Query psy13020
Match_columns 81
No_of_seqs 118 out of 1437
Neff 10.1
Searched_HMMs 46136
Date Fri Aug 16 17:20:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13020.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13020hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0207|consensus 99.0 4.2E-09 9E-14 71.3 8.2 78 2-80 22-103 (951)
2 PF00403 HMA: Heavy-metal-asso 99.0 1.9E-09 4.1E-14 51.7 4.8 33 49-81 1-33 (62)
3 KOG0207|consensus 98.8 2.6E-08 5.6E-13 67.6 8.0 79 3-81 98-181 (951)
4 COG2608 CopZ Copper chaperone 98.8 1.4E-08 2.9E-13 50.2 4.8 35 47-81 3-37 (71)
5 COG2217 ZntA Cation transport 98.0 1.3E-05 2.7E-10 54.3 4.4 34 47-81 3-36 (713)
6 PRK10671 copA copper exporting 98.0 0.00015 3.3E-09 50.0 9.3 73 4-81 33-134 (834)
7 PRK10671 copA copper exporting 97.8 3.6E-05 7.9E-10 52.9 4.5 35 47-81 4-38 (834)
8 PF00403 HMA: Heavy-metal-asso 97.8 0.00018 3.8E-09 34.2 5.2 36 3-38 27-62 (62)
9 TIGR00003 copper ion binding p 97.2 0.002 4.4E-08 29.1 5.0 33 48-80 4-36 (68)
10 COG2608 CopZ Copper chaperone 97.2 0.0022 4.7E-08 31.5 5.1 38 3-40 31-68 (71)
11 PLN02957 copper, zinc superoxi 96.9 0.004 8.8E-08 37.3 5.2 35 46-81 6-40 (238)
12 KOG4656|consensus 96.9 0.0014 3.1E-08 38.5 3.0 33 48-81 9-41 (247)
13 KOG1603|consensus 96.9 0.0018 3.8E-08 32.0 3.0 29 52-80 10-38 (73)
14 PRK11033 zntA zinc/cadmium/mer 96.7 0.0044 9.5E-08 42.6 4.8 36 46-81 53-88 (741)
15 TIGR02052 MerP mercuric transp 89.6 1.4 3.1E-05 21.3 4.9 33 47-79 24-56 (92)
16 COG2217 ZntA Cation transport 85.2 2.6 5.6E-05 29.6 4.6 38 3-40 30-68 (713)
17 PRK13748 putative mercuric red 84.4 3.3 7.1E-05 27.8 4.8 32 49-80 3-34 (561)
18 cd00371 HMA Heavy-metal-associ 82.2 2.5 5.4E-05 16.9 4.2 25 52-76 4-28 (63)
19 PF08002 DUF1697: Protein of u 66.6 12 0.00026 20.7 3.2 51 22-73 18-69 (137)
20 PF11491 DUF3213: Protein of u 66.0 9.5 0.00021 19.5 2.4 36 5-40 29-64 (88)
21 PF01206 TusA: Sulfurtransfera 64.4 14 0.00031 17.4 3.4 24 49-72 2-25 (70)
22 PF04805 Pox_E10: E10-like pro 57.9 6.8 0.00015 19.1 1.0 24 53-76 14-37 (70)
23 PF01883 DUF59: Domain of unkn 56.5 18 0.0004 17.2 2.5 33 47-79 37-72 (72)
24 PF14424 Toxin-deaminase: The 56.3 33 0.00072 19.0 4.2 31 46-76 97-127 (133)
25 PRK05528 methionine sulfoxide 50.9 18 0.0004 20.6 2.2 27 52-81 5-31 (156)
26 PHA03005 sulfhydryl oxidase; P 49.9 14 0.00031 19.2 1.5 29 52-80 38-66 (96)
27 PRK14054 methionine sulfoxide 45.9 21 0.00047 20.7 2.0 26 52-80 7-32 (172)
28 PF01514 YscJ_FliF: Secretory 43.9 34 0.00075 20.2 2.7 21 61-81 117-137 (206)
29 PRK11152 ilvM acetolactate syn 40.7 49 0.0011 16.4 6.4 64 13-79 5-75 (76)
30 PF02680 DUF211: Uncharacteriz 40.3 38 0.00082 17.8 2.2 33 7-39 42-74 (95)
31 PRK00058 methionine sulfoxide 39.1 28 0.0006 21.0 1.8 29 50-81 47-75 (213)
32 PF01625 PMSR: Peptide methion 39.0 41 0.00089 19.1 2.4 26 52-80 4-29 (155)
33 TIGR00401 msrA methionine-S-su 38.3 32 0.00069 19.4 1.9 26 53-81 5-30 (149)
34 cd04888 ACT_PheB-BS C-terminal 38.2 47 0.001 15.5 7.9 65 15-79 4-74 (76)
35 TIGR02544 III_secr_YscJ type I 34.9 47 0.001 19.5 2.3 21 61-81 109-129 (193)
36 COG4669 EscJ Type III secretor 34.8 57 0.0012 20.2 2.7 21 60-80 110-130 (246)
37 COG0735 Fur Fe2+/Zn2+ uptake r 33.5 90 0.002 17.3 4.0 27 30-63 116-142 (145)
38 PRK10509 bacterioferritin-asso 31.8 29 0.00063 16.6 1.0 43 23-70 9-52 (64)
39 PRK00435 ef1B elongation facto 31.8 80 0.0017 16.2 6.0 65 15-79 9-82 (88)
40 PF04324 Fer2_BFD: BFD-like [2 31.4 19 0.00042 16.2 0.3 16 54-69 37-52 (55)
41 PRK13014 methionine sulfoxide 30.6 32 0.00069 20.3 1.1 28 51-81 11-38 (186)
42 PRK15348 type III secretion sy 30.2 64 0.0014 20.0 2.4 21 61-81 109-129 (249)
43 COG3309 VapD Uncharacterized v 29.8 92 0.002 16.3 3.2 44 26-73 26-69 (96)
44 COG2092 EFB1 Translation elong 29.7 90 0.002 16.1 5.8 66 14-79 8-82 (88)
45 PRK05974 phosphoribosylformylg 29.6 81 0.0018 15.6 7.3 68 13-80 4-77 (80)
46 PF08478 POTRA_1: POTRA domain 28.9 71 0.0015 14.7 2.5 21 60-80 35-55 (69)
47 PF14437 MafB19-deam: MafB19-l 28.8 1.2E+02 0.0026 17.3 3.9 33 46-79 100-132 (146)
48 TIGR00489 aEF-1_beta translati 28.5 94 0.002 16.0 6.3 63 15-79 9-82 (88)
49 TIGR00302 phosphoribosylformyl 26.8 93 0.002 15.4 7.3 66 13-78 4-75 (80)
50 PF15644 Tox-PL: Papain fold t 26.0 71 0.0015 16.8 1.9 18 56-73 2-19 (111)
51 PRK11200 grxA glutaredoxin 1; 26.0 93 0.002 15.1 2.6 14 56-70 10-23 (85)
52 COG1888 Uncharacterized protei 25.4 1.1E+02 0.0025 16.0 4.1 34 7-40 44-77 (97)
53 PF10217 DUF2039: Uncharacteri 24.6 64 0.0014 16.8 1.5 18 50-68 27-44 (92)
54 COG1913 Predicted Zn-dependent 23.7 67 0.0014 18.9 1.6 19 53-71 161-179 (181)
55 PF14599 zinc_ribbon_6: Zinc-r 23.6 32 0.00069 16.4 0.3 17 46-62 40-56 (61)
56 COG4248 Uncharacterized protei 23.3 31 0.00067 23.6 0.3 23 47-69 312-334 (637)
57 TIGR02945 SUF_assoc FeS assemb 23.1 1.2E+02 0.0026 15.4 3.9 34 47-80 40-76 (99)
58 PRK04435 hypothetical protein; 22.9 1.5E+02 0.0033 16.5 7.5 58 22-79 80-143 (147)
59 PRK11018 hypothetical protein; 21.9 1.2E+02 0.0026 14.9 3.5 25 48-72 9-33 (78)
60 COG2151 PaaD Predicted metal-s 21.6 1.5E+02 0.0033 15.9 3.5 33 49-81 54-89 (111)
61 cd04878 ACT_AHAS N-terminal AC 21.5 99 0.0021 13.8 6.2 62 14-77 3-71 (72)
62 PHA03075 glutaredoxin-like pro 21.3 1.6E+02 0.0035 16.2 3.5 21 19-39 98-118 (123)
63 PF09580 Spore_YhcN_YlaJ: Spor 21.0 1.4E+02 0.0031 16.8 2.7 22 58-79 74-95 (177)
64 PF05922 Inhibitor_I9: Peptida 20.8 1.2E+02 0.0025 14.4 2.4 28 52-80 49-76 (82)
65 PF08210 APOBEC_N: APOBEC-like 20.5 2E+02 0.0043 16.9 3.4 30 46-75 74-109 (188)
66 cd08969 MeNeil3_N N-terminal d 20.3 85 0.0018 17.7 1.5 24 52-75 2-25 (140)
No 1
>KOG0207|consensus
Probab=98.99 E-value=4.2e-09 Score=71.31 Aligned_cols=78 Identities=38% Similarity=0.647 Sum_probs=68.1
Q ss_pred CceEEEEecCCeEEEEEcCCCCCHHHHHHHHHhcCCcccCCCC----CceEEEEeccccchhHHHHHHHHhcCCCCeeEE
Q psy13020 2 RKRHQVSLEQKNANIRFNPIITNEETLRISIEDMGFDARLPST----NDEATFTVDGMKCQSCVKKIEATIGEKPGVIAV 77 (81)
Q Consensus 2 ~~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~g~~~~~~~~----~~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~ 77 (81)
+++..+++.++++.+.|+ ...+++.+.+.+++.||++..... ..+..+++.||+|.+|...+++.+++.+|+..+
T Consensus 22 ~~~i~vsl~~~~~~v~~~-~~~~~~~i~~~ied~gf~~~~~~~~~~~~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~ 100 (951)
T KOG0207|consen 22 VQKIEVSLAQKRANVSYD-NIVSPESIKETIEDMGFEASLLSDSEITASKCYLSVNGMTCASCVATIERNLRKIEGVESA 100 (951)
T ss_pred ceeEEEEeccccceEEEe-eccCHHHHHHHhhcccceeeecccCccccceeEEEecCceeHHHHHHHHHHhhccCCcceE
Confidence 467889999999999999 778999999999999999865432 246789999999999999999999999999887
Q ss_pred EEe
Q psy13020 78 KVS 80 (81)
Q Consensus 78 ~~~ 80 (81)
.+.
T Consensus 101 ~va 103 (951)
T KOG0207|consen 101 VVA 103 (951)
T ss_pred EEE
Confidence 654
No 2
