Query 029137
Match_columns 198
No_of_seqs 190 out of 1104
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:05:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029137.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029137hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.6 2.5E-14 5.3E-19 102.6 8.8 69 7-75 3-71 (73)
2 PF00403 HMA: Heavy-metal-asso 99.4 4.5E-13 9.7E-18 91.7 7.6 58 12-70 1-62 (62)
3 COG2608 CopZ Copper chaperone 99.3 1.9E-11 4.2E-16 87.3 7.9 66 8-74 1-70 (71)
4 KOG4656 Copper chaperone for s 99.0 6.9E-10 1.5E-14 94.9 8.3 72 7-79 5-76 (247)
5 PLN02957 copper, zinc superoxi 98.5 6.9E-07 1.5E-11 77.2 10.2 73 6-79 3-75 (238)
6 PRK10671 copA copper exporting 98.3 1.8E-06 4E-11 85.9 8.2 66 8-76 2-68 (834)
7 TIGR00003 copper ion binding p 97.9 0.00016 3.5E-09 45.0 8.4 61 9-70 2-66 (68)
8 COG2217 ZntA Cation transport 97.7 9.8E-05 2.1E-09 73.2 7.5 63 9-73 2-69 (713)
9 PRK10671 copA copper exporting 97.0 0.0019 4.2E-08 64.6 7.9 64 10-74 100-164 (834)
10 KOG0207 Cation transport ATPas 96.7 0.0036 7.8E-08 63.4 7.0 66 9-75 146-215 (951)
11 PRK11033 zntA zinc/cadmium/mer 96.2 0.013 2.8E-07 58.3 7.3 64 8-73 52-118 (741)
12 KOG0207 Cation transport ATPas 96.2 0.0089 1.9E-07 60.7 6.1 62 16-78 2-65 (951)
13 TIGR02052 MerP mercuric transp 93.5 1.3 2.8E-05 30.2 9.1 64 9-73 23-90 (92)
14 PF02680 DUF211: Uncharacteriz 89.4 2.1 4.5E-05 32.8 6.9 66 8-74 4-77 (95)
15 PF01883 DUF59: Domain of unkn 89.3 0.58 1.3E-05 32.6 3.7 33 9-41 34-72 (72)
16 cd00371 HMA Heavy-metal-associ 87.3 3.3 7.2E-05 22.6 7.1 49 16-64 6-56 (63)
17 COG1888 Uncharacterized protei 87.2 4 8.8E-05 31.1 7.2 67 8-75 5-80 (97)
18 PRK13748 putative mercuric red 86.5 4 8.7E-05 38.6 8.6 64 12-76 3-69 (561)
19 PF14437 MafB19-deam: MafB19-l 70.9 10 0.00023 31.0 5.2 42 8-50 99-142 (146)
20 TIGR03406 FeS_long_SufT probab 64.3 9.7 0.00021 31.8 3.8 35 10-44 114-154 (174)
21 cd04888 ACT_PheB-BS C-terminal 62.1 23 0.00051 23.8 4.9 33 9-41 41-74 (76)
22 TIGR02945 SUF_assoc FeS assemb 61.4 13 0.00027 27.4 3.6 35 10-44 38-78 (99)
23 PRK14054 methionine sulfoxide 53.8 42 0.00092 28.0 5.9 51 9-64 4-76 (172)
24 PF04972 BON: BON domain; Int 53.3 11 0.00024 25.1 2.0 33 24-57 2-37 (64)
25 PF14492 EFG_II: Elongation Fa 52.5 74 0.0016 22.4 6.3 62 11-73 6-73 (75)
26 PRK11670 antiporter inner memb 52.3 40 0.00087 31.0 6.1 67 9-76 47-144 (369)
27 PRK10553 assembly protein for 50.9 66 0.0014 23.9 6.0 44 21-64 17-61 (87)
28 PRK06418 transcription elongat 50.4 54 0.0012 27.3 6.0 69 9-77 6-99 (166)
29 PF13732 DUF4162: Domain of un 48.6 50 0.0011 23.0 4.9 42 30-74 26-69 (84)
30 COG2151 PaaD Predicted metal-s 48.3 30 0.00065 27.0 3.9 34 10-43 50-89 (111)
31 TIGR02159 PA_CoA_Oxy4 phenylac 47.6 23 0.00051 28.7 3.4 34 9-43 25-64 (146)
32 PF13291 ACT_4: ACT domain; PD 47.0 56 0.0012 22.6 4.9 33 8-40 47-79 (80)
33 cd02410 archeal_CPSF_KH The ar 46.2 56 0.0012 26.8 5.4 70 9-78 37-116 (145)
34 PF03927 NapD: NapD protein; 45.3 99 0.0021 22.3 6.1 43 21-64 15-58 (79)
35 TIGR02189 GlrX-like_plant Glut 43.4 97 0.0021 22.8 6.0 52 9-69 8-59 (99)
36 PF08712 Nfu_N: Scaffold prote 41.9 80 0.0017 23.2 5.2 40 24-65 37-78 (87)
37 PF05046 Img2: Mitochondrial l 41.9 1.4E+02 0.003 21.9 6.7 58 9-68 28-86 (87)
38 PRK05528 methionine sulfoxide 40.5 99 0.0021 25.4 6.0 45 20-64 8-69 (156)
39 PRK11200 grxA glutaredoxin 1; 39.3 74 0.0016 22.3 4.6 34 11-45 3-40 (85)
40 PF04468 PSP1: PSP1 C-terminal 38.1 1.1E+02 0.0023 22.5 5.4 53 20-73 29-85 (88)
41 PF09580 Spore_YhcN_YlaJ: Spor 37.8 84 0.0018 25.3 5.2 33 20-52 74-106 (177)
42 PF13192 Thioredoxin_3: Thiore 37.5 40 0.00087 23.4 2.9 14 10-24 2-15 (76)
43 PF03927 NapD: NapD protein; 37.0 95 0.0021 22.4 4.9 33 9-41 39-71 (79)
44 PF01206 TusA: Sulfurtransfera 36.6 86 0.0019 21.2 4.5 53 12-74 2-57 (70)
45 cd03028 GRX_PICOT_like Glutare 36.0 1.3E+02 0.0028 21.6 5.5 41 18-70 22-62 (90)
46 COG3643 Glutamate formiminotra 35.8 38 0.00082 30.5 3.0 54 21-74 18-73 (302)
47 PF00679 EFG_C: Elongation fac 33.8 1.3E+02 0.0028 21.5 5.2 58 7-68 5-66 (89)
48 TIGR00489 aEF-1_beta translati 32.9 85 0.0018 23.4 4.1 35 8-42 48-83 (88)
49 PRK13014 methionine sulfoxide 32.4 99 0.0022 26.2 5.0 36 7-47 7-42 (186)
50 TIGR02190 GlrX-dom Glutaredoxi 31.9 1.1E+02 0.0024 21.2 4.5 35 8-44 7-41 (79)
51 PF05663 DUF809: Protein of un 31.8 1.2E+02 0.0026 23.8 4.9 44 20-64 47-90 (138)
52 PRK00435 ef1B elongation facto 31.5 86 0.0019 23.4 4.0 35 8-42 48-83 (88)
53 COG1094 Predicted RNA-binding 31.1 97 0.0021 26.6 4.7 38 23-61 26-66 (194)
54 cd04877 ACT_TyrR N-terminal AC 30.6 1.2E+02 0.0026 20.7 4.4 30 11-40 39-68 (74)
55 PRK00058 methionine sulfoxide 30.3 1.5E+02 0.0032 25.8 5.7 27 20-46 52-78 (213)
56 cd06167 LabA_like LabA_like pr 30.0 66 0.0014 24.6 3.3 30 47-77 103-132 (149)
57 PRK10555 aminoglycoside/multid 29.1 82 0.0018 32.9 4.7 43 22-64 158-208 (1037)
58 cd03029 GRX_hybridPRX5 Glutare 28.5 1.3E+02 0.0029 20.1 4.3 33 11-45 3-35 (72)
59 smart00838 EFG_C Elongation fa 28.4 2.1E+02 0.0046 20.1 5.8 47 14-61 7-54 (85)
60 cd03713 EFG_mtEFG_C EFG_mtEFG_ 27.4 2.1E+02 0.0046 19.7 5.9 47 13-60 4-51 (78)
61 PRK11198 LysM domain/BON super 27.1 1.2E+02 0.0027 24.1 4.5 43 22-64 27-70 (147)
62 PF08002 DUF1697: Protein of u 26.2 2.7E+02 0.0059 21.9 6.3 50 24-74 22-75 (137)
63 COG2092 EFB1 Translation elong 26.0 1.2E+02 0.0026 22.9 3.9 36 7-42 47-83 (88)
64 cd04097 mtEFG1_C mtEFG1_C: C-t 26.0 2.3E+02 0.005 19.6 5.5 46 14-60 5-51 (78)
65 cd02066 GRX_family Glutaredoxi 25.9 1.7E+02 0.0036 18.5 4.3 30 12-43 3-32 (72)
66 cd03711 Tet_C Tet_C: C-terminu 25.7 2.3E+02 0.005 19.6 5.7 47 14-61 5-52 (78)
67 COG2177 FtsX Cell division pro 25.5 96 0.0021 28.0 3.9 48 9-69 61-108 (297)
68 COG3062 NapD Uncharacterized p 25.5 2.3E+02 0.0049 21.7 5.3 48 20-68 17-64 (94)
69 KOG2236 Uncharacterized conser 25.0 1.6E+02 0.0035 28.6 5.4 10 66-75 278-287 (483)
70 TIGR03143 AhpF_homolog putativ 24.8 2.2E+02 0.0048 27.3 6.5 34 10-43 479-515 (555)
71 PRK11152 ilvM acetolactate syn 24.7 1.6E+02 0.0035 21.2 4.3 33 8-42 44-76 (76)
72 PRK10638 glutaredoxin 3; Provi 24.7 1.5E+02 0.0033 20.5 4.2 33 10-44 3-35 (83)
73 KOG3890 Mitochondrial 28S ribo 24.4 33 0.00071 31.8 0.8 16 180-195 175-190 (391)
74 PRK11023 outer membrane lipopr 24.4 1.6E+02 0.0036 24.4 4.9 48 17-64 45-95 (191)
75 cd03420 SirA_RHOD_Pry_redox Si 23.9 2.5E+02 0.0053 19.2 5.2 48 17-74 7-56 (69)
76 PF07837 FTCD_N: Formiminotran 23.4 2.1E+02 0.0044 24.2 5.3 45 20-64 15-61 (178)
77 PRK11023 outer membrane lipopr 23.1 2E+02 0.0043 23.9 5.2 41 20-60 126-168 (191)
78 cd03418 GRX_GRXb_1_3_like Glut 22.9 1.9E+02 0.0042 19.1 4.3 32 11-44 2-33 (75)
79 cd03710 BipA_TypA_C BipA_TypA_ 22.4 2.8E+02 0.006 19.3 5.6 45 15-60 6-52 (79)
80 cd04887 ACT_MalLac-Enz ACT_Mal 22.4 2.4E+02 0.0053 18.6 5.0 32 10-41 41-72 (74)
81 PF02983 Pro_Al_protease: Alph 22.0 1.8E+02 0.0039 19.9 3.9 21 33-53 22-42 (62)
82 PRK10553 assembly protein for 21.9 2.3E+02 0.0051 21.0 4.8 35 9-43 42-76 (87)
83 PF04459 DUF512: Protein of un 21.4 5.1E+02 0.011 22.0 7.4 52 24-75 113-168 (204)
84 PRK09577 multidrug efflux prot 21.4 2.1E+02 0.0045 30.0 5.9 42 23-64 158-207 (1032)
85 PF10934 DUF2634: Protein of u 20.7 1.6E+02 0.0034 22.6 3.8 33 21-53 69-104 (112)
86 COG4004 Uncharacterized protei 20.6 1.3E+02 0.0028 23.1 3.1 22 31-52 37-58 (96)
87 PRK05550 bifunctional methioni 20.4 2.8E+02 0.0061 25.0 5.8 28 20-47 134-161 (283)
88 KOG1752 Glutaredoxin and relat 20.2 2.4E+02 0.0052 21.5 4.7 54 8-70 13-66 (104)
89 cd03027 GRX_DEP Glutaredoxin ( 20.2 2.6E+02 0.0057 18.7 4.5 33 11-45 3-35 (73)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.55 E-value=2.5e-14 Score=102.63 Aligned_cols=69 Identities=43% Similarity=0.654 Sum_probs=62.9
Q ss_pred cceEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccCCceEEcC
Q 029137 7 LQSTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVP 75 (198)
Q Consensus 7 ~~~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~~aeiV~ 75 (198)
..++.+++|+|||++|+.+|++.|+.++||.++.+|..+++|||.|.+||..|++.|++..++++.+|.
