Query 027936
Match_columns 216
No_of_seqs 187 out of 1108
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 03:44:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027936.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027936hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.5 9.9E-14 2.1E-18 101.1 8.6 68 25-92 3-70 (73)
2 PF00403 HMA: Heavy-metal-asso 99.4 6E-13 1.3E-17 92.4 7.6 58 30-88 1-62 (62)
3 COG2608 CopZ Copper chaperone 99.3 1.1E-11 2.3E-16 90.1 8.0 66 26-92 1-70 (71)
4 KOG4656 Copper chaperone for s 99.0 9.3E-10 2E-14 95.8 8.6 72 25-97 5-76 (247)
5 PLN02957 copper, zinc superoxi 98.5 1.2E-06 2.6E-11 76.9 10.0 71 25-96 4-74 (238)
6 PRK10671 copA copper exporting 98.3 1.4E-06 3E-11 88.1 7.9 65 26-93 2-67 (834)
7 TIGR00003 copper ion binding p 97.9 0.00013 2.8E-09 46.1 8.4 61 27-88 2-66 (68)
8 COG2217 ZntA Cation transport 97.8 5.3E-05 1.1E-09 76.3 7.4 63 27-91 2-69 (713)
9 PRK10671 copA copper exporting 97.1 0.0014 2.9E-08 66.7 7.8 65 27-92 99-164 (834)
10 KOG0207 Cation transport ATPas 96.6 0.0047 1E-07 63.6 7.0 65 27-92 146-214 (951)
11 PRK11033 zntA zinc/cadmium/mer 96.4 0.0081 1.8E-07 60.7 7.2 65 25-91 51-118 (741)
12 KOG0207 Cation transport ATPas 96.0 0.012 2.6E-07 60.7 6.0 61 34-95 2-64 (951)
13 TIGR02052 MerP mercuric transp 94.1 0.79 1.7E-05 31.7 9.1 63 28-91 24-90 (92)
14 COG1888 Uncharacterized protei 90.2 2 4.3E-05 33.5 7.5 68 24-92 3-79 (97)
15 PF02680 DUF211: Uncharacteriz 90.1 1.4 3.1E-05 34.3 6.7 66 25-92 3-77 (95)
16 cd00371 HMA Heavy-metal-associ 88.5 2.8 6.2E-05 23.2 7.2 49 34-82 6-56 (63)
17 PRK13748 putative mercuric red 87.8 2.9 6.2E-05 40.2 8.5 64 30-94 3-69 (561)
18 PF01883 DUF59: Domain of unkn 86.3 1.3 2.8E-05 31.3 4.0 33 27-59 34-72 (72)
19 PF14437 MafB19-deam: MafB19-l 73.4 8 0.00017 32.3 5.1 42 26-68 99-142 (146)
20 TIGR03406 FeS_long_SufT probab 63.5 9.8 0.00021 32.4 3.8 34 28-61 114-153 (174)
21 cd04888 ACT_PheB-BS C-terminal 62.4 20 0.00044 24.6 4.7 34 26-59 40-74 (76)
22 TIGR02945 SUF_assoc FeS assemb 62.4 11 0.00024 28.1 3.6 35 28-62 38-78 (99)
23 PF13291 ACT_4: ACT domain; PD 54.8 35 0.00077 24.0 5.0 35 24-58 45-79 (80)
24 PF14492 EFG_II: Elongation Fa 54.6 65 0.0014 23.1 6.4 61 30-91 7-73 (75)
25 PF04972 BON: BON domain; Int 54.2 9 0.00019 26.0 1.7 39 42-81 2-43 (64)
26 PRK06418 transcription elongat 53.5 53 0.0012 27.9 6.5 70 26-95 5-99 (166)
27 PRK10553 assembly protein for 51.0 59 0.0013 24.7 5.8 43 40-82 18-61 (87)
28 PF01206 TusA: Sulfurtransfera 49.4 45 0.00097 23.1 4.7 53 30-92 2-57 (70)
29 PF03927 NapD: NapD protein; 47.3 67 0.0014 23.6 5.5 42 40-82 16-58 (79)