>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=98.98 E-value=1.9e-09 Score=51.66 Aligned_cols=33 Identities=48% Similarity=0.901 Sum_probs=31.1
Q ss_pred EEEeccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 49 TFTVDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 49 ~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
+|.+.||+|++|+.++++.|.+++||..+.+|+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~ 33 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDL 33 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEET
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEEC
Confidence 478999999999999999999999999999986
No 3
>KOG0207|consensus
Probab=98.84 E-value=2.6e-08 Score=67.62 Aligned_cols=79 Identities=35% Similarity=0.595 Sum_probs=70.5
Q ss_pred ceEEEEecCCeEEEEEcCCCCCHHHHHHHHHhcCCcccCCCC-----CceEEEEeccccchhHHHHHHHHhcCCCCeeEE
Q psy13020 3 KRHQVSLEQKNANIRFNPIITNEETLRISIEDMGFDARLPST-----NDEATFTVDGMKCQSCVKKIEATIGEKPGVIAV 77 (81)
Q Consensus 3 ~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~g~~~~~~~~-----~~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~ 77 (81)
.++.+.+..+.+++.|||..+....+.+.++++||++..++. .....|.+.||.|.+|..+++..+.+++||.+.
T Consensus 98 ~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~~~~~~~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~ 177 (951)
T KOG0207|consen 98 ESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESVNGNSNQKIYLDVLGMTCASCVSKIESILERLRGVKSF 177 (951)
T ss_pred ceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhcccCCCCCcEEEEeecccccchhhhhHHHHhhccCeeEE
Confidence 467888999999999999999999999999999999865442 147899999999999999999999999999999
Q ss_pred EEeC
Q psy13020 78 KVSH 81 (81)
Q Consensus 78 ~~~~ 81 (81)
+++.
T Consensus 178 sv~~ 181 (951)
T KOG0207|consen 178 SVSL 181 (951)
T ss_pred EEec
Confidence 8864
No 4
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.82 E-value=1.4e-08 Score=50.16 Aligned_cols=35 Identities=40% Similarity=0.746 Sum_probs=32.6
Q ss_pred eEEEEeccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 47 EATFTVDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 47 ~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
...+.+.||+|.+|+..+++.|..++|+..+.+|+
T Consensus 3 ~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l 37 (71)
T COG2608 3 KTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDL 37 (71)
T ss_pred eEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEc
Confidence 45799999999999999999999999999999885
No 5
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.98 E-value=1.3e-05 Score=54.34 Aligned_cols=34 Identities=35% Similarity=0.820 Sum_probs=31.9
Q ss_pred eEEEEeccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 47 EATFTVDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 47 ~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
+..+.+.||+|++|+.++| .|.+.+|+..+.+||
T Consensus 3 ~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~ 36 (713)
T COG2217 3 ETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNL 36 (713)
T ss_pred eeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeec
Confidence 5679999999999999999 999999999999986
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.96 E-value=0.00015 Score=49.96 Aligned_cols=73 Identities=27% Similarity=0.569 Sum_probs=54.8
Q ss_pred eEEEEecCCeEEEEEcCCCCCHHHHHHHHHhcCCcccCCCC-----------------------------CceEEEEecc
Q psy13020 4 RHQVSLEQKNANIRFNPIITNEETLRISIEDMGFDARLPST-----------------------------NDEATFTVDG 54 (81)
Q Consensus 4 ~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~g~~~~~~~~-----------------------------~~~~~~~i~g 54 (81)
++.+++ ++..+..+ .+.+.+.+.++++||.+..... ..+..+.+.|
T Consensus 33 ~v~v~~--~~~~v~~~---~~~~~i~~~i~~~Gy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~G 107 (834)
T PRK10671 33 QADVSI--TEAHVTGT---ASAEALIETIKQAGYDASVSHPKAKPLTESSIPSEALTAASEELPAATADDDDSQQLLLSG 107 (834)
T ss_pred eEEEee--eEEEEEec---CCHHHHHHHHHhcCCcccccccccccccccccCchhhhhhhhhccccccCcCceEEEEeCC
Confidence 456676 34455432 3578999999999998764210 0145688999
Q ss_pred ccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 55 MKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 55 ~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
|+|..|+..+++.+...+|+..+.+|+
T Consensus 108 m~Ca~Ca~~Ie~~L~~~~GV~~a~vnl 134 (834)
T PRK10671 108 MSCASCVSRVQNALQSVPGVTQARVNL 134 (834)
T ss_pred cCcHHHHHHHHHHHhcCCCceeeeeec
Confidence 999999999999999999998887764
No 7
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.82 E-value=3.6e-05 Score=52.94 Aligned_cols=35 Identities=31% Similarity=0.715 Sum_probs=32.6
Q ss_pred eEEEEeccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 47 EATFTVDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 47 ~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
+..+.+.||+|.+|+.++++.+.+++|+..+.+|+
T Consensus 4 ~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~ 38 (834)
T PRK10671 4 TIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSI 38 (834)
T ss_pred EEEEEECCcccHHHHHHHHHHHhcCCCcceEEEee
Confidence 56899999999999999999999999999998875
No 8
>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=97.75 E-value=0.00018 Score=34.16 Aligned_cols=36 Identities=31% Similarity=0.512 Sum_probs=32.6
Q ss_pred ceEEEEecCCeEEEEEcCCCCCHHHHHHHHHhcCCc
Q psy13020 3 KRHQVSLEQKNANIRFNPIITNEETLRISIEDMGFD 38 (81)
Q Consensus 3 ~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~g~~ 38 (81)
.++.+++.++++.|.+++..++++++.+.++++||+
T Consensus 27 ~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 27 KSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred cEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 467899999999999998878889999999999985
No 9
>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=97.22 E-value=0.002 Score=29.14 Aligned_cols=33 Identities=48% Similarity=0.707 Sum_probs=28.1
Q ss_pred EEEEeccccchhHHHHHHHHhcCCCCeeEEEEe
Q psy13020 48 ATFTVDGMKCQSCVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 48 ~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~ 80 (81)
..+.+.|+.|..|...++..+...+++....++
T Consensus 4 ~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~ 36 (68)
T TIGR00003 4 FTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVK 36 (68)
T ss_pred EEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEE
Confidence 468899999999999999999888887766554
No 10
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=97.20 E-value=0.0022 Score=31.50 Aligned_cols=38 Identities=26% Similarity=0.422 Sum_probs=34.2
Q ss_pred ceEEEEecCCeEEEEEcCCCCCHHHHHHHHHhcCCccc
Q psy13020 3 KRHQVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 40 (81)
Q Consensus 3 ~~~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~g~~~~ 40 (81)
.++.+++..++..+.+++...+.+++.++++++||.+.