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEec
Confidence 467899999999999999999999999999999999999999999999999999999964447777663
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=99.44 E-value=4.5e-13 Score=91.71 Aligned_cols=58 Identities=28% Similarity=0.503 Sum_probs=53.4
Q ss_pred EEEE-eecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeC---CHHHHHHHHHhccCCc
Q 029137 12 VLKI-RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTM---DVKELVPYLKEKLKRN 70 (198)
Q Consensus 12 vLkV-~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~v---dp~~L~~~L~kk~G~~ 70 (198)
+|+| +|+|++|+++|+++|++++||.++.+|+.+++|+|+++. ++.+|.++|+ ++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhCcC
Confidence 6889 599999999999999999999999999999999999874 5699999999 89874
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.27 E-value=1.9e-11 Score=87.31 Aligned_cols=66 Identities=23% Similarity=0.465 Sum_probs=58.5
Q ss_pred ceEEEEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEe--e-eCCHHHHHHHHHhccCCceEEc
Q 029137 8 QSTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK--G-TMDVKELVPYLKEKLKRNVEVV 74 (198)
Q Consensus 8 ~~tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~--G-~vdp~~L~~~L~kk~G~~aeiV 74 (198)
+++++|+|. |+|.+|+.+|+++|.+++||.+|.+|+..++++|+ + .++...|+++|. .+||.+..+
T Consensus 1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~~~ 70 (71)
T COG2608 1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVEEI 70 (71)
T ss_pred CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCeeec
Confidence 467899996 99999999999999999999999999999666655 5 489999999999 999988764
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.05 E-value=6.9e-10 Score=94.90 Aligned_cols=72 Identities=19% Similarity=0.377 Sum_probs=66.6
Q ss_pred cceEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccCCceEEcCCCCC
Q 029137 7 LQSTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVPAKKD 79 (198)
Q Consensus 7 ~~~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~~aeiV~p~k~ 79 (198)
..-+++|.|.|||++|+..|+..|..++||.+|+||+..+.|.|.+...+.+|...|+ .+|+++.+....+.
T Consensus 5 ~~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le-~tGr~Avl~G~G~p 76 (247)
T KOG4656|consen 5 DTYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLE-NTGRDAVLRGAGKP 76 (247)
T ss_pred CceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHH-hhChheEEecCCch
Confidence 3456899999999999999999999999999999999999999999999999999999 99999999876543
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.53 E-value=6.9e-07 Score=77.20 Aligned_cols=73 Identities=22% Similarity=0.438 Sum_probs=65.9
Q ss_pred ccceEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccCCceEEcCCCCC
Q 029137 6 VLQSTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVPAKKD 79 (198)
Q Consensus 6 ~~~~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~~aeiV~p~k~ 79 (198)
+.++++.|.|.|+|+.|+.+|+++|.+++||.++.+|+..++++|...++...|+..|+ ++|+.+++++....
T Consensus 3 ~~~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe-~~Gy~a~~~~~~~~ 75 (238)
T PLN02957 3 LPELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALE-QTGRKARLIGQGDP 75 (238)
T ss_pred CCcEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHH-HcCCcEEEecCCCc
Confidence 45678889999999999999999999999999999999999999998888999999998 99999988866443
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.30 E-value=1.8e-06 Score=85.88 Aligned_cols=66 Identities=20% Similarity=0.384 Sum_probs=59.3
Q ss_pred ceEEEEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccCCceEEcCC
Q 029137 8 QSTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVPA 76 (198)
Q Consensus 8 ~~tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~~aeiV~p 76 (198)
+++++|+|+ |+|.+|+.+|+++|.+++||.+|.+|+ ++++|++..++..|...|+ .+||.+.++.+
T Consensus 2 ~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~--~~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~~ 68 (834)
T PRK10671 2 SQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSI--TEAHVTGTASAEALIETIK-QAGYDASVSHP 68 (834)
T ss_pred CeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEee--eEEEEEecCCHHHHHHHHH-hcCCccccccc
Confidence 367999996 999999999999999999999999999 4667777789999999999 99999998753
No 7
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.89 E-value=0.00016 Score=45.03 Aligned_cols=61 Identities=18% Similarity=0.300 Sum_probs=50.6
Q ss_pred eEEEEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee---eCCHHHHHHHHHhccCCc
Q 029137 9 STVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRN 70 (198)
Q Consensus 9 ~tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G---~vdp~~L~~~L~kk~G~~ 70 (198)
+++.+.|. |+|..|+..|++.+..+.+|..+.+++....+.|.. ..+...+...|. ..|+.
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~ 66 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYE 66 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCC
Confidence 45678896 999999999999999999999999999999988874 256777777775 66654
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.70 E-value=9.8e-05 Score=73.17 Aligned_cols=63 Identities=21% Similarity=0.402 Sum_probs=56.7
Q ss_pred eEEEEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeee---CC-HHHHHHHHHhccCCceEE
Q 029137 9 STVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MD-VKELVPYLKEKLKRNVEV 73 (198)
Q Consensus 9 ~tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~---vd-p~~L~~~L~kk~G~~aei 73 (198)
.++.|.|. |||..|+.+|+ +|.+++||.++.+++.+++++|..+ .+ +..+...++ .+||.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCccccc
Confidence 46789996 99999999999 9999999999999999999999854 45 789999998 99998876
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.04 E-value=0.0019 Score=64.57 Aligned_cols=64 Identities=19% Similarity=0.414 Sum_probs=56.6
Q ss_pred EEEEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccCCceEEc
Q 029137 10 TVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 74 (198)
Q Consensus 10 tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~~aeiV 74 (198)
+++|.|. |+|..|+.+|++.|.+++||.++.+++.++++.|.+..++..+...|+ .+|+.+.++
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~-~~Gy~a~~~ 164 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVE-KAGYGAEAI 164 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHH-hcCCCcccc
Confidence 5678886 999999999999999999999999999999999887778888888888 899876544
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.75 E-value=0.0036 Score=63.40 Aligned_cols=66 Identities=20% Similarity=0.430 Sum_probs=59.4
Q ss_pred eEEEEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeee---CCHHHHHHHHHhccCCceEEcC
Q 029137 9 STVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MDVKELVPYLKEKLKRNVEVVP 75 (198)
Q Consensus 9 ~tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~---vdp~~L~~~L~kk~G~~aeiV~ 75 (198)
.+++|.|. |.|..|..+|++.|.+++||.++.+|..++++.|.-. +.+-.+++.|. .+|+.+.+..
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~~~~~~~~ 215 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETGFEASVRP 215 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhcccceeee
Confidence 68999996 9999999999999999999999999999999999854 78999999998 8888776653
No 11
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.24 E-value=0.013 Score=58.31 Aligned_cols=64 Identities=14% Similarity=0.302 Sum_probs=52.3
Q ss_pred ceEEEEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeee--CCHHHHHHHHHhccCCceEE
Q 029137 8 QSTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLKEKLKRNVEV 73 (198)
Q Consensus 8 ~~tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~--vdp~~L~~~L~kk~G~~aei 73 (198)
..++.|.|. |+|..|+.+|++.|.+++||.++.+++.+.++.|... .+ ..+...++ .+|+.+..
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~-~~I~~aI~-~~Gy~a~~ 118 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIR-AQVESAVQ-KAGFSLRD 118 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccch-HHHHHHHH-hccccccc
Confidence 356778886 9999999999999999999999999999999888643 23 66667777 78887643
No 12
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.23 E-value=0.0089 Score=60.67 Aligned_cols=62 Identities=13% Similarity=0.325 Sum_probs=56.5
Q ss_pred eecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeee--CCHHHHHHHHHhccCCceEEcCCCC
Q 029137 16 RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLKEKLKRNVEVVPAKK 78 (198)
Q Consensus 16 ~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~--vdp~~L~~~L~kk~G~~aeiV~p~k 78 (198)
.|+|..|.+.|++++.+.+||.++.|++.+++.+|.-+ ++++.|.++|. -.|+.+.++....