30 PRK14054 methionine sulfoxide 45.2 41 0.0009 28.6 4.6 46 37-82 9-76 (172)
31 TIGR02190 GlrX-dom Glutaredoxi 45.2 52 0.0011 23.3 4.6 37 24-62 5-41 (79)
32 PF13732 DUF4162: Domain of un 44.9 60 0.0013 23.0 4.9 42 48-92 26-69 (84)
33 COG2151 PaaD Predicted metal-s 44.2 36 0.00078 27.1 3.9 34 28-61 50-89 (111)
34 cd02410 archeal_CPSF_KH The ar 42.1 68 0.0015 26.8 5.3 69 28-96 38-116 (145)
35 PF08002 DUF1697: Protein of u 41.3 1E+02 0.0023 24.8 6.3 50 42-92 22-75 (137)
36 PF13192 Thioredoxin_3: Thiore 39.6 36 0.00078 24.1 3.0 14 28-42 2-15 (76)
37 PRK11200 grxA glutaredoxin 1; 38.5 77 0.0017 22.6 4.6 34 29-63 3-40 (85)
38 PF08712 Nfu_N: Scaffold prote 37.8 68 0.0015 24.0 4.4 40 42-83 37-78 (87)
39 PF04468 PSP1: PSP1 C-terminal 36.7 1E+02 0.0022 23.0 5.2 53 38-91 29-85 (88)
40 KOG3411 40S ribosomal protein 35.5 33 0.00071 28.5 2.4 42 38-82 97-139 (143)
41 PF05046 Img2: Mitochondrial l 35.2 1.9E+02 0.0041 21.6 6.7 59 26-86 27-86 (87)
42 PF03958 Secretin_N: Bacterial 35.1 1.2E+02 0.0025 21.3 5.1 29 53-82 45-74 (82)
43 PRK11670 antiporter inner memb 35.0 1.1E+02 0.0024 28.6 6.2 66 28-94 48-144 (369)
44 TIGR02159 PA_CoA_Oxy4 phenylac 35.0 52 0.0011 27.2 3.6 33 28-61 26-64 (146)
45 PF09580 Spore_YhcN_YlaJ: Spor 34.2 95 0.0021 25.4 5.1 34 36-69 72-105 (177)
46 cd04877 ACT_TyrR N-terminal AC 34.2 91 0.002 21.7 4.4 30 29-58 39-68 (74)
47 PRK04435 hypothetical protein; 33.5 92 0.002 25.4 4.8 33 27-59 110-143 (147)
48 PRK05528 methionine sulfoxide 33.1 94 0.002 26.0 4.9 46 37-82 7-69 (156)
49 KOG2236 Uncharacterized conser 32.7 93 0.002 30.7 5.4 10 84-93 278-287 (483)
50 PRK11152 ilvM acetolactate syn 31.1 1.1E+02 0.0025 22.4 4.6 36 23-60 41-76 (76)
51 cd04887 ACT_MalLac-Enz ACT_Mal 29.9 1.6E+02 0.0036 19.9 5.0 35 25-59 38-72 (74)
52 PF08210 APOBEC_N: APOBEC-like 29.8 69 0.0015 27.3 3.6 66 25-94 72-147 (188)
53 COG3643 Glutamate formiminotra 29.3 51 0.0011 30.3 2.8 55 38-92 17-73 (302)
54 PF00679 EFG_C: Elongation fac 29.3 1.7E+02 0.0037 21.3 5.3 48 38-86 15-66 (89)
55 cd03027 GRX_DEP Glutaredoxin ( 28.4 1.4E+02 0.0031 20.4 4.6 32 29-62 3-34 (73)
56 cd06167 LabA_like LabA_like pr 28.4 73 0.0016 24.8 3.4 29 66-95 104-132 (149)
57 TIGR00489 aEF-1_beta translati 28.3 1.1E+02 0.0023 23.4 4.0 23 38-60 61-83 (88)
58 PRK11018 hypothetical protein; 28.2 2.3E+02 0.0051 20.4 6.1 57 28-92 8-65 (78)
59 PRK00435 ef1B elongation facto 28.1 1E+02 0.0022 23.5 3.9 33 28-60 50-83 (88)
60 TIGR02189 GlrX-like_plant Glut 27.9 1.8E+02 0.0039 21.8 5.3 51 28-87 9-59 (99)
61 PF03927 NapD: NapD protein; 27.6 1.6E+02 0.0035 21.6 4.8 33 27-59 39-71 (79)