T Consensus 31 ~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~ 68 (71)
T COG2608 31 ASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVE 68 (71)
T ss_pred eEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCee
Confidence 46789999999999999977899999999999999864
No 11
>PLN02957 copper, zinc superoxide dismutase
Probab=96.88 E-value=0.004 Score=37.33 Aligned_cols=35 Identities=34% Similarity=0.563 Sum_probs=30.2
Q ss_pred ceEEEEeccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 46 DEATFTVDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 46 ~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
.+..+.+ +|.|..|+..+++.|.+.+|+..+.+|+
T Consensus 6 ~~~~~~V-gMsC~~Ca~~Iek~L~~~~GV~~v~vn~ 40 (238)
T PLN02957 6 LLTEFMV-DMKCEGCVAAVKNKLETLEGVKAVEVDL 40 (238)
T ss_pred EEEEEEE-CccCHHHHHHHHHHHhcCCCeEEEEEEc
Confidence 4567778 7999999999999999999998877764
No 12
>KOG4656|consensus
Probab=96.85 E-value=0.0014 Score=38.54 Aligned_cols=33 Identities=39% Similarity=0.758 Sum_probs=28.4
Q ss_pred EEEEeccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 48 ATFTVDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 48 ~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
..|.+ .|+|.+|+..+.+.|...+||.++++++
T Consensus 9 ~efaV-~M~cescvnavk~~L~~V~Gi~~vevdl 41 (247)
T KOG4656|consen 9 AEFAV-QMTCESCVNAVKACLKGVPGINSVEVDL 41 (247)
T ss_pred EEEEE-echhHHHHHHHHHHhccCCCcceEEEEh
Confidence 34444 6999999999999999999999999874
No 13
>KOG1603|consensus
Probab=96.85 E-value=0.0018 Score=31.96 Aligned_cols=29 Identities=24% Similarity=0.595 Sum_probs=26.0
Q ss_pred eccccchhHHHHHHHHhcCCCCeeEEEEe
Q psy13020 52 VDGMKCQSCVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 52 i~g~~c~~C~~~i~~~l~~~~gv~~~~~~ 80 (81)
-..|+|.+|...+.+.+..+.||..+.++
T Consensus 10 kv~~~C~gc~~kV~~~l~~~~GV~~v~id 38 (73)
T KOG1603|consen 10 KVNMHCEGCARKVKRVLQKLKGVESVDID 38 (73)
T ss_pred EECcccccHHHHHHHHhhccCCeEEEEec
Confidence 34799999999999999999999988776
No 14
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.70 E-value=0.0044 Score=42.63 Aligned_cols=36 Identities=33% Similarity=0.665 Sum_probs=32.2
Q ss_pred ceEEEEeccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 46 DEATFTVDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 46 ~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
.+..+.+.||+|++|+..+++.+...+|+..+.+++
T Consensus 53 ~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~ 88 (741)
T PRK11033 53 TRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLF 88 (741)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEc
Confidence 467789999999999999999999999998887764
No 15
>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=89.64 E-value=1.4 Score=21.30 Aligned_cols=33 Identities=30% Similarity=0.585 Sum_probs=26.1
Q ss_pred eEEEEeccccchhHHHHHHHHhcCCCCeeEEEE
Q psy13020 47 EATFTVDGMKCQSCVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 47 ~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~ 79 (81)
...+.+.|+.|..|...++..+...+++.....
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~ 56 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEV 56 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEE
Confidence 456778999999999999988888877655443
No 16
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=85.16 E-value=2.6 Score=29.62 Aligned_cols=38 Identities=21% Similarity=0.476 Sum_probs=32.7
Q ss_pred ceEEEEecCCeEEEEEcCCCCC-HHHHHHHHHhcCCccc
Q psy13020 3 KRHQVSLEQKNANIRFNPIITN-EETLRISIEDMGFDAR 40 (81)
Q Consensus 3 ~~~~v~~~~~~~~v~~~~~~~~-~~~i~~~i~~~g~~~~ 40 (81)
.++.+|+.++++.+.+++.... .+++...++..||...
T Consensus 30 ~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~ 68 (713)
T COG2217 30 EEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSAR 68 (713)
T ss_pred eEEEeecccceEEEEecccccccHHHHHHHHHhcCcccc
Confidence 4688999999999999976555 7899999999999864
No 17
>PRK13748 putative mercuric reductase; Provisional
Probab=84.36 E-value=3.3 Score=27.76 Aligned_cols=32 Identities=34% Similarity=0.773 Sum_probs=25.8
Q ss_pred EEEeccccchhHHHHHHHHhcCCCCeeEEEEe
Q psy13020 49 TFTVDGMKCQSCVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 49 ~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~ 80 (81)
.+.+.|+.|.+|...++..+...+++.....+
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~ 34 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVS 34 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEE
Confidence 35688999999999999999888886655443
No 18
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=82.20 E-value=2.5 Score=16.86 Aligned_cols=25 Identities=48% Similarity=0.958 Sum_probs=18.1
Q ss_pred eccccchhHHHHHHHHhcCCCCeeE
Q psy13020 52 VDGMKCQSCVKKIEATIGEKPGVIA 76 (81)
Q Consensus 52 i~g~~c~~C~~~i~~~l~~~~gv~~ 76 (81)
+.++.|..|...+...+...+++..
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~ 28 (63)
T cd00371 4 VEGMTCAGCVSKIEKALEKLPGVES 28 (63)
T ss_pred ECCeEcHHHHHHHHHHHhcCCCEeE
Confidence 5677788888888777776666543
No 19
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=66.59 E-value=12 Score=20.69 Aligned_cols=51 Identities=25% Similarity=0.359 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHhcCCc-ccCCCCCceEEEEeccccchhHHHHHHHHhcCCCC
Q psy13020 22 ITNEETLRISIEDMGFD-ARLPSTNDEATFTVDGMKCQSCVKKIEATIGEKPG 73 (81)
Q Consensus 22 ~~~~~~i~~~i~~~g~~-~~~~~~~~~~~~~i~g~~c~~C~~~i~~~l~~~~g 73 (81)
++.+.++.+..+++||. +...-...-+.+. .....+....++++.|...-|
T Consensus 18 ki~MaeLr~~l~~~Gf~~V~Tyi~SGNvvf~-~~~~~~~l~~~ie~~l~~~fG 69 (137)
T PF08002_consen 18 KIKMAELREALEDLGFTNVRTYIQSGNVVFE-SDRDPAELAAKIEKALEERFG 69 (137)
T ss_dssp ---HHHHHHHHHHCT-EEEEEETTTTEEEEE-ESS-HHHHHHHHHHHHHHH-T
T ss_pred cccHHHHHHHHHHcCCCCceEEEeeCCEEEe-cCCChHHHHHHHHHHHHHhcC
Confidence 46789999999999997 3321122455666 777778888888888876654
No 20
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=65.96 E-value=9.5 Score=19.48 Aligned_cols=36 Identities=14% Similarity=0.092 Sum_probs=18.5
Q ss_pred EEEEecCCeEEEEEcCCCCCHHHHHHHHHhcCCccc
Q psy13020 5 HQVSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 40 (81)
Q Consensus 5 ~~v~~~~~~~~v~~~~~~~~~~~i~~~i~~~g~~~~ 40 (81)
+.+|-=.+.+.|.+|+..++.+++.+..+..++++.