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~gf~~~~~~~~~ 65 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMGFEASLLSDSE 65 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-cccceeeecccCc
Confidence 59999999999999999999999999999999988854 89999999998 9999999886643
No 13
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=93.46 E-value=1.3 Score=30.18 Aligned_cols=64 Identities=20% Similarity=0.302 Sum_probs=47.4
Q ss_pred eEEEEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee---eCCHHHHHHHHHhccCCceEE
Q 029137 9 STVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNVEV 73 (198)
Q Consensus 9 ~tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G---~vdp~~L~~~L~kk~G~~aei 73 (198)
.++.+.+. ++|..|..+++..+....+|....++.....+.+.- ..+...+...+. ..++.+++
T Consensus 23 ~~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~ 90 (92)
T TIGR02052 23 QTVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSSL 90 (92)
T ss_pred eEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeEe
Confidence 35567775 999999999999999999998888888887766652 245666655555 66666543
No 14
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=89.37 E-value=2.1 Score=32.76 Aligned_cols=66 Identities=24% Similarity=0.395 Sum_probs=45.5
Q ss_pred ceEEEEEEeecChhHHHHHHHHHhcCCCccEEEE-----eCCCC--eEEEeee-CCHHHHHHHHHhccCCceEEc
Q 029137 8 QSTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTI-----DGGKD--LVTVKGT-MDVKELVPYLKEKLKRNVEVV 74 (198)
Q Consensus 8 ~~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~V-----D~~~~--kVtV~G~-vdp~~L~~~L~kk~G~~aeiV 74 (198)
.+.++|-|-.--.--.-.+-++|.+++||..|.+ |..+. ++||.|. +|.+.|.++|. .+|-.+.++
T Consensus 4 irRlVLDVlKP~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHSI 77 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHSI 77 (95)
T ss_dssp EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEEE
T ss_pred eeEEEEEeecCCCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEee
Confidence 4567777753344445578888999999887764 44444 4456686 99999999999 899887765
No 15
>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=89.34 E-value=0.58 Score=32.57 Aligned_cols=33 Identities=21% Similarity=0.448 Sum_probs=24.1
Q ss_pred eEEEEEEeecChhHH------HHHHHHHhcCCCccEEEE
Q 029137 9 STVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTI 41 (198)
Q Consensus 9 ~tvvLkV~MhC~gCa------~kI~kaL~kl~GV~sV~V 41 (198)
.++.|.+.+...+|. +.|+.+|..++||.+|+|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 567777777776665 788899999999999976
No 16
>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=87.26 E-value=3.3 Score=22.58 Aligned_cols=49 Identities=33% Similarity=0.556 Sum_probs=35.3
Q ss_pred eecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeee--CCHHHHHHHHH
Q 029137 16 RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLK 64 (198)
Q Consensus 16 ~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~--vdp~~L~~~L~ 64 (198)
.++|..|...+...+....++....+++....+.+... .+...+...+.
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE 56 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH
Confidence 48899999999999989999887778877776666532 24444433443
No 17
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=87.18 E-value=4 Score=31.14 Aligned_cols=67 Identities=24% Similarity=0.347 Sum_probs=47.5
Q ss_pred ceEEEEEEe-ecChhHHHHHHHHHhcCCCccEEEE-----eC--CCCeEEEeee-CCHHHHHHHHHhccCCceEEcC
Q 029137 8 QSTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTI-----DG--GKDLVTVKGT-MDVKELVPYLKEKLKRNVEVVP 75 (198)
Q Consensus 8 ~~tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~V-----D~--~~~kVtV~G~-vdp~~L~~~L~kk~G~~aeiV~ 75 (198)
...++|.|- -|-.--.--+-+.|+++.||+-|.+ |. .+=++||.|+ +|-+.|.+.|. .+|--+.++.
T Consensus 5 iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSiD 80 (97)
T COG1888 5 IRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSID 80 (97)
T ss_pred ceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeehh
Confidence 355666664 3434455567778899999877654 33 3456677786 99999999998 8998887663
No 18
>PRK13748 putative mercuric reductase; Provisional
Probab=86.48 E-value=4 Score=38.64 Aligned_cols=64 Identities=20% Similarity=0.325 Sum_probs=49.5
Q ss_pred EEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee--eCCHHHHHHHHHhccCCceEEcCC
Q 029137 12 VLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVVPA 76 (198)
Q Consensus 12 vLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G--~vdp~~L~~~L~kk~G~~aeiV~p 76 (198)
.+.+. |+|..|..+++..+..++++....+++....+.+.. ..+...+...+. ..++.+++...
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g~~~~~~~~ 69 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLGYRATLADA 69 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcCCeeeccCc
Confidence 35564 999999999999999999999999999888877763 245666666666 67777665544
No 19
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=70.94 E-value=10 Score=31.04 Aligned_cols=42 Identities=19% Similarity=0.264 Sum_probs=33.9
Q ss_pred ceEEEEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCC-CCeEEE
Q 029137 8 QSTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGG-KDLVTV 50 (198)
Q Consensus 8 ~~tvvLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~-~~kVtV 50 (198)
-..++|.|+ --|..|..-|.....++ |+.++.|-.. ++++.+
T Consensus 99 g~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~~ 142 (146)
T PF14437_consen 99 GRSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVYY 142 (146)
T ss_pred CCeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEEE
Confidence 356788887 78999999999888775 8999998876 776654
No 20
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=64.29 E-value=9.7 Score=31.81 Aligned_cols=35 Identities=20% Similarity=0.384 Sum_probs=26.8
Q ss_pred EEEEEEeecChhHH------HHHHHHHhcCCCccEEEEeCC
Q 029137 10 TVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTIDGG 44 (198)
Q Consensus 10 tvvLkV~MhC~gCa------~kI~kaL~kl~GV~sV~VD~~ 44 (198)
++.+.+.+...+|. ..|+.+|..++||.+|.|++.
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l~ 154 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVELV 154 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEEE
Confidence 56677777766665 458899999999999988753
No 21
>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=62.11 E-value=23 Score=23.84 Aligned_cols=33 Identities=18% Similarity=0.319 Sum_probs=25.4
Q ss_pred eEEEEEEeecChh-HHHHHHHHHhcCCCccEEEE
Q 029137 9 STVVLKIRLHCEG-CISKIKKIIYKTKGVDNVTI 41 (198)
Q Consensus 9 ~tvvLkV~MhC~g-Ca~kI~kaL~kl~GV~sV~V 41 (198)
..+.|.|..+-.. --.+|.+.|++++||.+|.+
T Consensus 41 ~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 41 ANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 4455666555554 78899999999999999875
No 22
>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=61.41 E-value=13 Score=27.40 Aligned_cols=35 Identities=20% Similarity=0.392 Sum_probs=24.9
Q ss_pred EEEEEEeecChhHH------HHHHHHHhcCCCccEEEEeCC
Q 029137 10 TVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTIDGG 44 (198)
Q Consensus 10 tvvLkV~MhC~gCa------~kI~kaL~kl~GV~sV~VD~~ 44 (198)
.+.+.|.+...+|. ..|+.+|..++||++|.|++.
T Consensus 38 ~v~i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 38 HVDIQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred eEEEEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEEEE
Confidence 45556655544443 458888999999999998864
No 23
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=53.76 E-value=42 Score=27.99 Aligned_cols=51 Identities=22% Similarity=0.298 Sum_probs=37.5
Q ss_pred eEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCCCe-------------------EEEeee---CCHHHHHHHHH
Q 029137 9 STVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDL-------------------VTVKGT---MDVKELVPYLK 64 (198)
Q Consensus 9 ~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~k-------------------VtV~G~---vdp~~L~~~L~ 64 (198)
.+++|- .||=..++..+.+++||.++.+=.+++. |.|+-+ ++-++|+...-
T Consensus 4 ~~a~fa-----gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~ 76 (172)
T PRK14054 4 ETAVLA-----GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF 76 (172)
T ss_pred eEEEEE-----cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence 445554 6888888889999999999999887665 455533 66777777655
No 24
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=53.25 E-value=11 Score=25.11 Aligned_cols=33 Identities=15% Similarity=0.339 Sum_probs=17.4
Q ss_pred HHHHHHHhc---CCCccEEEEeCCCCeEEEeeeCCHH
Q 029137 24 SKIKKIIYK---TKGVDNVTIDGGKDLVTVKGTMDVK 57 (198)
Q Consensus 24 ~kI~kaL~k---l~GV~sV~VD~~~~kVtV~G~vdp~ 57 (198)
.+|+.+|.. +++- ++.+....+.|+++|.++-.
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~s~ 37 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEVPSQ 37 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEESSC
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeCcHH
Confidence 467777765 4555 57888889999999987433
No 25
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=52.46 E-value=74 Score=22.41 Aligned_cols=62 Identities=18% Similarity=0.246 Sum_probs=42.5
Q ss_pred EEEEEeecChhHHHHHHHHHhcC----CCccEEEEeCCCCeEEEee--eCCHHHHHHHHHhccCCceEE
Q 029137 11 VVLKIRLHCEGCISKIKKIIYKT----KGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEV 73 (198)
Q Consensus 11 vvLkV~MhC~gCa~kI~kaL~kl----~GV~sV~VD~~~~kVtV~G--~vdp~~L~~~L~kk~G~~aei 73 (198)
+.+.|.-.-.+=..++..+|.++ +++ .+..|..++.+.|.| .+-.+.++++|+++.|-.+++
T Consensus 6 ~~~~i~p~~~~d~~kl~~aL~~l~~eDP~l-~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~~ 73 (75)
T PF14492_consen 6 LSVAIEPKNKEDEPKLSEALQKLSEEDPSL-RVERDEETGELILSGMGELHLEVLLERLKRRFGVEVEF 73 (75)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHH-TTS-EEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEEE
T ss_pred EEEEEEECCHhHHHHHHHHHHHHHhcCCeE-EEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeEe
Confidence 33444433444555666666544 455 589999999999885 578899999999777766654
No 26
>PRK11670 antiporter inner membrane protein; Provisional
Probab=52.26 E-value=40 Score=30.97 Aligned_cols=67 Identities=12% Similarity=0.167 Sum_probs=43.4
Q ss_pred eEEEEEEeecChhH------HHHHHHHHhcCCCccEEEEeCCC------------------CeEEEe---e----eCCHH
Q 029137 9 STVVLKIRLHCEGC------ISKIKKIIYKTKGVDNVTIDGGK------------------DLVTVK---G----TMDVK 57 (198)
Q Consensus 9 ~tvvLkV~MhC~gC------a~kI~kaL~kl~GV~sV~VD~~~------------------~kVtV~---G----~vdp~ 57 (198)
.++.|.|.+.-..| .+.|+.+|..++||.+|.+.+.. ..+.|. | +.-..
T Consensus 47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~av 126 (369)
T PRK11670 47 DTLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAV 126 (369)
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHH
Confidence 35666666544444 35689999999999988765532 223343 2 13455
Q ss_pred HHHHHHHhccCCceEEcCC
Q 029137 58 ELVPYLKEKLKRNVEVVPA 76 (198)
Q Consensus 58 ~L~~~L~kk~G~~aeiV~p 76 (198)
.|...|. +.|++|-++.-
T Consensus 127 NLA~aLA-~~G~rVlLID~ 144 (369)
T PRK11670 127 NLALALA-AEGAKVGILDA 144 (369)
T ss_pred HHHHHHH-HCCCcEEEEeC
Confidence 6667777 78999988844
No 27
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=50.86 E-value=66 Score=23.92 Aligned_cols=44 Identities=18% Similarity=0.172 Sum_probs=30.1
Q ss_pred hHHHHHHHHHhcCCCccEEEEeCCCCeEEEee-eCCHHHHHHHHH
Q 029137 21 GCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG-TMDVKELVPYLK 64 (198)
Q Consensus 21 gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G-~vdp~~L~~~L~ 64 (198)
.=...|.++|..++|++=...|...+|+.|+= ..+...+++.|.