62 PRK13014 methionine sulfoxide 27.4 84 0.0018 27.1 3.7 46 37-82 14-81 (186)
63 cd03029 GRX_hybridPRX5 Glutare 27.2 1.5E+02 0.0032 20.2 4.4 32 29-62 3-34 (72)
64 PRK11198 LysM domain/BON super 27.2 1.1E+02 0.0025 24.8 4.4 45 38-82 25-70 (147)
65 COG2177 FtsX Cell division pro 27.1 83 0.0018 28.9 3.9 48 27-87 61-108 (297)
66 PRK10638 glutaredoxin 3; Provi 27.1 1.3E+02 0.0029 21.3 4.3 33 28-62 3-35 (83)
67 COG1094 Predicted RNA-binding 27.0 1.3E+02 0.0028 26.4 4.8 36 42-78 27-65 (194)
68 PRK00058 methionine sulfoxide 26.9 1.1E+02 0.0025 26.9 4.5 46 37-82 51-118 (213)
69 PF05663 DUF809: Protein of un 26.7 1.7E+02 0.0036 23.4 5.0 45 37-82 46-90 (138)
70 COG3062 NapD Uncharacterized p 26.6 1.9E+02 0.0041 22.6 5.2 45 38-82 17-61 (94)
71 PRK11023 outer membrane lipopr 26.6 1.4E+02 0.003 25.3 5.0 42 38-79 126-169 (191)
72 PF00462 Glutaredoxin: Glutare 26.1 1.9E+02 0.0041 19.0 4.7 32 31-64 3-34 (60)
73 cd04883 ACT_AcuB C-terminal AC 26.0 2.1E+02 0.0045 19.2 7.1 60 30-90 3-69 (72)
74 PRK11023 outer membrane lipopr 25.9 1.2E+02 0.0026 25.7 4.4 48 35-82 45-95 (191)
75 PRK05412 putative nucleotide-b 25.6 1.4E+02 0.0031 25.3 4.8 44 37-82 101-146 (161)
76 cd02066 GRX_family Glutaredoxi 25.3 1.9E+02 0.0041 18.5 4.6 31 29-61 2-32 (72)
77 cd03420 SirA_RHOD_Pry_redox Si 24.9 2.3E+02 0.0051 19.7 5.2 48 35-92 7-56 (69)
78 PF08777 RRM_3: RNA binding mo 24.6 3.2E+02 0.0069 21.0 6.2 54 29-82 2-58 (105)
79 COG2092 EFB1 Translation elong 24.4 1.3E+02 0.0027 23.3 3.8 35 26-60 48-83 (88)
80 smart00838 EFG_C Elongation fa 24.0 2.8E+02 0.006 19.9 5.7 40 39-79 15-54 (85)
81 PRK07334 threonine dehydratase 23.3 5E+02 0.011 24.3 8.4 64 28-92 326-402 (403)
82 cd04878 ACT_AHAS N-terminal AC 23.1 1.8E+02 0.0039 18.8 4.1 32 25-57 40-71 (72)
83 PRK10555 aminoglycoside/multid 23.0 1.2E+02 0.0025 32.4 4.5 43 40-82 158-208 (1037)
84 cd03421 SirA_like_N SirA_like_ 22.9 2.1E+02 0.0046 19.5 4.6 46 35-91 7-54 (67)
85 TIGR02194 GlrX_NrdH Glutaredox 22.1 1.7E+02 0.0036 20.1 3.9 27 34-62 6-32 (72)
86 PF14424 Toxin-deaminase: The 22.0 1.6E+02 0.0034 23.9 4.2 30 27-56 97-127 (133)
87 PF07837 FTCD_N: Formiminotran 21.9 2E+02 0.0043 24.8 5.0 45 38-82 15-61 (178)
88 cd03418 GRX_GRXb_1_3_like Glut 21.9 2E+02 0.0044 19.3 4.3 31 29-61 2-32 (75)
89 TIGR02200 GlrX_actino Glutared 21.5 2E+02 0.0043 19.2 4.2 30 29-60 2-31 (77)
90 COG1666 Uncharacterized protei 21.5 1.7E+02 0.0038 24.9 4.4 44 37-82 105-150 (165)
91 PF04461 DUF520: Protein of un 21.1 1E+02 0.0022 26.2 3.0 44 37-82 101-146 (160)
92 PF00352 TBP: Transcription fa 20.9 1E+02 0.0023 22.5 2.8 54 28-82 8-76 (86)