T Consensus 29 vFiNgYar~g~VifDe~kl~~e~lL~~le~~kpEVi 64 (88)
T PF11491_consen 29 VFINGYARNGFVIFDESKLSKEELLEMLEEFKPEVI 64 (88)
T ss_dssp ----TTSS--EEE--B-S-SHHHH---HHHTTT-SS
T ss_pred eeecccccceEEEECcccCCHHHHHHHHHhcChhhe
Confidence 445556788899999999999999999998888763
No 21
>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=64.38 E-value=14 Score=17.43 Aligned_cols=24 Identities=25% Similarity=0.509 Sum_probs=17.8
Q ss_pred EEEeccccchhHHHHHHHHhcCCC
Q psy13020 49 TFTVDGMKCQSCVKKIEATIGEKP 72 (81)
Q Consensus 49 ~~~i~g~~c~~C~~~i~~~l~~~~ 72 (81)
.+.+.|..|+.....+.+++..++
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~ 25 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELP 25 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSG
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcC
Confidence 456678888888888888888864
No 22
>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=57.85 E-value=6.8 Score=19.14 Aligned_cols=24 Identities=13% Similarity=0.315 Sum_probs=17.8
Q ss_pred ccccchhHHHHHHHHhcCCCCeeE
Q psy13020 53 DGMKCQSCVKKIEATIGEKPGVIA 76 (81)
Q Consensus 53 ~g~~c~~C~~~i~~~l~~~~gv~~ 76 (81)
.-+.|+.|.....+++.+..-..+
T Consensus 14 ~tLPC~~Cr~HA~~ai~kNNiMSs 37 (70)
T PF04805_consen 14 STLPCPECRIHAKEAIQKNNIMSS 37 (70)
T ss_pred hcCCCHHHHHHHHHHHHhcCcccc
Confidence 457799999999888877654443
No 23
>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=56.52 E-value=18 Score=17.21 Aligned_cols=33 Identities=24% Similarity=0.439 Sum_probs=19.9
Q ss_pred eEEEEeccccchh---HHHHHHHHhcCCCCeeEEEE
Q psy13020 47 EATFTVDGMKCQS---CVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 47 ~~~~~i~g~~c~~---C~~~i~~~l~~~~gv~~~~~ 79 (81)
.+.+.+....|+. =...+++.|..++|+.++++
T Consensus 37 ~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 37 SVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 4445555555553 24566778999999988765
No 24
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=56.33 E-value=33 Score=18.95 Aligned_cols=31 Identities=19% Similarity=0.322 Sum_probs=26.2
Q ss_pred ceEEEEeccccchhHHHHHHHHhcCCCCeeE
Q psy13020 46 DEATFTVDGMKCQSCVKKIEATIGEKPGVIA 76 (81)
Q Consensus 46 ~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~ 76 (81)
.++.+-..-..|.+|...|++-....|.+.-
T Consensus 97 G~i~l~te~~pC~SC~~vi~qF~~~~pni~~ 127 (133)
T PF14424_consen 97 GTIDLFTELPPCESCSNVIEQFKKDFPNIKV 127 (133)
T ss_pred ceEEEEecCCcChhHHHHHHHHHHHCCCcEE
Confidence 5677778888999999999999888888764
No 25
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=50.87 E-value=18 Score=20.59 Aligned_cols=27 Identities=26% Similarity=0.261 Sum_probs=19.2
Q ss_pred eccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 52 VDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 52 i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
+.++.|-+|. +..+.+++||..+.+.+
T Consensus 5 ~fagGCFWg~---E~~f~~l~GV~~t~vGY 31 (156)
T PRK05528 5 YFAGGCLWGV---QAFFKTLPGVIHTEAGR 31 (156)
T ss_pred EEecCCchhh---HHHHhcCCCEEEEEEEc
Confidence 3456677665 55778889999888753
No 26
>PHA03005 sulfhydryl oxidase; Provisional
Probab=49.92 E-value=14 Score=19.25 Aligned_cols=29 Identities=10% Similarity=0.340 Sum_probs=20.4
Q ss_pred eccccchhHHHHHHHHhcCCCCeeEEEEe
Q psy13020 52 VDGMKCQSCVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 52 i~g~~c~~C~~~i~~~l~~~~gv~~~~~~ 80 (81)
+.-+.|+.|.....+++.+..-..+..+|
T Consensus 38 ~~tLPC~~Cr~HA~~ai~knnimSs~diN 66 (96)
T PHA03005 38 CSTLPCPACRRHAKEAIEKNNIMSSNDLN 66 (96)
T ss_pred hhcCCCHHHHHHHHHHHhhcCccccCCcc
Confidence 34577999999999988876554444433
No 27
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=45.89 E-value=21 Score=20.65 Aligned_cols=26 Identities=31% Similarity=0.353 Sum_probs=18.7
Q ss_pred eccccchhHHHHHHHHhcCCCCeeEEEEe
Q psy13020 52 VDGMKCQSCVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 52 i~g~~c~~C~~~i~~~l~~~~gv~~~~~~ 80 (81)
+.++.|-+|. +..+.+++||..+.+.
T Consensus 7 ~fagGCFWg~---E~~f~~~~GV~~t~vG 32 (172)
T PRK14054 7 VLAGGCFWGM---EAPFDRVKGVISTRVG 32 (172)
T ss_pred EEEcCChhhh---HHHHccCCCEEEEEee
Confidence 3456676665 5577889999988775
No 28
>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=43.89 E-value=34 Score=20.25 Aligned_cols=21 Identities=29% Similarity=0.313 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCCCeeEEEEeC
Q psy13020 61 VKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 61 ~~~i~~~l~~~~gv~~~~~~~ 81 (81)
...+++.++.++||..++|.+
T Consensus 117 e~eL~~tI~~i~gV~~A~V~l 137 (206)
T PF01514_consen 117 EGELERTIESIDGVESARVHL 137 (206)
T ss_dssp HHHHHHHHTTSTTEEEEEEEE
T ss_pred HHHHHHHHHcCCCeeEEEEEE
Confidence 456677899999999999863
No 29
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=40.72 E-value=49 Score=16.42 Aligned_cols=64 Identities=14% Similarity=0.123 Sum_probs=44.7
Q ss_pred eEEEEEcCCCCCHHHHHHHHHhcCCcccCCC-------CCceEEEEeccccchhHHHHHHHHhcCCCCeeEEEE
Q psy13020 13 NANIRFNPIITNEETLRISIEDMGFDARLPS-------TNDEATFTVDGMKCQSCVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 13 ~~~v~~~~~~~~~~~i~~~i~~~g~~~~~~~-------~~~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~ 79 (81)
...+..+..+-....+...+..-||.+..++ ...+.++.+. .......+.+.|.++.+|..+.+
T Consensus 5 ~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~~~sriti~v~---~~~~i~ql~kQL~KL~dV~~V~~ 75 (76)
T PRK11152 5 QLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDAQNINIELTVA---SERPIDLLSSQLNKLVDVAHVEI 75 (76)
T ss_pred EEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCCCEEEEEEEEC---CCchHHHHHHHHhcCcCeEEEEE
Confidence 3344444444567888999999999875322 1135566663 46688899999999999998875
No 30
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=40.32 E-value=38 Score=17.77 Aligned_cols=33 Identities=21% Similarity=0.258 Sum_probs=23.4
Q ss_pred EEecCCeEEEEEcCCCCCHHHHHHHHHhcCCcc
Q psy13020 7 VSLEQKNANIRFNPIITNEETLRISIEDMGFDA 39 (81)
Q Consensus 7 v~~~~~~~~v~~~~~~~~~~~i~~~i~~~g~~~ 39 (81)
++..+++..+......++.+++.+++++.|-.+
T Consensus 42 vD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~I 74 (95)
T PF02680_consen 42 VDVETENLKITIEGDDIDFDEIKEAIEELGGVI 74 (95)
T ss_dssp E-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EE
T ss_pred eeccccEEEEEEEeCCCCHHHHHHHHHHcCCeE
Confidence 345566777777666688999999999998654
No 31
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=39.08 E-value=28 Score=20.98 Aligned_cols=29 Identities=24% Similarity=0.291 Sum_probs=20.5
Q ss_pred EEeccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 50 FTVDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 50 ~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
..+.|+.|.+|.. ..+.+++||..+.+.+
T Consensus 47 ~a~fagGCFWg~E---~~F~~l~GV~~t~vGY 75 (213)
T PRK00058 47 QAIFGMGCFWGAE---RLFWQLPGVYSTAVGY 75 (213)
T ss_pred EEEEEccCcchhH---HHHhcCCCEEEEEeee
Confidence 4455677777764 5677789999887753
No 32
>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=39.00 E-value=41 Score=19.12 Aligned_cols=26 Identities=35% Similarity=0.404 Sum_probs=18.8
Q ss_pred eccccchhHHHHHHHHhcCCCCeeEEEEe
Q psy13020 52 VDGMKCQSCVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 52 i~g~~c~~C~~~i~~~l~~~~gv~~~~~~ 80 (81)
+.|+.|-+|. +..+.+++||....+.