T Consensus 17 e~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 17 ERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 44778999999999998555666777877662 344554544444
No 28
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=50.37 E-value=54 Score=27.33 Aligned_cols=69 Identities=29% Similarity=0.406 Sum_probs=44.4
Q ss_pred eEEEEEEeecChhHHHHH------------HHHHhcC------CCccEEEEeCCCCeEE-Ee--ee---C-CHHHHHHHH
Q 029137 9 STVVLKIRLHCEGCISKI------------KKIIYKT------KGVDNVTIDGGKDLVT-VK--GT---M-DVKELVPYL 63 (198)
Q Consensus 9 ~tvvLkV~MhC~gCa~kI------------~kaL~kl------~GV~sV~VD~~~~kVt-V~--G~---v-dp~~L~~~L 63 (198)
-.+-++-.+-|++|.++| .++|.++ .+++-...=...++|. |. |. + ---..+++|
T Consensus 6 ~~~c~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l 85 (166)
T PRK06418 6 CEVCVKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKAL 85 (166)
T ss_pred eeEEeccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHH
Confidence 346667779999999875 5677776 3443333222346666 33 33 1 123668888
Q ss_pred HhccCCceEEcCCC
Q 029137 64 KEKLKRNVEVVPAK 77 (198)
Q Consensus 64 ~kk~G~~aeiV~p~ 77 (198)
++.+|+++++|.-.
T Consensus 86 ~~~lgk~VevVE~s 99 (166)
T PRK06418 86 SRKLGKKVRVVEKT 99 (166)
T ss_pred HHHhCCcEEEEEcC
Confidence 88999999999643
No 29
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=48.61 E-value=50 Score=23.00 Aligned_cols=42 Identities=19% Similarity=0.286 Sum_probs=31.3
Q ss_pred HhcCCCccEEEEeCCCC--eEEEeeeCCHHHHHHHHHhccCCceEEc
Q 029137 30 IYKTKGVDNVTIDGGKD--LVTVKGTMDVKELVPYLKEKLKRNVEVV 74 (198)
Q Consensus 30 L~kl~GV~sV~VD~~~~--kVtV~G~vdp~~L~~~L~kk~G~~aeiV 74 (198)
|..++||.++..+- .+ ++.|....+...|+..|. ..|. +..+
T Consensus 26 l~~~~~v~~v~~~~-~~~~~i~l~~~~~~~~ll~~l~-~~g~-I~~f 69 (84)
T PF13732_consen 26 LEELPGVESVEQDG-DGKLRIKLEDEETANELLQELI-EKGI-IRSF 69 (84)
T ss_pred HhhCCCeEEEEEeC-CcEEEEEECCcccHHHHHHHHH-hCCC-eeEE
Confidence 88889999998753 44 445556678899999998 6777 6544
No 30
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=48.29 E-value=30 Score=27.00 Aligned_cols=34 Identities=24% Similarity=0.521 Sum_probs=25.9
Q ss_pred EEEEEEeecChhH------HHHHHHHHhcCCCccEEEEeC
Q 029137 10 TVVLKIRLHCEGC------ISKIKKIIYKTKGVDNVTIDG 43 (198)
Q Consensus 10 tvvLkV~MhC~gC------a~kI~kaL~kl~GV~sV~VD~ 43 (198)
.+.+++.++-.+| ...|+.+|..++||+++.|++
T Consensus 50 ~v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 50 LVKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred eEEEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 3445555666666 678999999999999998865
No 31
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=47.56 E-value=23 Score=28.66 Aligned_cols=34 Identities=26% Similarity=0.475 Sum_probs=23.2
Q ss_pred eEEEEEEeecChhHHH------HHHHHHhcCCCccEEEEeC
Q 029137 9 STVVLKIRLHCEGCIS------KIKKIIYKTKGVDNVTIDG 43 (198)
Q Consensus 9 ~tvvLkV~MhC~gCa~------kI~kaL~kl~GV~sV~VD~ 43 (198)
..+.+.|.+.-.+|.. .|+.+|..+ ||.+|.|++
T Consensus 25 d~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~-Gv~~V~V~i 64 (146)
T TIGR02159 25 GGVVVKFTPTYSGCPALEVIRQDIRDAVRAL-GVEVVEVST 64 (146)
T ss_pred CEEEEEEEeCCCCCchHHHHHHHHHHHHHhc-CCCeEEEeE
Confidence 3566677777666653 477888776 888877753
No 32
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=47.05 E-value=56 Score=22.57 Aligned_cols=33 Identities=15% Similarity=0.257 Sum_probs=26.0
Q ss_pred ceEEEEEEeecChhHHHHHHHHHhcCCCccEEE
Q 029137 8 QSTVVLKIRLHCEGCISKIKKIIYKTKGVDNVT 40 (198)
Q Consensus 8 ~~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~ 40 (198)
...+.|.|...--.=-..|...|++++||.+|.
T Consensus 47 ~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 47 TARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 456677777777677778999999999998874
No 33
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=46.16 E-value=56 Score=26.77 Aligned_cols=70 Identities=14% Similarity=0.194 Sum_probs=48.2
Q ss_pred eEEEEEEe----ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeee-----C-CHHHHHHHHHhccCCceEEcCCCC
Q 029137 9 STVVLKIR----LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT-----M-DVKELVPYLKEKLKRNVEVVPAKK 78 (198)
Q Consensus 9 ~tvvLkV~----MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~-----v-dp~~L~~~L~kk~G~~aeiV~p~k 78 (198)
+.++++.+ |.=+--+..|++.+=.-.||.++.+|..++.|+|... + -....+..|..++|+...++..++
T Consensus 37 KRIvvR~dps~l~~~e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 37 KRIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred ceEEEcCChhhcCCHHHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 44555553 3345566677777766679999999999999998732 1 234444555569999999886554
No 34
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=45.30 E-value=99 Score=22.26 Aligned_cols=43 Identities=14% Similarity=0.230 Sum_probs=29.9
Q ss_pred hHHHHHHHHHhcCCCccEEEEeCCCCeEEEe-eeCCHHHHHHHHH
Q 029137 21 GCISKIKKIIYKTKGVDNVTIDGGKDLVTVK-GTMDVKELVPYLK 64 (198)
Q Consensus 21 gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~-G~vdp~~L~~~L~ 64 (198)
.=...|.++|..++||+=...|-. +++.|+ -..+...+.+.|.
T Consensus 15 ~~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 15 ERLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp CCHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred hhHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 445789999999999964445545 666665 4456666666666
No 35
>TIGR02189 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa.
Probab=43.38 E-value=97 Score=22.85 Aligned_cols=52 Identities=21% Similarity=0.238 Sum_probs=33.4
Q ss_pred eEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccCC
Q 029137 9 STVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKR 69 (198)
Q Consensus 9 ~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~ 69 (198)
..|++-..-.|..|. ++++.|.++ ||.-..+|+.. ..+..++++.|.+.+|.
T Consensus 8 ~~Vvvysk~~Cp~C~-~ak~~L~~~-~i~~~~vdid~-------~~~~~~~~~~l~~~tg~ 59 (99)
T TIGR02189 8 KAVVIFSRSSCCMCH-VVKRLLLTL-GVNPAVHEIDK-------EPAGKDIENALSRLGCS 59 (99)
T ss_pred CCEEEEECCCCHHHH-HHHHHHHHc-CCCCEEEEcCC-------CccHHHHHHHHHHhcCC
Confidence 445555568999999 777777765 67544455442 23446677777755665
No 36
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=41.91 E-value=80 Score=23.17 Aligned_cols=40 Identities=30% Similarity=0.538 Sum_probs=30.5
Q ss_pred HHHHHHHhcCCCccEEEEeCCCCeEEEee--eCCHHHHHHHHHh
Q 029137 24 SKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKE 65 (198)
Q Consensus 24 ~kI~kaL~kl~GV~sV~VD~~~~kVtV~G--~vdp~~L~~~L~k 65 (198)
.-+-+.|..++||.+|-+. .+=|||+- .++...|...|..
T Consensus 37 spLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~~ 78 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIRE 78 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHHH
Confidence 5566778899999998764 77888884 4889999888874
No 37
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=41.89 E-value=1.4e+02 Score=21.93 Aligned_cols=58 Identities=19% Similarity=0.194 Sum_probs=42.6
Q ss_pred eEEEEEEeecChhHHHHHHHHHhcCCC-ccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccC
Q 029137 9 STVVLKIRLHCEGCISKIKKIIYKTKG-VDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLK 68 (198)
Q Consensus 9 ~tvvLkV~MhC~gCa~kI~kaL~kl~G-V~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G 68 (198)
.|++=+|+-+=..+.+.+.+.|..... -..+.|+..++.|.|.|.. ...|.++|. ..|
T Consensus 28 ~T~IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~-~~~Vk~wL~-~~G 86 (87)
T PF05046_consen 28 ITVIRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDH-VEEVKKWLL-EKG 86 (87)
T ss_pred EEEEEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCcc-HHHHHHHHH-HCc
Confidence 455556665567888888888865544 2357788999999999985 777888887 444
No 38
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=40.47 E-value=99 Score=25.42 Aligned_cols=45 Identities=18% Similarity=0.310 Sum_probs=32.9
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCCCe--------------EEEee---eCCHHHHHHHHH
Q 029137 20 EGCISKIKKIIYKTKGVDNVTIDGGKDL--------------VTVKG---TMDVKELVPYLK 64 (198)
Q Consensus 20 ~gCa~kI~kaL~kl~GV~sV~VD~~~~k--------------VtV~G---~vdp~~L~~~L~ 64 (198)
.||=--++..+.+++||.++.+-.+.+. |.|+- .++-+.|++..-
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~ 69 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLF 69 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHH
Confidence 6788888889999999999998876543 33432 256677777665
No 39
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=39.34 E-value=74 Score=22.25 Aligned_cols=34 Identities=26% Similarity=0.330 Sum_probs=24.1
Q ss_pred EEEEEeecChhHHHHHHHHHhcC----CCccEEEEeCCC
Q 029137 11 VVLKIRLHCEGCISKIKKIIYKT----KGVDNVTIDGGK 45 (198)
Q Consensus 11 vvLkV~MhC~gCa~kI~kaL~kl----~GV~sV~VD~~~ 45 (198)
|++-..-.|..|. ++++.|.++ .||.-..+|...