93 cd03028 GRX_PICOT_like Glutare 20.8 2.4E+02 0.0052 20.5 4.7 41 36-88 22-62 (90)
94 PF14535 AMP-binding_C_2: AMP- 20.6 3.2E+02 0.0069 20.2 5.4 55 42-96 7-81 (96)
95 cd03713 EFG_mtEFG_C EFG_mtEFG_ 20.2 3.1E+02 0.0068 19.1 6.0 46 32-78 5-51 (78)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.50 E-value=9.9e-14 Score=101.05 Aligned_cols=68 Identities=44% Similarity=0.686 Sum_probs=62.3
Q ss_pred CceEEEEEEeecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHHhccCCcEEEc
Q 027936 25 GVVTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 25 ~~~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G~~veiV 92 (216)
..++++|+|.|||++|+.+|++.|+.++||.++.+|...++|||.|.+|+..|++.|++..+.++.++
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEe
Confidence 45788999999999999999999999999999999999999999999999999999995444777766
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=99.43 E-value=6e-13 Score=92.43 Aligned_cols=58 Identities=28% Similarity=0.514 Sum_probs=53.3
Q ss_pred EEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeec---CCHHHHHHHHHhccCCc
Q 027936 30 VLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MDVKELVPYLKEKLKRN 88 (216)
Q Consensus 30 ~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~---vd~~~L~~~L~kk~G~~ 88 (216)
+|+|. |+|.+|+++|+++|++++||.++.+|+.+++|+|.+. +++.+|.++|+ ++||.
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 68994 9999999999999999999999999999999999987 45699999999 88873
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.30 E-value=1.1e-11 Score=90.09 Aligned_cols=66 Identities=23% Similarity=0.495 Sum_probs=58.6
Q ss_pred ceEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEE--ee-cCCHHHHHHHHHhccCCcEEEc
Q 027936 26 VVTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTV--KG-TMDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 26 ~~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV--~G-~vd~~~L~~~L~kk~G~~veiV 92 (216)
+++++|+|. |+|.+|+.+|+++|..++||.+|.+|+..++++| ++ .++.+.|+++|. .+||.+..+
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 9999999999999999999999999999966665 45 589999999999 999988754
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.03 E-value=9.3e-10 Score=95.75 Aligned_cols=72 Identities=19% Similarity=0.399 Sum_probs=67.3
Q ss_pred CceEEEEEEeecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHHhccCCcEEEcCCCCC
Q 027936 25 GVVTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVPAKKD 97 (216)
Q Consensus 25 ~~~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G~~veiV~p~k~ 97 (216)
..-+++|.|.|||++|++.|+..|..++||++|++|+..+.|.|.+++.+++|...|+ .+|+++.+....+.
