|-+.++..+.+++||....+-...+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 457888899999999998888865444
No 40
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=20.58 E-value=1.7e+02 Score=17.69 Aligned_cols=21 Identities=29% Similarity=0.485 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCCCeeEEEEEc
Q 034633 17 VGAVKRVLGKMDGVETFDIDL 37 (88)
Q Consensus 17 ~~~i~~~l~~~~g~~~~~~~~ 37 (88)
...+++.|++++|+...++..
T Consensus 111 eQ~le~tLs~mDGVi~ArV~I 131 (246)
T COG4669 111 EQQLEQTLSKMDGVISARVHI 131 (246)
T ss_pred HHHHHHHHHhcCceEEEEEEE
Confidence 456888999999988888763
No 41
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=20.57 E-value=1.9e+02 Score=16.74 Aligned_cols=20 Identities=30% Similarity=0.629 Sum_probs=16.8
Q ss_pred HHHHHHHhcCCCCeeEEEEE
Q 034633 17 VGAVKRVLGKMDGVETFDID 36 (88)
Q Consensus 17 ~~~i~~~l~~~~g~~~~~~~ 36 (88)
...+++.+..++||..++++
T Consensus 117 e~eL~~tI~~i~gV~~A~V~ 136 (206)
T PF01514_consen 117 EGELERTIESIDGVESARVH 136 (206)
T ss_dssp HHHHHHHHTTSTTEEEEEEE
T ss_pred HHHHHHHHHcCCCeeEEEEE
Confidence 34678889999999999987
Done!