T Consensus 3 v~iy~~~~C~~C~-~a~~~L~~l~~~~~~i~~~~idi~~ 40 (85)
T PRK11200 3 VVIFGRPGCPYCV-RAKELAEKLSEERDDFDYRYVDIHA 40 (85)
T ss_pred EEEEeCCCChhHH-HHHHHHHhhcccccCCcEEEEECCC
Confidence 4444456899998 677788776 677777777654
No 40
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=38.13 E-value=1.1e+02 Score=22.49 Aligned_cols=53 Identities=23% Similarity=0.288 Sum_probs=40.0
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCCCeEEEe----eeCCHHHHHHHHHhccCCceEE
Q 029137 20 EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK----GTMDVKELVPYLKEKLKRNVEV 73 (198)
Q Consensus 20 ~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~----G~vdp~~L~~~L~kk~G~~aei 73 (198)
.-|.+.|...-..+. +.+|+..+..++++|- +.+|-..|+..|.+..+.++++
T Consensus 29 ~~c~~~~~~~~L~m~-lvd~e~~~D~~k~~fyy~a~~rvDFR~Lvr~L~~~f~~RIem 85 (88)
T PF04468_consen 29 KFCRELVKELGLPMK-LVDVEYQFDGSKLTFYYTAESRVDFRELVRDLAREFKTRIEM 85 (88)
T ss_pred HHHHHHHHHcCCCeE-EEEEEEEcCCCEEEEEEEeCCcCcHHHHHHHHHHHhCceEEE
Confidence 456666666555444 5678888899999986 3489999999999877777765
No 41
>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=37.79 E-value=84 Score=25.25 Aligned_cols=33 Identities=21% Similarity=0.210 Sum_probs=27.3
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee
Q 029137 20 EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG 52 (198)
Q Consensus 20 ~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G 52 (198)
..=+.+|.+.|.+++||+++.|=...+.+.|--
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav 106 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATVVVTDDNAYVAV 106 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEECCEEEEEE
Confidence 345789999999999999999888888877653
No 42
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=37.54 E-value=40 Score=23.40 Aligned_cols=14 Identities=14% Similarity=0.394 Sum_probs=10.1
Q ss_pred EEEEEEeecChhHHH
Q 029137 10 TVVLKIRLHCEGCIS 24 (198)
Q Consensus 10 tvvLkV~MhC~gCa~ 24 (198)
+|.+ +...|..|..
T Consensus 2 ~I~v-~~~~C~~C~~ 15 (76)
T PF13192_consen 2 KIKV-FSPGCPYCPE 15 (76)
T ss_dssp EEEE-ECSSCTTHHH
T ss_pred EEEE-eCCCCCCcHH
Confidence 4555 6777999983
No 43
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=37.01 E-value=95 Score=22.35 Aligned_cols=33 Identities=15% Similarity=0.182 Sum_probs=28.2
Q ss_pred eEEEEEEeecChhHHHHHHHHHhcCCCccEEEE
Q 029137 9 STVVLKIRLHCEGCISKIKKIIYKTKGVDNVTI 41 (198)
Q Consensus 9 ~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~V 41 (198)
-++++.|.-....-...+-++|..++||.++..
T Consensus 39 GKiVVtiE~~~~~~~~~~~~~i~~l~GVlsa~l 71 (79)
T PF03927_consen 39 GKIVVTIEAESSEEEVDLIDAINALPGVLSASL 71 (79)
T ss_dssp TEEEEEEEESSHHHHHHHHHHHCCSTTEEEEEE
T ss_pred CeEEEEEEeCChHHHHHHHHHHHcCCCceEEEE
Confidence 567778888888888889999999999998875
No 44
>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=36.61 E-value=86 Score=21.21 Aligned_cols=53 Identities=21% Similarity=0.252 Sum_probs=36.3
Q ss_pred EEEEe-ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeee--CCHHHHHHHHHhccCCceEEc
Q 029137 12 VLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLKEKLKRNVEVV 74 (198)
Q Consensus 12 vLkV~-MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~--vdp~~L~~~L~kk~G~~aeiV 74 (198)
+|-+. +.|+...-+++++|.+++. .+.+.|..+ .....|..+++ ..|+.+..+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~---------G~~l~v~~d~~~~~~di~~~~~-~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPP---------GEVLEVLVDDPAAVEDIPRWCE-ENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGT---------T-EEEEEESSTTHHHHHHHHHH-HHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCC---------CCEEEEEECCccHHHHHHHHHH-HCCCEEEEE
Confidence 34554 8999999999999998742 234444443 45577888887 899976554
No 45
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=36.03 E-value=1.3e+02 Score=21.58 Aligned_cols=41 Identities=32% Similarity=0.281 Sum_probs=26.8
Q ss_pred cChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccCCc
Q 029137 18 HCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRN 70 (198)
Q Consensus 18 hC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~~ 70 (198)
.|..|. ++++.|... ||.-..+|... + ..++..|.+.+|..
T Consensus 22 ~Cp~C~-~ak~~L~~~-~i~y~~idv~~---------~-~~~~~~l~~~~g~~ 62 (90)
T cd03028 22 RCGFSR-KVVQILNQL-GVDFGTFDILE---------D-EEVRQGLKEYSNWP 62 (90)
T ss_pred CCcHHH-HHHHHHHHc-CCCeEEEEcCC---------C-HHHHHHHHHHhCCC
Confidence 688887 677777665 67766677542 2 45677777566653
No 46
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=35.75 E-value=38 Score=30.48 Aligned_cols=54 Identities=15% Similarity=0.107 Sum_probs=36.1
Q ss_pred hHHHHHHHHHhcCCCccEEEEeC--CCCeEEEeeeCCHHHHHHHHHhccCCceEEc
Q 029137 21 GCISKIKKIIYKTKGVDNVTIDG--GKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 74 (198)
Q Consensus 21 gCa~kI~kaL~kl~GV~sV~VD~--~~~kVtV~G~vdp~~L~~~L~kk~G~~aeiV 74 (198)
.-+.+|..++..+++|.=+.+++ ..++-.|+-.-|++.++.+.-+-+++-++++
T Consensus 18 ~~ie~i~a~~~~~~~v~ildve~danhNRsViT~vgdp~~~~~A~f~~ik~AaelI 73 (302)
T COG3643 18 EKIEKIVAAAKSIPTVKILDVEMDANHNRSVITLVGDPSKVVNAAFALIKKAAELI 73 (302)
T ss_pred HHHHHHHHHHhcCCceEEEEeccCCCCCceEEEEecChHHHHHHHHHHHHHHHHhh
Confidence 34567777888888876555544 5666667777788888877765555544433
No 47
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=33.76 E-value=1.3e+02 Score=21.50 Aligned_cols=58 Identities=21% Similarity=0.276 Sum_probs=36.2
Q ss_pred cceEEEEEEeecChhHHHHHHHHHhcCCC-ccEEEEeCCCCeEEEeeeCCHHHH---HHHHHhccC
Q 029137 7 LQSTVVLKIRLHCEGCISKIKKIIYKTKG-VDNVTIDGGKDLVTVKGTMDVKEL---VPYLKEKLK 68 (198)
Q Consensus 7 ~~~tvvLkV~MhC~gCa~kI~kaL~kl~G-V~sV~VD~~~~kVtV~G~vdp~~L---~~~L~kk~G 68 (198)
+...+++.++ ..+..+|...|.+..| |.+...+ .++.++|++.+....+ ...|+..+.
T Consensus 5 P~~~~~I~~p---~~~~g~v~~~l~~r~g~i~~~~~~-~~~~~~i~~~iP~~~~~gf~~~Lr~~T~ 66 (89)
T PF00679_consen 5 PIMSVEISVP---EEYLGKVISDLSKRRGEILSMDPI-GGDRVVIEAEIPVRELFGFRSELRSLTS 66 (89)
T ss_dssp EEEEEEEEEE---GGGHHHHHHHHHHTT-EEEEEEEE-STTEEEEEEEEEGGGHTTHHHHHHHHTT
T ss_pred CEEEEEEEEC---HHHHHHHHHHhcccccEEEechhh-hhhheeEEEEEChhhhhhHHHHhhccCC
Confidence 3444555544 6888999999999888 3344333 5889999987554433 455553333
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=32.87 E-value=85 Score=23.44 Aligned_cols=35 Identities=14% Similarity=0.251 Sum_probs=25.5
Q ss_pred ceEEEEEEeecC-hhHHHHHHHHHhcCCCccEEEEe
Q 029137 8 QSTVVLKIRLHC-EGCISKIKKIIYKTKGVDNVTID 42 (198)
Q Consensus 8 ~~tvvLkV~MhC-~gCa~kI~kaL~kl~GV~sV~VD 42 (198)
...+.+.+-|-. .+-...|+.+|++++||++|++-
T Consensus 48 LkaL~~~~vv~D~~g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 48 LVAINVMVVMGDAEGGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred ceeeEEEEEEecCCcChHHHHHHHhcCCCccEEEEE
Confidence 344444444433 36679999999999999999875
No 49
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=32.43 E-value=99 Score=26.18 Aligned_cols=36 Identities=17% Similarity=0.203 Sum_probs=27.7
Q ss_pred cceEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCCCe
Q 029137 7 LQSTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDL 47 (198)
Q Consensus 7 ~~~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~k 47 (198)
.+.+++|- .||=--++..+.+++||.++.+=.+++.
T Consensus 7 ~~~~a~~a-----gGCFWg~E~~f~~l~GV~~t~vGYagG~ 42 (186)
T PRK13014 7 GMETATFA-----GGCFWGVEGVFQHVPGVVSVVSGYSGGH 42 (186)
T ss_pred CccEEEEe-----cCCceeeHHHHccCCCEEEEEeeecCCC
Confidence 34556665 6777778888889999999999887664
No 50
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=31.95 E-value=1.1e+02 Score=21.18 Aligned_cols=35 Identities=29% Similarity=0.372 Sum_probs=25.1
Q ss_pred ceEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCC
Q 029137 8 QSTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGG 44 (198)
Q Consensus 8 ~~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~ 44 (198)
...|+|-..-.|..|. ++++.|... ||.-..+|+.
T Consensus 7 ~~~V~ly~~~~Cp~C~-~ak~~L~~~-gi~y~~idi~ 41 (79)
T TIGR02190 7 PESVVVFTKPGCPFCA-KAKATLKEK-GYDFEEIPLG 41 (79)
T ss_pred CCCEEEEECCCCHhHH-HHHHHHHHc-CCCcEEEECC
Confidence 3456666678999998 777777654 7776666654
No 51
>PF05663 DUF809: Protein of unknown function (DUF809); InterPro: IPR008527 This family consists of several proteins of unknown function Raphanus sativus (Radish) and Brassica napus (Rape).
Probab=31.78 E-value=1.2e+02 Score=23.77 Aligned_cols=44 Identities=14% Similarity=0.124 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHH
Q 029137 20 EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLK 64 (198)
Q Consensus 20 ~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~ 64 (198)
.+|-+.+ +.|.+++=--....-.-.-++||...+.-+.+...+.