T Consensus 4 ~fa~GCFW~~---e~~f~~~~GV~~t~vG 29 (155)
T PF01625_consen 4 YFAGGCFWGV---EAAFRRLPGVISTRVG 29 (155)
T ss_dssp EEEESSHHHH---HHHHHTSTTEEEEEEE
T ss_pred EEecCCCeEh---HHHHhhCCCEEEEEec
Confidence 3456677665 5678888999988765
No 33
>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=38.31 E-value=32 Score=19.43 Aligned_cols=26 Identities=27% Similarity=0.143 Sum_probs=18.2
Q ss_pred ccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 53 DGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 53 ~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
.++.|-+|. +..+.+++||..+.+.+
T Consensus 5 ~agGCFWg~---E~~f~~~~GV~~t~~GY 30 (149)
T TIGR00401 5 FAGGCFWGV---EKYFWLIPGVYSTAVGY 30 (149)
T ss_pred EecCCchhh---HHHHhcCCCEEEEEEee
Confidence 456677665 45677889999887753
No 34
>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=38.18 E-value=47 Score=15.51 Aligned_cols=65 Identities=11% Similarity=0.092 Sum_probs=39.9
Q ss_pred EEEEcCCCCCHHHHHHHHHhcCCcccCCC----CC--ceEEEEeccccchhHHHHHHHHhcCCCCeeEEEE
Q psy13020 15 NIRFNPIITNEETLRISIEDMGFDARLPS----TN--DEATFTVDGMKCQSCVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 15 ~v~~~~~~~~~~~i~~~i~~~g~~~~~~~----~~--~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~ 79 (81)
.+...+.+-...++...+.+.+.++..+. .. ....+.+.--.-..--..+-+.|++++||.++.+
T Consensus 4 ~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 4 SLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 34444434457888999988887753221 11 2344444332222356788889999999998864
No 35
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=34.91 E-value=47 Score=19.55 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=16.2
Q ss_pred HHHHHHHhcCCCCeeEEEEeC
Q psy13020 61 VKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 61 ~~~i~~~l~~~~gv~~~~~~~ 81 (81)
...+++.+.+++||..++|++
T Consensus 109 e~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 109 EQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHhcCCeeeeEEEE
Confidence 345667888999999998863
No 36
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=34.84 E-value=57 Score=20.17 Aligned_cols=21 Identities=29% Similarity=0.483 Sum_probs=17.3
Q ss_pred HHHHHHHHhcCCCCeeEEEEe
Q psy13020 60 CVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 60 C~~~i~~~l~~~~gv~~~~~~ 80 (81)
-...++..|+.++||..++|.
T Consensus 110 ~eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 110 KEQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HHHHHHHHHHhcCceEEEEEE
Confidence 456788899999999998873
No 37
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=33.53 E-value=90 Score=17.35 Aligned_cols=27 Identities=26% Similarity=0.653 Sum_probs=18.3
Q ss_pred HHHHhcCCcccCCCCCceEEEEeccccchhHHHH
Q psy13020 30 ISIEDMGFDARLPSTNDEATFTVDGMKCQSCVKK 63 (81)
Q Consensus 30 ~~i~~~g~~~~~~~~~~~~~~~i~g~~c~~C~~~ 63 (81)
......||.+ ....+.+.|. |+.|...
T Consensus 116 ~~~~~~Gf~i------~~~~l~~~G~-C~~C~~~ 142 (145)
T COG0735 116 EIAKKLGFKL------KDHTLEIYGI-CPDCQAK 142 (145)
T ss_pred HHHHhcCCee------eeeEEEEEEE-CcchHhh
Confidence 3334568886 3557778888 8888764
No 38
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=31.82 E-value=29 Score=16.55 Aligned_cols=43 Identities=12% Similarity=0.386 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHhcCCc-ccCCCCCceEEEEeccccchhHHHHHHHHhcC
Q psy13020 23 TNEETLRISIEDMGFD-ARLPSTNDEATFTVDGMKCQSCVKKIEATIGE 70 (81)
Q Consensus 23 ~~~~~i~~~i~~~g~~-~~~~~~~~~~~~~i~g~~c~~C~~~i~~~l~~ 70 (81)
++..+|.+++...|-. .. .-....=-|-.|..|...+.+.|..
T Consensus 9 Vtd~~I~~ai~~~g~~s~~-----~l~~~~~~g~~CG~C~~~i~~il~~ 52 (64)
T PRK10509 9 VSDKKIRQAVRQFHPQSFQ-----QLRKFVPVGNQCGKCIRAAREVMQD 52 (64)
T ss_pred CCHHHHHHHHHHcCCCCHH-----HHHHhcCCCCCccchHHHHHHHHHH
Confidence 4566788888754422 11 0000111256799999888877644
No 39
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=31.77 E-value=80 Score=16.21 Aligned_cols=65 Identities=14% Similarity=0.136 Sum_probs=35.6
Q ss_pred EEEEcCCCCCHHHHHHHHHhc---CCcccCCC------CCceEEEEeccccchhHHHHHHHHhcCCCCeeEEEE
Q psy13020 15 NIRFNPIITNEETLRISIEDM---GFDARLPS------TNDEATFTVDGMKCQSCVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 15 ~v~~~~~~~~~~~i~~~i~~~---g~~~~~~~------~~~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~ 79 (81)
.|.+.+..++.+++.+.++.. |+...-.. .-....+.+---....-...+++.+.+.+||.++.+
T Consensus 9 ~V~P~d~e~Dl~~L~~~ik~~~~~g~~~~~~~~ePIaFGLkaL~i~~vv~D~~~~td~lee~i~~~e~Vqsvei 82 (88)
T PRK00435 9 KVMPESPEVDLDELKEKIKEVLPEGYKINGIEEEPIAFGLKALKLYVIMPDEEGGTEPVEEAFANVEGVESVEV 82 (88)
T ss_pred EECCCCCCcCHHHHHHHHHHhCcCCcEEeEeEEEEeeccceeEEEEEEEEcCCcCcHHHHHHHhccCCCcEEEE
Confidence 344545557888888888754 33221000 001111111111113456889999999999988765
No 40
>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=31.39 E-value=19 Score=16.25 Aligned_cols=16 Identities=31% Similarity=0.814 Sum_probs=3.4
Q ss_pred cccchhHHHHHHHHhc
Q psy13020 54 GMKCQSCVKKIEATIG 69 (81)
Q Consensus 54 g~~c~~C~~~i~~~l~ 69 (81)
|..|.+|...+...|.