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 4567899999999999999999999999999999999999999999999999999999 99999999877554
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.46 E-value=1.2e-06 Score=76.94 Aligned_cols=71 Identities=23% Similarity=0.450 Sum_probs=64.0
Q ss_pred CceEEEEEEeecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHHhccCCcEEEcCCCC
Q 027936 25 GVVTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVPAKK 96 (216)
Q Consensus 25 ~~~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G~~veiV~p~k 96 (216)
...++.|.|.|+|..|+.+|+++|..++||.++.+|+..++++|...++...|+..|+ ++|+.++++....
T Consensus 4 ~~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe-~~Gy~a~~~~~~~ 74 (238)
T PLN02957 4 PELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALE-QTGRKARLIGQGD 74 (238)
T ss_pred CcEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHH-HcCCcEEEecCCC
Confidence 3456788889999999999999999999999999999999999998888999999999 9999998886643
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.32 E-value=1.4e-06 Score=88.11 Aligned_cols=65 Identities=20% Similarity=0.367 Sum_probs=59.0
Q ss_pred ceEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHHhccCCcEEEcC
Q 027936 26 VVTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVVP 93 (216)
Q Consensus 26 ~~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G~~veiV~ 93 (216)
+++++|+|. |+|.+|+.+|+++|.+++||.+|.+|+. +++|++..+...|...|+ .+||.+.++.
T Consensus 2 ~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~ 67 (834)
T PRK10671 2 SQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIK-QAGYDASVSH 67 (834)
T ss_pred CeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHH-hcCCcccccc
Confidence 468999996 9999999999999999999999999994 567777789999999999 9999999875
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=97.92 E-value=0.00013 Score=46.09 Aligned_cols=61 Identities=18% Similarity=0.291 Sum_probs=50.5
Q ss_pred eEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee---cCCHHHHHHHHHhccCCc
Q 027936 27 VTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRN 88 (216)
Q Consensus 27 ~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G---~vd~~~L~~~L~kk~G~~ 88 (216)
+++.|.|. |+|..|+..|++.|..+.+|..+.+++....++|.. ..+...+...|. ..|+.
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~ 66 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYE 66 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCC
Confidence 46678996 999999999999999999999999999999988863 356777777776 66654
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.79 E-value=5.3e-05 Score=76.27 Aligned_cols=63 Identities=21% Similarity=0.392 Sum_probs=56.7
Q ss_pred eEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeec---CC-HHHHHHHHHhccCCcEEE
Q 027936 27 VTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MD-VKELVPYLKEKLKRNVEV 91 (216)
Q Consensus 27 ~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~---vd-~~~L~~~L~kk~G~~vei 91 (216)
.++.|.|. |||..|+.+|+ +|.+++||..+.+++.+++++|... .+ .+.+...++ .+||.+..
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 9999999999999999999999743 56 789999999 99998876
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.12 E-value=0.0014 Score=66.71 Aligned_cols=65 Identities=18% Similarity=0.393 Sum_probs=57.4
Q ss_pred eEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHHhccCCcEEEc
Q 027936 27 VTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 27 ~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G~~veiV 92 (216)
.+++|.|. |+|..|+..|++.|..++||.++.+++.+++++|.+..++..|...|+ .+|+.+.++
T Consensus 99 ~~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~-~~Gy~a~~~ 164 (834)
T PRK10671 99 DSQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVE-KAGYGAEAI 164 (834)
T ss_pred ceEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHH-hcCCCcccc
Confidence 35778886 999999999999999999999999999999999887778888888898 899987644
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.62 E-value=0.0047 Score=63.62 Aligned_cols=65 Identities=18% Similarity=0.386 Sum_probs=58.4
Q ss_pred eEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee---cCCHHHHHHHHHhccCCcEEEc
Q 027936 27 VTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 27 ~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G---~vd~~~L~~~L~kk~G~~veiV 92 (216)
.++.|.|. |.|.+|..+|++.|.+++||.++.+++.+++++|.- .+.+..+++.|. .+++...+.