T Consensus 47 qhclrtm-rhleklkipyefqygwlgvkitiksnvpndevtkkvs 90 (138)
T PF05663_consen 47 QHCLRTM-RHLEKLKIPYEFQYGWLGVKITIKSNVPNDEVTKKVS 90 (138)
T ss_pred HHHHHHH-HHHHhcCCCeeeeecceeEEEEEecCCCchHhhhccC
Confidence 4565443 3355554322333334455677777777777766655
No 52
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=31.46 E-value=86 Score=23.42 Aligned_cols=35 Identities=17% Similarity=0.341 Sum_probs=26.3
Q ss_pred ceEEEEEEeecC-hhHHHHHHHHHhcCCCccEEEEe
Q 029137 8 QSTVVLKIRLHC-EGCISKIKKIIYKTKGVDNVTID 42 (198)
Q Consensus 8 ~~tvvLkV~MhC-~gCa~kI~kaL~kl~GV~sV~VD 42 (198)
...+.+.+-|-+ .+-...|+.+|..++||+||+|-
T Consensus 48 LkaL~i~~vv~D~~~~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 48 LKALKLYVIMPDEEGGTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred ceeEEEEEEEEcCCcCcHHHHHHHhccCCCcEEEEE
Confidence 344445554544 47889999999999999999875
No 53
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=31.12 E-value=97 Score=26.59 Aligned_cols=38 Identities=32% Similarity=0.409 Sum_probs=30.1
Q ss_pred HHHHHHHHhcCCCccEEEEeCCCCeEEEeee---CCHHHHHH
Q 029137 23 ISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MDVKELVP 61 (198)
Q Consensus 23 a~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~---vdp~~L~~ 61 (198)
...|.+.|.+..||+ +.+|..++.|+|..+ .||..+++
T Consensus 26 ~g~v~k~ie~~~~~~-~~iD~~~~~V~i~~~~~t~Dp~~~~k 66 (194)
T COG1094 26 WGEVKKAIEEKTGVK-LRIDSKTGSVTIRTTRKTEDPLALLK 66 (194)
T ss_pred cccchHHHHhhcCeE-EEEECCCCeEEEEecCCCCChHHHHH
Confidence 456888898888885 999999999999865 57765543
No 54
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=30.58 E-value=1.2e+02 Score=20.72 Aligned_cols=30 Identities=17% Similarity=0.194 Sum_probs=21.3
Q ss_pred EEEEEeecChhHHHHHHHHHhcCCCccEEE
Q 029137 11 VVLKIRLHCEGCISKIKKIIYKTKGVDNVT 40 (198)
Q Consensus 11 vvLkV~MhC~gCa~kI~kaL~kl~GV~sV~ 40 (198)
+.|.+...--.=-..|.+.|++++||.+|.
T Consensus 39 i~l~i~v~~~~~L~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 39 IYLNFPTIEFEKLQTLMPEIRRIDGVEDVK 68 (74)
T ss_pred EEEEeEecCHHHHHHHHHHHhCCCCceEEE
Confidence 455555444444578888899999999886
No 55
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=30.28 E-value=1.5e+02 Score=25.77 Aligned_cols=27 Identities=15% Similarity=0.380 Sum_probs=23.3
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCCC
Q 029137 20 EGCISKIKKIIYKTKGVDNVTIDGGKD 46 (198)
Q Consensus 20 ~gCa~kI~kaL~kl~GV~sV~VD~~~~ 46 (198)
.||-.-++..+.+++||.++.+=.+.+
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG 78 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGG 78 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCC
Confidence 688888888899999999999988754
No 56
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=30.00 E-value=66 Score=24.63 Aligned_cols=30 Identities=37% Similarity=0.444 Sum_probs=25.7
Q ss_pred eEEEeeeCCHHHHHHHHHhccCCceEEcCCC
Q 029137 47 LVTVKGTMDVKELVPYLKEKLKRNVEVVPAK 77 (198)
Q Consensus 47 kVtV~G~vdp~~L~~~L~kk~G~~aeiV~p~ 77 (198)
-|.|+|+.|-..++..|+ ..|++|.++++.
T Consensus 103 ivLvSgD~Df~~~i~~lr-~~G~~V~v~~~~ 132 (149)
T cd06167 103 IVLVSGDSDFVPLVERLR-ELGKRVIVVGFE 132 (149)
T ss_pred EEEEECCccHHHHHHHHH-HcCCEEEEEccC
Confidence 344778899999999999 789999999876
No 57
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=29.10 E-value=82 Score=32.92 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=34.2
Q ss_pred HHHHHHHHHhcCCCccEEEEeCCCCeEEEee--------eCCHHHHHHHHH
Q 029137 22 CISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--------TMDVKELVPYLK 64 (198)
Q Consensus 22 Ca~kI~kaL~kl~GV~sV~VD~~~~kVtV~G--------~vdp~~L~~~L~ 64 (198)
=++.|+..|.+++||.+|.+......+.|.- .+++..|..+|+
T Consensus 158 ~~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~ 208 (1037)
T PRK10555 158 VASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIE 208 (1037)
T ss_pred HHHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 4577999999999999999987656566662 267888888888
No 58
>cd03029 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH - GSH reductase - GSH - GRX domain of hybrid - PRX domain of hybrid - peroxide substrate.
Probab=28.48 E-value=1.3e+02 Score=20.08 Aligned_cols=33 Identities=27% Similarity=0.407 Sum_probs=22.3
Q ss_pred EEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCC
Q 029137 11 VVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGK 45 (198)
Q Consensus 11 vvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~ 45 (198)
|+|-..-.|..|. ++++.|.+. ||.-..+|...
T Consensus 3 v~lys~~~Cp~C~-~ak~~L~~~-~i~~~~~~v~~ 35 (72)
T cd03029 3 VSLFTKPGCPFCA-RAKAALQEN-GISYEEIPLGK 35 (72)
T ss_pred EEEEECCCCHHHH-HHHHHHHHc-CCCcEEEECCC
Confidence 4444457899999 567777754 77766666543
No 59
>smart00838 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
Probab=28.37 E-value=2.1e+02 Score=20.07 Aligned_cols=47 Identities=11% Similarity=0.188 Sum_probs=31.6
Q ss_pred EEeecC-hhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHH
Q 029137 14 KIRLHC-EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVP 61 (198)
Q Consensus 14 kV~MhC-~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~ 61 (198)
.+.+.| ..+...|...|.+..|.- +.++..+..++|.+.+....+..
T Consensus 7 ~~~I~~p~~~~g~v~~~l~~rrG~i-~~~~~~~~~~~i~~~iP~~~~~~ 54 (85)
T smart00838 7 KVEVTVPEEYMGDVIGDLNSRRGKI-EGMEQRGGAQVIKAKVPLSEMFG 54 (85)
T ss_pred EEEEEeCHHHHHHHHHHHHHcCCEE-ECeeccCCcEEEEEECCHHHHhc
Confidence 334444 367778999998888854 34444456788999887766643
No 60
>cd03713 EFG_mtEFG_C EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide
Probab=27.37 E-value=2.1e+02 Score=19.66 Aligned_cols=47 Identities=9% Similarity=0.199 Sum_probs=31.7
Q ss_pred EEEeecCh-hHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHH
Q 029137 13 LKIRLHCE-GCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELV 60 (198)
Q Consensus 13 LkV~MhC~-gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~ 60 (198)
++|.++|. .+..+|...|.+..|.. +..+..++.+.|++.+....+.
T Consensus 4 ~~~~I~~p~~~~g~v~~~l~~rrg~i-~~~~~~~~~~~i~~~iP~~e~~ 51 (78)
T cd03713 4 MKVEVTVPEEYMGDVIGDLSSRRGQI-LGTESRGGWKVIKAEVPLAEMF 51 (78)
T ss_pred EEEEEEcCHHHHHHHHHHHHHcCCce-EceeccCCcEEEEEEcCHHHHh
Confidence 34555663 67778999998888854 2333445678899987766653
No 61
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=27.08 E-value=1.2e+02 Score=24.14 Aligned_cols=43 Identities=21% Similarity=0.210 Sum_probs=28.8
Q ss_pred HHHHHHHHHhcC-CCccEEEEeCCCCeEEEeeeCCHHHHHHHHH
Q 029137 22 CISKIKKIIYKT-KGVDNVTIDGGKDLVTVKGTMDVKELVPYLK 64 (198)
Q Consensus 22 Ca~kI~kaL~kl-~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~ 64 (198)
=+..|.++|.+. -++..+.|....+.|++.|.+.-...+.++.
T Consensus 27 ~~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~ 70 (147)
T PRK11198 27 AADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKIL 70 (147)
T ss_pred HHHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHH
Confidence 345667777542 1344456666799999999987666666665
No 62
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=26.21 E-value=2.7e+02 Score=21.95 Aligned_cols=50 Identities=22% Similarity=0.282 Sum_probs=33.5
Q ss_pred HHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHH----HHHhccCCceEEc
Q 029137 24 SKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVP----YLKEKLKRNVEVV 74 (198)
Q Consensus 24 ~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~----~L~kk~G~~aeiV 74 (198)
..++..|..+ |-..|.+=++++-|.++...++..|.. .|.+..|+.+.++
T Consensus 22 aeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v~ 75 (137)
T PF08002_consen 22 AELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPVI 75 (137)
T ss_dssp HHHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---EE
T ss_pred HHHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEEE
Confidence 4667777776 899999999999999997777766654 4555688877544
No 63
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=26.03 E-value=1.2e+02 Score=22.92 Aligned_cols=36 Identities=17% Similarity=0.321 Sum_probs=27.7
Q ss_pred cceEEEEEEeec-ChhHHHHHHHHHhcCCCccEEEEe
Q 029137 7 LQSTVVLKIRLH-CEGCISKIKKIIYKTKGVDNVTID 42 (198)
Q Consensus 7 ~~~tvvLkV~Mh-C~gCa~kI~kaL~kl~GV~sV~VD 42 (198)
....+.|.|-|. -+|-...|+.+|..+.||+++++-
T Consensus 47 GLkal~l~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 47 GLKALKLYVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred eeeeEEEEEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 345566666664 357788999999999999999874
No 64
>cd04097 mtEFG1_C mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (desig
Probab=25.97 E-value=2.3e+02 Score=19.62 Aligned_cols=46 Identities=20% Similarity=0.365 Sum_probs=30.1
Q ss_pred EEeecCh-hHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHH
Q 029137 14 KIRLHCE-GCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELV 60 (198)
Q Consensus 14 kV~MhC~-gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~ 60 (198)
+|.+.|. .+..+|...|.+..|.- +..+...+.+.|.+.+....+.
T Consensus 5 ~~~I~~p~~~~g~v~~~l~~rrg~i-~~~~~~~~~~~i~~~~P~~e~~ 51 (78)
T cd04097 5 KVEVTAPTEFQGNVIGLLNKRKGTI-VDTDTGEDEFTLEAEVPLNDMF 51 (78)
T ss_pred EEEEEecHHHHHHHHHHHHHCCCEE-eceEecCCeEEEEEEECHHHhh
Confidence 4444553 56778888898888854 2333344678899987766653
No 65
>cd02066 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which
Probab=25.93 E-value=1.7e+02 Score=18.47 Aligned_cols=30 Identities=20% Similarity=0.336 Sum_probs=19.2
Q ss_pred EEEEeecChhHHHHHHHHHhcCCCccEEEEeC
Q 029137 12 VLKIRLHCEGCISKIKKIIYKTKGVDNVTIDG 43 (198)
Q Consensus 12 vLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~ 43 (198)
+|-..-.|..|. +++..|.+.. |.-..+|.