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 7789999987766554
No 41
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=30.58 E-value=32 Score=20.26 Aligned_cols=28 Identities=21% Similarity=0.241 Sum_probs=20.1
Q ss_pred EeccccchhHHHHHHHHhcCCCCeeEEEEeC
Q psy13020 51 TVDGMKCQSCVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 51 ~i~g~~c~~C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
.+.++.|-+|.. ..+.+++||..+.+.+
T Consensus 11 a~~agGCFWg~E---~~f~~l~GV~~t~vGY 38 (186)
T PRK13014 11 ATFAGGCFWGVE---GVFQHVPGVVSVVSGY 38 (186)
T ss_pred EEEecCCceeeH---HHHccCCCEEEEEeee
Confidence 455677887764 5677889999887753
No 42
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=30.24 E-value=64 Score=19.96 Aligned_cols=21 Identities=33% Similarity=0.517 Sum_probs=17.7
Q ss_pred HHHHHHHhcCCCCeeEEEEeC
Q psy13020 61 VKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 61 ~~~i~~~l~~~~gv~~~~~~~ 81 (81)
...+++.+..++||..++|++
T Consensus 109 egELarTI~~idgV~~ArVhL 129 (249)
T PRK15348 109 EQRIEGMLSQMEGVINAKVTI 129 (249)
T ss_pred HHHHHHHHHhCCCeeEeEEEE
Confidence 466888999999999999863
No 43
>COG3309 VapD Uncharacterized virulence-associated protein D [Function unknown]
Probab=29.84 E-value=92 Score=16.29 Aligned_cols=44 Identities=11% Similarity=0.187 Sum_probs=33.7
Q ss_pred HHHHHHHHhcCCcccCCCCCceEEEEeccccchhHHHHHHHHhcCCCC
Q psy13020 26 ETLRISIEDMGFDARLPSTNDEATFTVDGMKCQSCVKKIEATIGEKPG 73 (81)
Q Consensus 26 ~~i~~~i~~~g~~~~~~~~~~~~~~~i~g~~c~~C~~~i~~~l~~~~g 73 (81)
.+|.+.++..||+-. +..+.+.-.|..-..|...+.+.+.+.+.
T Consensus 26 ~Dir~~L~~~gF~~t----QGSVYl~~~~i~~~~~~~~~q~~~~q~~w 69 (96)
T COG3309 26 DDIRRVLERHGFENT----QGSVYLNDEGINQAAGTLAAQNLAKQFQW 69 (96)
T ss_pred HHHHHHHHHcCcccc----cceEEEccchHHHHHHHHHHHHHHHHhHH
Confidence 467778888999864 46778888888888888888887766643
No 44
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=29.67 E-value=90 Score=16.14 Aligned_cols=66 Identities=17% Similarity=0.140 Sum_probs=39.0
Q ss_pred EEEEEcCCCCCHHHHHHHHHhc---CCcccCCCC------CceEEEEeccccchhHHHHHHHHhcCCCCeeEEEE
Q psy13020 14 ANIRFNPIITNEETLRISIEDM---GFDARLPST------NDEATFTVDGMKCQSCVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 14 ~~v~~~~~~~~~~~i~~~i~~~---g~~~~~~~~------~~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~ 79 (81)
..|.+++..++.+.+.+.+... ||...-+.. -.-..+.+-.-.-.+-...+++.|....||.++++
T Consensus 8 lkV~P~d~evdl~~L~~~ik~~l~~g~~~~~~~~epIaFGLkal~l~vvv~D~Eg~td~~ee~l~~vegV~svev 82 (88)
T COG2092 8 LKVMPDDPEVDLEELEEKIKEKLPEGYELIKIEEEPIAFGLKALKLYVVVEDKEGGTDALEEALEEVEGVESVEV 82 (88)
T ss_pred EEecCCCCCCCHHHHHHHHHHhccccceeccceeEeeeeeeeeEEEEEEEcccccCcHHHHHHHhhccCcceEEE
Confidence 4455666668889888888653 444221100 01112222223344457789999999999988765
No 45
>PRK05974 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed
Probab=29.63 E-value=81 Score=15.59 Aligned_cols=68 Identities=9% Similarity=0.250 Sum_probs=38.2
Q ss_pred eEEEEEcCCCCCH--HHHHHHHHhcCCc-ccCCCCCceEEEEeccc---cchhHHHHHHHHhcCCCCeeEEEEe
Q psy13020 13 NANIRFNPIITNE--ETLRISIEDMGFD-ARLPSTNDEATFTVDGM---KCQSCVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 13 ~~~v~~~~~~~~~--~~i~~~i~~~g~~-~~~~~~~~~~~~~i~g~---~c~~C~~~i~~~l~~~~gv~~~~~~ 80 (81)
+..|.+.+...++ +.+.+.+...||+ +.-....+.+.+.+.+- .-...+..+-+.|...|-+...+++
T Consensus 4 ~V~V~~k~gv~Dp~G~ai~~~l~~lg~~~v~~Vr~~k~~~l~~~~~~~~~a~~~v~~i~~~lL~Npvie~~~i~ 77 (80)
T PRK05974 4 KVTVTLKEGVLDPQGQAIKGALGSLGYDGVEDVRQGKYFELELEGESEEKAEADLKEMCEKLLANPVIEDYRIE 77 (80)
T ss_pred EEEEEECCCCcChHHHHHHHHHHHcCCCCcceEEEEEEEEEEEcCCchhhhHHHHHHHHHHhcCCceeeEEEEE
Confidence 3455666655555 4678888888997 32111123344544452 2344566776777666766665543
No 46
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=28.91 E-value=71 Score=14.73 Aligned_cols=21 Identities=43% Similarity=0.452 Sum_probs=17.4
Q ss_pred HHHHHHHHhcCCCCeeEEEEe
Q psy13020 60 CVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 60 C~~~i~~~l~~~~gv~~~~~~ 80 (81)
-...+++.|.+.|.|.++.+.
T Consensus 35 ~~~~~~~~l~~~p~V~~v~V~ 55 (69)
T PF08478_consen 35 DLKKIEQRLEKLPWVKSVSVS 55 (69)
T ss_dssp HHHHHHHCCCCTTTEEEEEEE
T ss_pred CHHHHHHHHHcCCCEEEEEEE
Confidence 467888899999999988874
No 47
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=28.83 E-value=1.2e+02 Score=17.26 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=24.4
Q ss_pred ceEEEEeccccchhHHHHHHHHhcCCCCeeEEEE
Q psy13020 46 DEATFTVDGMKCQSCVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 46 ~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~ 79 (81)
...++.|+-..|..|...|.....++ |+....+
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I 132 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTI 132 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHHc-CCCeEEE
Confidence 67788899889999998887766655 5544433
No 48
>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=28.49 E-value=94 Score=15.96 Aligned_cols=63 Identities=16% Similarity=0.178 Sum_probs=35.8
Q ss_pred EEEEcCCCCCHHHHHHHHHhc---CCcccCCCC------Cc--eEEEEeccccchhHHHHHHHHhcCCCCeeEEEE
Q psy13020 15 NIRFNPIITNEETLRISIEDM---GFDARLPST------ND--EATFTVDGMKCQSCVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 15 ~v~~~~~~~~~~~i~~~i~~~---g~~~~~~~~------~~--~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~ 79 (81)
.|.+....++.+++.+.++.. |+.+.-... -. .....+..- ..-...+++.+.+.+||.++++
T Consensus 9 kV~P~s~evDle~L~~~ik~~~~~g~~~~~~~~ePiaFGLkaL~~~~vv~D~--~g~td~lee~i~~ve~V~svev 82 (88)
T TIGR00489 9 KVMPESPDVDLEALKEKIKERIPEGVEIRKIDEEPIAFGLVAINVMVVMGDA--EGGTEAAEESLSGIEGVESVEV 82 (88)
T ss_pred EECCCCCccCHHHHHHHHHHhCcCCcEEeeeEEEeeeccceeeEEEEEEecC--CcChHHHHHHHhcCCCccEEEE
Confidence 344545557888888888764 332210000 01 112222222 2345889999999999988875
No 49
>TIGR00302 phosphoribosylformylglycinamidine synthase, purS protein. In species such as Bacillus subtilis in which FGAM synthetase is split into two ORFs purL and purQ, this small protein, previously called yexA, is required for FGAM synthetase activity. Although the article does not make it clear whether this is a subunit or an accessory protein, it is encoded as part of the operon, which suggests stochiometric amounts, = subunit.