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~~~~~~~ 214 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETGFEASVR 214 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhcccceee
Confidence 78999996 999999999999999999999999999999999864 378899999999 888876554
No 11
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.42 E-value=0.0081 Score=60.67 Aligned_cols=65 Identities=14% Similarity=0.280 Sum_probs=53.1
Q ss_pred CceEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeec--CCHHHHHHHHHhccCCcEEE
Q 027936 25 GVVTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLKEKLKRNVEV 91 (216)
Q Consensus 25 ~~~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~--vd~~~L~~~L~kk~G~~vei 91 (216)
...++.|+|. |+|.+|+.+|+++|..++||.++.+++.+.+++|... .+ ..+...++ .+|+.+..
T Consensus 51 ~~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~-~~I~~aI~-~~Gy~a~~ 118 (741)
T PRK11033 51 SGTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIR-AQVESAVQ-KAGFSLRD 118 (741)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccch-HHHHHHHH-hccccccc
Confidence 3456788896 9999999999999999999999999999999888632 23 66677777 78887653
No 12
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.02 E-value=0.012 Score=60.72 Aligned_cols=61 Identities=13% Similarity=0.321 Sum_probs=55.6
Q ss_pred eecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee--cCCHHHHHHHHHhccCCcEEEcCCC
Q 027936 34 RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVVPAK 95 (216)
Q Consensus 34 ~MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G--~vd~~~L~~~L~kk~G~~veiV~p~ 95 (216)
.|+|..|.+.|+++|.+.+||.++.+++.+++.+|.- .++++.|.+.|. ..|+.+.++...
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~gf~~~~~~~~ 64 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMGFEASLLSDS 64 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-cccceeeecccC
Confidence 5999999999999999999999999999999999864 488999999999 999999888653
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=94.13 E-value=0.79 Score=31.71 Aligned_cols=63 Identities=21% Similarity=0.306 Sum_probs=47.3
Q ss_pred EEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee---cCCHHHHHHHHHhccCCcEEE
Q 027936 28 TVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG---TMDVKELVPYLKEKLKRNVEV 91 (216)
Q Consensus 28 tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G---~vd~~~L~~~L~kk~G~~vei 91 (216)
++.+.+. ++|..|...++..+....+|..+.++.....+.+.- ..+...+...+. ..++.+++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~ 90 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSSL 90 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeEe
Confidence 5566775 999999999999999999998888888887766642 246666656665 66766543
No 14
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=90.23 E-value=2 Score=33.45 Aligned_cols=68 Identities=25% Similarity=0.396 Sum_probs=48.5
Q ss_pred CCceEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEE-----eCC--CCeEEEeec-CCHHHHHHHHHhccCCcEEEc
Q 027936 24 DGVVTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTI-----DGG--KDLVTVKGT-MDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 24 ~~~~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~v-----D~~--t~kVtV~G~-vd~~~L~~~L~kk~G~~veiV 92 (216)
.....++|.|- -|-+--.--+-+.|+++.||+-|.+ |.. +=++||.|+ +|-+.|.+.|+ .+|--+.+|
T Consensus 3 ~~iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSi 79 (97)
T COG1888 3 KGIRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSI 79 (97)
T ss_pred ccceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeeh
Confidence 34566777774 3434445567778999999887654 333 445667786 99999999999 999888766
No 15
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=90.10 E-value=1.4 Score=34.25 Aligned_cols=66 Identities=26% Similarity=0.454 Sum_probs=46.0
Q ss_pred CceEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEE-----eCCCCe--EEEeec-CCHHHHHHHHHhccCCcEEEc
Q 027936 25 GVVTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTI-----DGGKDL--VTVKGT-MDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 25 ~~~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~v-----D~~t~k--VtV~G~-vd~~~L~~~L~kk~G~~veiV 92 (216)
.+..++|-|- -|-. -.--+-++|.+++||..|.+ |..+.. +||.|. +|.+.|.++|+ .+|-.+..|
T Consensus 3 ~irRlVLDVlKP~~p-~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHSI 77 (95)
T PF02680_consen 3 GIRRLVLDVLKPHEP-SIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHSI 77 (95)
T ss_dssp SEEEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEEE
T ss_pred ceeEEEEEeecCCCC-CHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEee
Confidence 4567788884 3444 45577888999999887764 444444 455686 99999999999 999887665
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=88.49 E-value=2.8 Score=23.19 Aligned_cols=49 Identities=33% Similarity=0.556 Sum_probs=35.5
Q ss_pred eecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeec--CCHHHHHHHHH
Q 027936 34 RLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLK 82 (216)
Q Consensus 34 ~MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~--vd~~~L~~~L~ 82 (216)
.++|..|...+...+..+.++....+++....+.+... .+...+...+.