T Consensus 3 ~ly~~~~Cp~C~-~~~~~L~~~~-i~~~~~di 32 (72)
T cd02066 3 VVFSKSTCPYCK-RAKRLLESLG-IEFEEIDI 32 (72)
T ss_pred EEEECCCCHHHH-HHHHHHHHcC-CcEEEEEC
Confidence 344446799998 7778787664 55444444
No 66
>cd03711 Tet_C Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=25.72 E-value=2.3e+02 Score=19.59 Aligned_cols=47 Identities=17% Similarity=0.140 Sum_probs=32.1
Q ss_pred EEeecCh-hHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHH
Q 029137 14 KIRLHCE-GCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVP 61 (198)
Q Consensus 14 kV~MhC~-gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~ 61 (198)
++.+.|. .+..+|...|.+..|.-. ..+..++.+.|++.+....+..
T Consensus 5 ~~~i~~p~~~~g~v~~~l~~rrg~i~-~~~~~~~~~~i~~~~P~~~~~g 52 (78)
T cd03711 5 RFELEVPQDALGRAMSDLAKMGATFE-DPQIKGDEVTLEGTIPVATSQD 52 (78)
T ss_pred EEEEEcCHHHHHHHHHHHHHcCCEee-CcEecCCEEEEEEEECHHHHhh
Confidence 3444553 677899999988888542 3444557899999877766643
No 67
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=25.53 E-value=96 Score=27.99 Aligned_cols=48 Identities=23% Similarity=0.224 Sum_probs=36.2
Q ss_pred eEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccCC
Q 029137 9 STVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKR 69 (198)
Q Consensus 9 ~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~ 69 (198)
.++.|+++.+ ..|++.|+..|..++||.++.+ ++.++-.+.|++.+|.
T Consensus 61 i~vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~------------~sre~~l~~L~~~lg~ 108 (297)
T COG2177 61 ITVYLQIDAD-QDDAALVREKIEGIPGVKSVRF------------ISREEALKELQPWLGF 108 (297)
T ss_pred EEEEEecCCC-hHHHHHHHHHHhcCCCcceEEE------------eCHHHHHHHHHHHcCc
Confidence 3444555555 9999999999999999998875 4666667777766664
No 68
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=25.46 E-value=2.3e+02 Score=21.71 Aligned_cols=48 Identities=19% Similarity=0.267 Sum_probs=32.6
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccC
Q 029137 20 EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLK 68 (198)
Q Consensus 20 ~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G 68 (198)
+.-...|+.+|+.++|++=-.-|...+.|.|.-.-+...|+..|. .+.
T Consensus 17 pe~l~av~~~L~~ip~~EV~~~d~~GKlVVVie~~~~~~l~~tie-~i~ 64 (94)
T COG3062 17 PERLSAVKTALLAIPGCEVYGEDAEGKLVVVIEAEDSETLLETIE-SIR 64 (94)
T ss_pred HHHHHHHHHHHhcCCCcEeeccCCCceEEEEEEcCchHHHHHHHH-HHh
Confidence 456788999999999998444444434444555567777777776 443
No 69
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.98 E-value=1.6e+02 Score=28.61 Aligned_cols=10 Identities=20% Similarity=0.248 Sum_probs=5.4
Q ss_pred ccCCceEEcC
Q 029137 66 KLKRNVEVVP 75 (198)
Q Consensus 66 k~G~~aeiV~ 75 (198)
++|..|-.++
T Consensus 278 ~ig~~vy~ap 287 (483)
T KOG2236|consen 278 CIGEKVYYAP 287 (483)
T ss_pred ccCCeeEecC
Confidence 4555555554
No 70
>TIGR03143 AhpF_homolog putative alkyl hydroperoxide reductase F subunit. This family of thioredoxin reductase homologs is found adjacent to alkylhydroperoxide reductase C subunit predominantly in cases where there is only one C subunit in the genome and that genome is lacking the F subunit partner (also a thioredcxin reductase homolog) that is usually found (TIGR03140).
Probab=24.77 E-value=2.2e+02 Score=27.34 Aligned_cols=34 Identities=21% Similarity=0.398 Sum_probs=18.8
Q ss_pred EEEEEEeecChhHHHHH---HHHHhcCCCccEEEEeC
Q 029137 10 TVVLKIRLHCEGCISKI---KKIIYKTKGVDNVTIDG 43 (198)
Q Consensus 10 tvvLkV~MhC~gCa~kI---~kaL~kl~GV~sV~VD~ 43 (198)
.|.+-|..+|..|-+-+ .+.+...++|..-.+|.
T Consensus 479 ~i~v~~~~~C~~Cp~~~~~~~~~~~~~~~i~~~~i~~ 515 (555)
T TIGR03143 479 NIKIGVSLSCTLCPDVVLAAQRIASLNPNVEAEMIDV 515 (555)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHhCCCceEEEEEC
Confidence 33333468999998522 23334445665444443
No 71
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=24.69 E-value=1.6e+02 Score=21.22 Aligned_cols=33 Identities=21% Similarity=0.200 Sum_probs=26.0
Q ss_pred ceEEEEEEeecChhHHHHHHHHHhcCCCccEEEEe
Q 029137 8 QSTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTID 42 (198)
Q Consensus 8 ~~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD 42 (198)
...++|-|. -+.....|.+.|.++..|..|+++
T Consensus 44 ~sriti~v~--~~~~i~ql~kQL~KL~dV~~V~~~ 76 (76)
T PRK11152 44 NINIELTVA--SERPIDLLSSQLNKLVDVAHVEIL 76 (76)
T ss_pred EEEEEEEEC--CCchHHHHHHHHhcCcCeEEEEEC
Confidence 355555553 689999999999999999988764
No 72
>PRK10638 glutaredoxin 3; Provisional
Probab=24.66 E-value=1.5e+02 Score=20.53 Aligned_cols=33 Identities=24% Similarity=0.358 Sum_probs=22.7
Q ss_pred EEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCC
Q 029137 10 TVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGG 44 (198)
Q Consensus 10 tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~ 44 (198)
+|+|-..-.|..|. +++..|.. .||.-..+|..
T Consensus 3 ~v~ly~~~~Cp~C~-~a~~~L~~-~gi~y~~~dv~ 35 (83)
T PRK10638 3 NVEIYTKATCPFCH-RAKALLNS-KGVSFQEIPID 35 (83)
T ss_pred cEEEEECCCChhHH-HHHHHHHH-cCCCcEEEECC
Confidence 45555567899998 67777765 47776556554
No 73
>KOG3890 consensus Mitochondrial 28S ribosomal protein S22 [Translation, ribosomal structure and biogenesis]
Probab=24.43 E-value=33 Score=31.77 Aligned_cols=16 Identities=38% Similarity=0.742 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCCCcc
Q 029137 180 MYHAPQMFSDENPNAC 195 (198)
Q Consensus 180 ~~~~pq~FSDeNPnaC 195 (198)
+..+|-||||||=--|
T Consensus 175 ~~~tP~~F~eenL~~~ 190 (391)
T KOG3890|consen 175 QSYTPRMFAEENLAKC 190 (391)
T ss_pred ccCCCccccchHHHHH
Confidence 3568999999985444
No 74
>PRK11023 outer membrane lipoprotein; Provisional
Probab=24.39 E-value=1.6e+02 Score=24.41 Aligned_cols=48 Identities=13% Similarity=0.144 Sum_probs=35.5
Q ss_pred ecChhHHHHHHHHHhcCCCcc---EEEEeCCCCeEEEeeeCCHHHHHHHHH
Q 029137 17 LHCEGCISKIKKIIYKTKGVD---NVTIDGGKDLVTVKGTMDVKELVPYLK 64 (198)
Q Consensus 17 MhC~gCa~kI~kaL~kl~GV~---sV~VD~~~~kVtV~G~vdp~~L~~~L~ 64 (198)
+....=..+|+.+|..-+.+. ++.|...++.|+++|.++-........
T Consensus 45 ~dD~~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~A~ 95 (191)
T PRK11023 45 VDDGTLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERAK 95 (191)
T ss_pred ehhHHHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHHHH
Confidence 344556778888988777664 588888999999999987665555544
No 75
>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=23.88 E-value=2.5e+02 Score=19.24 Aligned_cols=48 Identities=25% Similarity=0.318 Sum_probs=34.9
Q ss_pred ecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeee--CCHHHHHHHHHhccCCceEEc
Q 029137 17 LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLKEKLKRNVEVV 74 (198)
Q Consensus 17 MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~--vdp~~L~~~L~kk~G~~aeiV 74 (198)
+.|+.=.-+++++|.+++. .+.+.|..+ .....|..+.+ ..|+.+..+
T Consensus 7 ~~CP~Pvl~~kkal~~l~~---------G~~l~V~~d~~~a~~di~~~~~-~~G~~~~~~ 56 (69)
T cd03420 7 LQCPGPILKLKKEIDKLQD---------GEQLEVKASDPGFARDAQAWCK-STGNTLISL 56 (69)
T ss_pred CcCCHHHHHHHHHHHcCCC---------CCEEEEEECCccHHHHHHHHHH-HcCCEEEEE
Confidence 8899999999999988762 233444433 45677888887 999988754
No 76
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=23.38 E-value=2.1e+02 Score=24.22 Aligned_cols=45 Identities=16% Similarity=0.107 Sum_probs=30.3
Q ss_pred hhHHHHHHHHHhcCCCcc--EEEEeCCCCeEEEeeeCCHHHHHHHHH
Q 029137 20 EGCISKIKKIIYKTKGVD--NVTIDGGKDLVTVKGTMDVKELVPYLK 64 (198)
Q Consensus 20 ~gCa~kI~kaL~kl~GV~--sV~VD~~~~kVtV~G~vdp~~L~~~L~ 64 (198)
..=+.+|.++++..+||. ++..|...++..+|-.-+++.|.+++-
T Consensus 15 ~~~ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~vG~p~~v~~a~~ 61 (178)
T PF07837_consen 15 KEVIEAIAKAARNVPGVKLLDVFSDADYNRSVITLVGEPEAVAEAAF 61 (178)
T ss_dssp HHHHHHHHHHCCTSTTEEEEEEEEETTTTEEEEEEEE-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCEEEecCCCCCCCCCeEEEeeChHHHHHHHH
Confidence 344678888888888855 455666888887775555666655544
No 77
>PRK11023 outer membrane lipoprotein; Provisional
Probab=23.07 E-value=2e+02 Score=23.94 Aligned_cols=41 Identities=15% Similarity=0.209 Sum_probs=29.0
Q ss_pred hhHHHHHHHHHhcCCCccE--EEEeCCCCeEEEeeeCCHHHHH
Q 029137 20 EGCISKIKKIIYKTKGVDN--VTIDGGKDLVTVKGTMDVKELV 60 (198)
Q Consensus 20 ~gCa~kI~kaL~kl~GV~s--V~VD~~~~kVtV~G~vdp~~L~ 60 (198)
..=..+|+.+|..-+.|.. +.|...++.|++.|.++..+..
T Consensus 126 ~~It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~ 168 (191)
T PRK11023 126 TWITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAK 168 (191)
T ss_pred HHHHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHH
Confidence 3466788888887766654 4455569999999988765543
No 78
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=22.87 E-value=1.9e+02 Score=19.11 Aligned_cols=32 Identities=31% Similarity=0.547 Sum_probs=20.7
Q ss_pred EEEEEeecChhHHHHHHHHHhcCCCccEEEEeCC
Q 029137 11 VVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGG 44 (198)
Q Consensus 11 vvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~ 44 (198)
|+|-..-.|..|. ++++.|.+. ||.-..+|..