Probab=26.82 E-value=93 Score=15.37 Aligned_cols=66 Identities=11% Similarity=0.210 Sum_probs=37.3
Q ss_pred eEEEEEcCCCCCH--HHHHHHHHhcCCc-ccCCCCCceEEEEecccc---chhHHHHHHHHhcCCCCeeEEE
Q psy13020 13 NANIRFNPIITNE--ETLRISIEDMGFD-ARLPSTNDEATFTVDGMK---CQSCVKKIEATIGEKPGVIAVK 78 (81)
Q Consensus 13 ~~~v~~~~~~~~~--~~i~~~i~~~g~~-~~~~~~~~~~~~~i~g~~---c~~C~~~i~~~l~~~~gv~~~~ 78 (81)
+..|.+.+...++ +.+...+.+.||+ +.-+...+.+.+.+.|.. -......+-+.|...|-+...+
T Consensus 4 ~I~V~~k~gV~Dp~G~ti~~~l~~lg~~~v~~Vr~~k~~~l~~~~~~~~~a~~~v~~i~~~lL~Npvie~~~ 75 (80)
T TIGR00302 4 EVYIRLKKGVLDPEGAAIQRALALLGYNEVKDVRTGKVIELTIEADSEEAVEREVEEMCEKLLANPVIHDYD 75 (80)
T ss_pred EEEEEECCCCcChHHHHHHHHHHHcCCCCcceEEEEEEEEEEEcCCChhhHHHHHHHHHHHhcCCceeeEEE
Confidence 4456666655555 5678888888997 321111233344446654 2345666666666666665544
No 50
>PF15644 Tox-PL: Papain fold toxin 1; PDB: 3B21_A.
Probab=26.03 E-value=71 Score=16.75 Aligned_cols=18 Identities=39% Similarity=0.748 Sum_probs=12.3
Q ss_pred cchhHHHHHHHHhcCCCC
Q psy13020 56 KCQSCVKKIEATIGEKPG 73 (81)
Q Consensus 56 ~c~~C~~~i~~~l~~~~g 73 (81)
.|..|+..++..+...|-
T Consensus 2 NC~~C~~A~~~~l~G~~~ 19 (111)
T PF15644_consen 2 NCQDCVVAVEARLRGYPV 19 (111)
T ss_dssp --HHHHHHHHHHHTTS--
T ss_pred cchhhHHHHHHHhCCCCe
Confidence 489999999998886654
No 51
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=25.96 E-value=93 Score=15.10 Aligned_cols=14 Identities=21% Similarity=0.586 Sum_probs=7.6
Q ss_pred cchhHHHHHHHHhcC
Q psy13020 56 KCQSCVKKIEATIGE 70 (81)
Q Consensus 56 ~c~~C~~~i~~~l~~ 70 (81)
.|+.|.. +.+.|.+
T Consensus 10 ~C~~C~~-a~~~L~~ 23 (85)
T PRK11200 10 GCPYCVR-AKELAEK 23 (85)
T ss_pred CChhHHH-HHHHHHh
Confidence 5888863 3333333
No 52
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.44 E-value=1.1e+02 Score=15.95 Aligned_cols=34 Identities=18% Similarity=0.282 Sum_probs=26.5
Q ss_pred EEecCCeEEEEEcCCCCCHHHHHHHHHhcCCccc
Q psy13020 7 VSLEQKNANIRFNPIITNEETLRISIEDMGFDAR 40 (81)
Q Consensus 7 v~~~~~~~~v~~~~~~~~~~~i~~~i~~~g~~~~ 40 (81)
++..+....+......++.+++.+.+++.|..+.
T Consensus 44 iD~et~~~~itIeG~~ldydei~~~iE~~Gg~IH 77 (97)
T COG1888 44 IDVETENLKITIEGTNLDYDEIEEVIEELGGAIH 77 (97)
T ss_pred eeehhcceEEEEEcCCCCHHHHHHHHHHcCCeee
Confidence 4456777777777667899999999999987653
No 53
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=24.64 E-value=64 Score=16.81 Aligned_cols=18 Identities=39% Similarity=0.879 Sum_probs=14.4
Q ss_pred EEeccccchhHHHHHHHHh
Q psy13020 50 FTVDGMKCQSCVKKIEATI 68 (81)
Q Consensus 50 ~~i~g~~c~~C~~~i~~~l 68 (81)
+.+.|+ |..|...|+..+
T Consensus 27 ~~~~gv-C~rC~~~IeWK~ 44 (92)
T PF10217_consen 27 LPIDGV-CQRCKDIIEWKV 44 (92)
T ss_pred Cccccc-cHhHHHHHHHHH
Confidence 556677 999999998864
No 54
>COG1913 Predicted Zn-dependent proteases [General function prediction only]
Probab=23.75 E-value=67 Score=18.92 Aligned_cols=19 Identities=26% Similarity=0.562 Sum_probs=15.1
Q ss_pred ccccchhHHHHHHHHhcCC
Q psy13020 53 DGMKCQSCVKKIEATIGEK 71 (81)
Q Consensus 53 ~g~~c~~C~~~i~~~l~~~ 71 (81)
..+.|.+|..+++..+...
T Consensus 161 s~~fC~~C~~kL~~~l~~~ 179 (181)
T COG1913 161 SPNFCNSCLRKLERKLKYS 179 (181)
T ss_pred chhhhHHHHHHHHHhhccC
Confidence 3467999999999887654
No 55
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=23.56 E-value=32 Score=16.43 Aligned_cols=17 Identities=35% Similarity=0.694 Sum_probs=7.8
Q ss_pred ceEEEEeccccchhHHH
Q psy13020 46 DEATFTVDGMKCQSCVK 62 (81)
Q Consensus 46 ~~~~~~i~g~~c~~C~~ 62 (81)
..+.+++-|+-|..|..
T Consensus 40 s~v~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 40 SEVPFHFLGHKCSHCGS 56 (61)
T ss_dssp EEEE--TT----TTTS-
T ss_pred cceeeeHhhhcCCCCCC
Confidence 45779999999999964
No 56
>COG4248 Uncharacterized protein with protein kinase and helix-hairpin-helix DNA-binding domains [General function prediction only]
Probab=23.31 E-value=31 Score=23.64 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=17.0
Q ss_pred eEEEEeccccchhHHHHHHHHhc
Q psy13020 47 EATFTVDGMKCQSCVKKIEATIG 69 (81)
Q Consensus 47 ~~~~~i~g~~c~~C~~~i~~~l~ 69 (81)
...+.+.+..|++|+..-+..+.