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE 56 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH
Confidence 48899999999999999999887888877776666532 24444443443
No 17
>PRK13748 putative mercuric reductase; Provisional
Probab=87.75 E-value=2.9 Score=40.23 Aligned_cols=64 Identities=20% Similarity=0.325 Sum_probs=49.8
Q ss_pred EEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee--cCCHHHHHHHHHhccCCcEEEcCC
Q 027936 30 VLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVVPA 94 (216)
Q Consensus 30 ~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G--~vd~~~L~~~L~kk~G~~veiV~p 94 (216)
.+.+. |+|..|..+++..+..+++|....+++....+.+.. ..+...+...+. ..++.++++..
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 45675 999999999999999999999999999888877763 245666666666 67777665544
No 18
>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=86.30 E-value=1.3 Score=31.32 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=23.3
Q ss_pred eEEEEEEeecchhHH------HHHHHHHhcCCCccEEEE
Q 027936 27 VTVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTI 59 (216)
Q Consensus 27 ~tv~LKV~MhC~gCa------~kI~KaL~kl~GVesV~v 59 (216)
.++.|.|.+.+.+|. ..|+.+|..++||.+|+|
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 456666666666665 788999999999999875
No 19
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=73.41 E-value=8 Score=32.30 Aligned_cols=42 Identities=19% Similarity=0.231 Sum_probs=34.5
Q ss_pred ceEEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCC-CCeEEE
Q 027936 26 VVTVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGG-KDLVTV 68 (216)
Q Consensus 26 ~~tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~-t~kVtV 68 (216)
-..++|.|+ -.|..|..-|....+++ |+.++.|... ++++.+
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 356788886 78999999999988888 9999999887 775554
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=63.49 E-value=9.8 Score=32.36 Aligned_cols=34 Identities=21% Similarity=0.428 Sum_probs=26.0
Q ss_pred EEEEEEeecchhHH------HHHHHHHhcCCCccEEEEeC
Q 027936 28 TVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTIDG 61 (216)
Q Consensus 28 tv~LKV~MhC~gCa------~kI~KaL~kl~GVesV~vD~ 61 (216)
+|.+.|.|...+|. ..|+.+|..++||.+|.|++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 46666666666665 44899999999999998875
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=62.41 E-value=20 Score=24.58 Aligned_cols=34 Identities=18% Similarity=0.280 Sum_probs=26.2
Q ss_pred ceEEEEEEeecchh-HHHHHHHHHhcCCCccEEEE
Q 027936 26 VVTVVLKIRLHCEG-CISKIKKIIYKTKGVDNVTI 59 (216)
Q Consensus 26 ~~tv~LKV~MhC~g-Ca~kI~KaL~kl~GVesV~v 59 (216)
...+.|.|..+-.. ....|.++|++++||.+|.+
T Consensus 40 ~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 40 RANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred eEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 34566666655555 88899999999999999875
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=62.40 E-value=11 Score=28.14 Aligned_cols=35 Identities=20% Similarity=0.392 Sum_probs=23.8
Q ss_pred EEEEEEeecchhHH------HHHHHHHhcCCCccEEEEeCC
Q 027936 28 TVVLKIRLHCEGCI------SKIKKIIYKTKGVDNVTIDGG 62 (216)
Q Consensus 28 tv~LKV~MhC~gCa------~kI~KaL~kl~GVesV~vD~~ 62 (216)
.+.+.|.+...+|. ..|+.+|..++||++|.|++.