T Consensus 2 i~ly~~~~Cp~C~-~ak~~L~~~-~i~~~~i~i~ 33 (75)
T cd03418 2 VEIYTKPNCPYCV-RAKALLDKK-GVDYEEIDVD 33 (75)
T ss_pred EEEEeCCCChHHH-HHHHHHHHC-CCcEEEEECC
Confidence 3444456799998 677777664 7765555543
No 79
>cd03710 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secreti
Probab=22.41 E-value=2.8e+02 Score=19.32 Aligned_cols=45 Identities=13% Similarity=0.204 Sum_probs=28.7
Q ss_pred EeecC-hhHHHHHHHHHhcCCCccEEEEeC-CCCeEEEeeeCCHHHHH
Q 029137 15 IRLHC-EGCISKIKKIIYKTKGVDNVTIDG-GKDLVTVKGTMDVKELV 60 (198)
Q Consensus 15 V~MhC-~gCa~kI~kaL~kl~GV~sV~VD~-~~~kVtV~G~vdp~~L~ 60 (198)
|.+.| ..|..+|...|.+..|... .++. .++.+.|++.+....+.
T Consensus 6 v~I~~P~~~~g~V~~~l~~rrg~i~-~~~~~~~~~~~i~~~~P~~~~~ 52 (79)
T cd03710 6 LTIDVPEEYSGAVIEKLGKRKGEMV-DMEPDGNGRTRLEFKIPSRGLI 52 (79)
T ss_pred EEEEeCchhhHHHHHHHHhCCCEEE-ccEECCCCEEEEEEEECHHHHc
Confidence 33344 3566688888988888432 2333 34678899987766653
No 80
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.38 E-value=2.4e+02 Score=18.64 Aligned_cols=32 Identities=9% Similarity=0.075 Sum_probs=21.4
Q ss_pred EEEEEEeecChhHHHHHHHHHhcCCCccEEEE
Q 029137 10 TVVLKIRLHCEGCISKIKKIIYKTKGVDNVTI 41 (198)
Q Consensus 10 tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~V 41 (198)
.+.|.|...-..=...|.+.|.+++||...++
T Consensus 41 ~~~~~vev~~~~~l~~i~~~L~~i~gV~~~~~ 72 (74)
T cd04887 41 VRDITVDAPSEEHAETIVAAVRALPEVKVLSV 72 (74)
T ss_pred EEEEEEEcCCHHHHHHHHHHHhcCCCeEEEEe
Confidence 34455555555555678888999999876554
No 81
>PF02983 Pro_Al_protease: Alpha-lytic protease prodomain; InterPro: IPR004236 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. The alpha-lytic protease prodomain is associated with serine peptidases, specifically the alpha-lytic endopeptidases and streptogrisin A, B, C, D and E, which are bacterial enzymes and which belong to MEROPS peptidase subfamily S1A (IPR001316 from INTERPRO). The protease precursor in Gram-negative bacterial proteases may be a general property of extracellular bacterial proteases []. The proteases are encoded with a large (166 amino acid) N-terminal pro region that is required transiently both in vivo and in vitro for the correct folding of the protease domain [, ]. The pro region also acts as a potent inhibitor of the mature enzyme []. ; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0005576 extracellular region; PDB: 3PRO_C 2PRO_B 4PRO_C.
Probab=21.96 E-value=1.8e+02 Score=19.94 Aligned_cols=21 Identities=19% Similarity=0.185 Sum_probs=18.2
Q ss_pred CCCccEEEEeCCCCeEEEeee
Q 029137 33 TKGVDNVTIDGGKDLVTVKGT 53 (198)
Q Consensus 33 l~GV~sV~VD~~~~kVtV~G~ 53 (198)
-.+|.+..||..+++|.|+..
T Consensus 22 ~~~~~~WyvD~~tn~VVV~a~ 42 (62)
T PF02983_consen 22 PVAVTSWYVDPRTNKVVVTAD 42 (62)
T ss_dssp GGCEEEEEEECCCTEEEEEEE
T ss_pred CCCcceEEEeCCCCeEEEEEC
Confidence 457899999999999999854
No 82
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=21.95 E-value=2.3e+02 Score=20.97 Aligned_cols=35 Identities=9% Similarity=0.121 Sum_probs=28.0
Q ss_pred eEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeC
Q 029137 9 STVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDG 43 (198)
Q Consensus 9 ~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~ 43 (198)
-++++.|.-.+.+=....-..|..++||.++..=+
T Consensus 42 GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVY 76 (87)
T PRK10553 42 GQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVY 76 (87)
T ss_pred CeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEE
Confidence 46777777777777778888899999999887644
No 83
>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins. It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).
Probab=21.41 E-value=5.1e+02 Score=22.04 Aligned_cols=52 Identities=17% Similarity=0.245 Sum_probs=32.3
Q ss_pred HHHHHHHhcCCCcc----EEEEeCCCCeEEEeeeCCHHHHHHHHHhccCCceEEcC
Q 029137 24 SKIKKIIYKTKGVD----NVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVP 75 (198)
Q Consensus 24 ~kI~kaL~kl~GV~----sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~~aeiV~ 75 (198)
+.+-+.|.+++|.. .|.=++=.+.|||.|-+...+|++.|+.+...+..+++
T Consensus 113 ~~~~~~l~~~~~~~v~V~~V~N~fFG~~ItVaGLLTg~Dii~~L~~~~~~d~lllP 168 (204)
T PF04459_consen 113 KPLVEKLNRIPGLEVEVVPVKNRFFGGTITVAGLLTGQDIIEQLKGKELGDLLLLP 168 (204)
T ss_pred HHHHHHHhccCCCeEEEEEeecCCCCCCeEEeeCccHHHHHHHhCcCCCCCEEEEC
Confidence 33334444556632 22233447789999999999999999843333455554
No 84
>PRK09577 multidrug efflux protein; Reviewed
Probab=21.37 E-value=2.1e+02 Score=30.02 Aligned_cols=42 Identities=10% Similarity=0.245 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCCccEEEEeCCCCeEEEee--------eCCHHHHHHHHH
Q 029137 23 ISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--------TMDVKELVPYLK 64 (198)
Q Consensus 23 a~kI~kaL~kl~GV~sV~VD~~~~kVtV~G--------~vdp~~L~~~L~ 64 (198)
++.|+..|.+++||.+|.++-...+|.|.- .+++..|..+|+
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~ 207 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVR 207 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHH
Confidence 568999999999999999987666666641 267788888888
No 85
>PF10934 DUF2634: Protein of unknown function (DUF2634); InterPro: IPR020288 This entry is represented by the Bacteriophage EJ-1, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Bacteriophage EJ-1, Orf60 function has not been characterised. It has been shown to be simialr to XkdS (P54331 from SWISSPROT), which is encoded on a phage-like element (prophage) of PSBX found in Bacillus subtilis.
Probab=20.67 E-value=1.6e+02 Score=22.61 Aligned_cols=33 Identities=18% Similarity=0.204 Sum_probs=26.0
Q ss_pred hHHHHHHHHHh---cCCCccEEEEeCCCCeEEEeee
Q 029137 21 GCISKIKKIIY---KTKGVDNVTIDGGKDLVTVKGT 53 (198)
Q Consensus 21 gCa~kI~kaL~---kl~GV~sV~VD~~~~kVtV~G~ 53 (198)
--.+.|+.+|. ++.+|+++.+....+.+.|+.+
T Consensus 69 Ei~r~I~EaL~~d~rI~~V~~f~f~~~~~~l~v~f~ 104 (112)
T PF10934_consen 69 EIEREIEEALLQDPRITSVENFSFEWEGDSLYVSFT 104 (112)
T ss_pred HHHHHHHHHHhcCCCcceEEEEEEEEECCEEEEEEE
Confidence 34677888885 6778888899999999988754
No 86
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.59 E-value=1.3e+02 Score=23.07 Aligned_cols=22 Identities=14% Similarity=0.262 Sum_probs=19.8
Q ss_pred hcCCCccEEEEeCCCCeEEEee
Q 029137 31 YKTKGVDNVTIDGGKDLVTVKG 52 (198)
Q Consensus 31 ~kl~GV~sV~VD~~~~kVtV~G 52 (198)
..++|++.|++...++++.|.+
T Consensus 37 as~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 37 ASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EecCCceEEEEecccceEEEec
Confidence 4578999999999999999987
No 87
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=20.42 E-value=2.8e+02 Score=25.04 Aligned_cols=28 Identities=21% Similarity=0.169 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCCCe
Q 029137 20 EGCISKIKKIIYKTKGVDNVTIDGGKDL 47 (198)
Q Consensus 20 ~gCa~kI~kaL~kl~GV~sV~VD~~~~k 47 (198)
.||=-.++..+.+++||.++.+=.+++.
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~ 161 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGD 161 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCC
Confidence 7888888889999999999999876553
No 88
>KOG1752 consensus Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]
Probab=20.24 E-value=2.4e+02 Score=21.52 Aligned_cols=54 Identities=22% Similarity=0.333 Sum_probs=35.5
Q ss_pred ceEEEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeeeCCHHHHHHHHHhccCCc
Q 029137 8 QSTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRN 70 (198)
Q Consensus 8 ~~tvvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~~kVtV~G~vdp~~L~~~L~kk~G~~ 70 (198)
...|++-..-.|.-|.. ++..|.. .||.-..+.++.. -+...|.++|.+.+|.+
T Consensus 13 ~~~VVifSKs~C~~c~~-~k~ll~~-~~v~~~vvELD~~-------~~g~eiq~~l~~~tg~~ 66 (104)
T KOG1752|consen 13 ENPVVIFSKSSCPYCHR-AKELLSD-LGVNPKVVELDED-------EDGSEIQKALKKLTGQR 66 (104)
T ss_pred cCCEEEEECCcCchHHH-HHHHHHh-CCCCCEEEEccCC-------CCcHHHHHHHHHhcCCC
Confidence 34454444588999997 7777766 5666555555443 45568888888666543
No 89
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=20.18 E-value=2.6e+02 Score=18.70 Aligned_cols=33 Identities=30% Similarity=0.553 Sum_probs=21.9
Q ss_pred EEEEEeecChhHHHHHHHHHhcCCCccEEEEeCCC
Q 029137 11 VVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGK 45 (198)
Q Consensus 11 vvLkV~MhC~gCa~kI~kaL~kl~GV~sV~VD~~~ 45 (198)
|+|-..-.|..|. ++++.|.. .||.-..+|+..
T Consensus 3 v~ly~~~~C~~C~-ka~~~L~~-~gi~~~~~di~~ 35 (73)
T cd03027 3 VTIYSRLGCEDCT-AVRLFLRE-KGLPYVEINIDI 35 (73)
T ss_pred EEEEecCCChhHH-HHHHHHHH-CCCceEEEECCC
Confidence 3444446899998 77777765 477766666543
Done!