T Consensus 312 ~H~y~~hl~~CPwCa~~~~g~~~ 334 (637)
T COG4248 312 MHVYPVHLTDCPWCALDNQGVIY 334 (637)
T ss_pred cccccCCCCCCchhhhcccCccc
Confidence 34588999999999985554443
No 57
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=23.08 E-value=1.2e+02 Score=15.36 Aligned_cols=34 Identities=24% Similarity=0.423 Sum_probs=22.1
Q ss_pred eEEEEeccccchhHH---HHHHHHhcCCCCeeEEEEe
Q psy13020 47 EATFTVDGMKCQSCV---KKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 47 ~~~~~i~g~~c~~C~---~~i~~~l~~~~gv~~~~~~ 80 (81)
.+.+.+....|+... ..++..+..++|+..+.++
T Consensus 40 ~i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~ 76 (99)
T TIGR02945 40 DIQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVE 76 (99)
T ss_pred EEEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEE
Confidence 455556556666543 3456678888888877765
No 58
>PRK04435 hypothetical protein; Provisional
Probab=22.93 E-value=1.5e+02 Score=16.50 Aligned_cols=58 Identities=12% Similarity=0.123 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHhcCCcccCCC----CC--ceEEEEeccccchhHHHHHHHHhcCCCCeeEEEE
Q psy13020 22 ITNEETLRISIEDMGFDARLPS----TN--DEATFTVDGMKCQSCVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 22 ~~~~~~i~~~i~~~g~~~~~~~----~~--~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~~~ 79 (81)
+-...++...+...|.++..++ .+ ....+.+.--.-......+-..|++++||..+.+
T Consensus 80 ~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 80 SGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTSSMEGDIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred CCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEEE
Confidence 3457888888888887753221 11 2344555443344467888899999999998764
No 59
>PRK11018 hypothetical protein; Provisional
Probab=21.88 E-value=1.2e+02 Score=14.87 Aligned_cols=25 Identities=8% Similarity=0.056 Sum_probs=18.9
Q ss_pred EEEEeccccchhHHHHHHHHhcCCC
Q psy13020 48 ATFTVDGMKCQSCVKKIEATIGEKP 72 (81)
Q Consensus 48 ~~~~i~g~~c~~C~~~i~~~l~~~~ 72 (81)
..+.+.|..|+.-..+..++|.+++
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~ 33 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLK 33 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCC
Confidence 4567778888887777777877775
No 60
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=21.62 E-value=1.5e+02 Score=15.95 Aligned_cols=33 Identities=30% Similarity=0.478 Sum_probs=22.4
Q ss_pred EEEeccccchh---HHHHHHHHhcCCCCeeEEEEeC
Q psy13020 49 TFTVDGMKCQS---CVKKIEATIGEKPGVIAVKVSH 81 (81)
Q Consensus 49 ~~~i~g~~c~~---C~~~i~~~l~~~~gv~~~~~~~ 81 (81)
.....-+.|+. =...++.++.+.+|+.++++++
T Consensus 54 ~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 54 KMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred EEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 33344455664 2456678899999999988864
No 61
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=21.47 E-value=99 Score=13.78 Aligned_cols=62 Identities=13% Similarity=0.132 Sum_probs=36.7
Q ss_pred EEEEEcCCCCCHHHHHHHHHhcCCcccCC---C----CCceEEEEeccccchhHHHHHHHHhcCCCCeeEE
Q psy13020 14 ANIRFNPIITNEETLRISIEDMGFDARLP---S----TNDEATFTVDGMKCQSCVKKIEATIGEKPGVIAV 77 (81)
Q Consensus 14 ~~v~~~~~~~~~~~i~~~i~~~g~~~~~~---~----~~~~~~~~i~g~~c~~C~~~i~~~l~~~~gv~~~ 77 (81)
..+...+..-...++...+.+.+..+... . ......+.+.... .-...+-+.|++++++..+
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 3 LSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVEGDD--DVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred EEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEECCH--HHHHHHHHHHhCCccEEEe
Confidence 34455444445778888888777764311 0 1123556665543 3455667788888888765
No 62
>PHA03075 glutaredoxin-like protein; Provisional
Probab=21.27 E-value=1.6e+02 Score=16.18 Aligned_cols=21 Identities=14% Similarity=0.291 Sum_probs=16.5
Q ss_pred cCCCCCHHHHHHHHHhcCCcc
Q psy13020 19 NPIITNEETLRISIEDMGFDA 39 (81)
Q Consensus 19 ~~~~~~~~~i~~~i~~~g~~~ 39 (81)
+...++.+++.+.++++.|.+
T Consensus 98 d~~~v~~d~L~~~Ie~a~ygv 118 (123)
T PHA03075 98 DKSFVDLDQLKEEIEKAPYGV 118 (123)
T ss_pred chhhcCHHHHHHHHHhCCCCc
Confidence 444567889999999998875
No 63
>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=21.03 E-value=1.4e+02 Score=16.81 Aligned_cols=22 Identities=27% Similarity=0.424 Sum_probs=17.9
Q ss_pred hhHHHHHHHHhcCCCCeeEEEE
Q psy13020 58 QSCVKKIEATIGEKPGVIAVKV 79 (81)
Q Consensus 58 ~~C~~~i~~~l~~~~gv~~~~~ 79 (81)
..-+..+...+.+++||..+.+
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~v 95 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATV 95 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEE
Confidence 3467888889999999998865
No 64
>PF05922 Inhibitor_I9: Peptidase inhibitor I9; InterPro: IPR010259 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes []. The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route []. The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus. Proteinase propeptide inhibitors (sometimes refered to as activation peptides) are responsible for the modulation of folding and activity of the pro-enzyme or zymogen. The pro-segment docks into the enzyme moiety shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology [], despite often low sequence identities []. The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology. This group of sequences contain the propeptide domain at the N terminus of peptidases belonging to MEROPS family S8A, subtilisins. A number of the members of this group of sequences belong to MEROPS inhibitor family I9, clan I-. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.; GO: 0004252 serine-type endopeptidase activity, 0042802 identical protein binding, 0043086 negative regulation of catalytic activity; PDB: 3CNQ_P 1SPB_P 3CO0_P 1ITP_A 1V5I_B 1SCJ_B 3P5B_P 2XTJ_P 2W2M_P 2P4E_P ....
Probab=20.80 E-value=1.2e+02 Score=14.38 Aligned_cols=28 Identities=18% Similarity=0.381 Sum_probs=19.0
Q ss_pred eccccchhHHHHHHHHhcCCCCeeEEEEe
Q psy13020 52 VDGMKCQSCVKKIEATIGEKPGVIAVKVS 80 (81)
Q Consensus 52 i~g~~c~~C~~~i~~~l~~~~gv~~~~~~ 80 (81)
+.|+.=.--... -+.|++.|+|..+..|
T Consensus 49 ~~Gfs~~l~~~~-i~~L~~~p~V~~Ve~D 76 (82)
T PF05922_consen 49 FNGFSAKLSEEE-IEKLRKDPGVKSVEPD 76 (82)
T ss_dssp SSEEEEEE-HHH-HHHHHTSTTEEEEEEE
T ss_pred EEEEEEEeCHHH-HHHHHcCCCeEEEEeC
Confidence 566555544433 4788999999998876
No 65
>PF08210 APOBEC_N: APOBEC-like N-terminal domain; InterPro: IPR013158 This domain is found at the N terminus of the Apolipoprotein B mRNA editing enzyme. Apobec-1 catalyzes C to U editing of apolipoprotein B (apoB) mRNA in the mammalian intestine. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination. APOBEC-3 like members contain two copies of this domain. This family also includes the functionally homologous activation induced deaminase, which is essential for the development of antibody diversity in B lymphocytes. RNA editing by APOBEC-1 requires homodimerisation and this complex interacts with RNA binding proteins to from the editosome [] (and references therein).; GO: 0008270 zinc ion binding, 0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines; PDB: 3IQS_A 3IR2_A 3V4J_B 2KEM_A 2KBO_A 3V4K_A 3E1U_A 2JYW_A 2RPZ_A.
Probab=20.46 E-value=2e+02 Score=16.87 Aligned_cols=30 Identities=23% Similarity=0.442 Sum_probs=23.8
Q ss_pred ceEEEEeccccchh----HHHHHHHHhcCC--CCee
Q psy13020 46 DEATFTVDGMKCQS----CVKKIEATIGEK--PGVI 75 (81)
Q Consensus 46 ~~~~~~i~g~~c~~----C~~~i~~~l~~~--~gv~ 75 (81)
.++++-+.=-.|.. |+.++.+-|.+. +++.
T Consensus 74 y~ITwy~SwSPC~~~~~~Ca~~i~~FL~~~~~~~v~ 109 (188)
T PF08210_consen 74 YRITWYLSWSPCPESDHCCAEKIAEFLKKHLKPNVS 109 (188)
T ss_dssp EEEEEEESSS--CC----HHHHHHHHHCCC--TTEE
T ss_pred EEEEEEEecCCCcchhhHHHHHHHHHHHHhCCCCCe
Confidence 46777788888999 999999999999 8764
No 66
>cd08969 MeNeil3_N N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3). This family contains the N-terminal domain of the Metazoan Neil3. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. In contrast, mouse NEIL3 (MmuNEIL3) forms a Schiff base intermediate via its N-
Probab=20.29 E-value=85 Score=17.71 Aligned_cols=24 Identities=29% Similarity=0.448 Sum_probs=17.1
Q ss_pred eccccchhHHHHHHHHhcCCCCee
Q psy13020 52 VDGMKCQSCVKKIEATIGEKPGVI 75 (81)
Q Consensus 52 i~g~~c~~C~~~i~~~l~~~~gv~ 75 (81)
+.|+.|.-+..+|...+....-+.
T Consensus 2 vegpgc~lngek~~~~v~~~q~v~ 25 (140)
T cd08969 2 VEGPGCTLNGEKIRARVEKGQRVV 25 (140)
T ss_pred ccCCccccccHHHHHHhhccceee
Confidence 568888888888888776554433
Done!