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 34445544444333 458889999999999998864
No 23
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=54.84 E-value=35 Score=24.02 Aligned_cols=35 Identities=20% Similarity=0.340 Sum_probs=28.4
Q ss_pred CCceEEEEEEeecchhHHHHHHHHHhcCCCccEEE
Q 027936 24 DGVVTVVLKIRLHCEGCISKIKKIIYKTKGVDNVT 58 (216)
Q Consensus 24 ~~~~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~ 58 (216)
+....+.|.|...--.--..|...|++++||.+|.
T Consensus 45 ~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 45 DGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp TTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred CCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 45667777787777778889999999999998874
No 24
>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=54.60 E-value=65 Score=23.11 Aligned_cols=61 Identities=18% Similarity=0.240 Sum_probs=41.6
Q ss_pred EEEEeecchhHHHHHHHHHhcC----CCccEEEEeCCCCeEEEee--cCCHHHHHHHHHhccCCcEEE
Q 027936 30 VLKIRLHCEGCISKIKKIIYKT----KGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEV 91 (216)
Q Consensus 30 ~LKV~MhC~gCa~kI~KaL~kl----~GVesV~vD~~t~kVtV~G--~vd~~~L~~~L~kk~G~~vei 91 (216)
.+.|.-.-..-..++..+|.+| +++ .+..|..++.+.|.| .+-.+-+++.|+++.|-.|++
T Consensus 7 ~~~i~p~~~~d~~kl~~aL~~l~~eDP~l-~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~~ 73 (75)
T PF14492_consen 7 SVAIEPKNKEDEPKLSEALQKLSEEDPSL-RVERDEETGELILSGMGELHLEVLLERLKRRFGVEVEF 73 (75)
T ss_dssp EEEEEESSHHHHHHHHHHHHHHHHH-TTS-EEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEEE
T ss_pred EEEEEECCHhHHHHHHHHHHHHHhcCCeE-EEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeEe
Confidence 3444433344455666666554 455 588999999999974 588899999999776655543
No 25
>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=54.22 E-value=9 Score=26.03 Aligned_cols=39 Identities=15% Similarity=0.252 Sum_probs=19.4
Q ss_pred HHHHHHHhc---CCCccEEEEeCCCCeEEEeecCCHHHHHHHH
Q 027936 42 SKIKKIIYK---TKGVDNVTIDGGKDLVTVKGTMDVKELVPYL 81 (216)
Q Consensus 42 ~kI~KaL~k---l~GVesV~vD~~t~kVtV~G~vd~~~L~~~L 81 (216)
.+|+.+|.. +++- .+.+....+.|+++|.++-......+
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~s~~~~~~a 43 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEVPSQEQRDAA 43 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEESSCHHHHHH
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeCcHHHHHHhH
Confidence 356777776 4455 57788889999999987543333333
No 26
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=53.47 E-value=53 Score=27.87 Aligned_cols=70 Identities=29% Similarity=0.413 Sum_probs=46.5
Q ss_pred ceEEEEEEeecchhHHHHH------------HHHHhcC------CCccEEEEeCCCCeEEEe---ec---C-CHHHHHHH
Q 027936 26 VVTVVLKIRLHCEGCISKI------------KKIIYKT------KGVDNVTIDGGKDLVTVK---GT---M-DVKELVPY 80 (216)
Q Consensus 26 ~~tv~LKV~MhC~gCa~kI------------~KaL~kl------~GVesV~vD~~t~kVtV~---G~---v-d~~~L~~~ 80 (216)
+-.+-+|-++-|+.|.++| .++|.+| .++.-...=...++|++. |. + -.-.++++
T Consensus 5 ~~~~c~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~ 84 (166)
T PRK06418 5 ICEVCVKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKA 84 (166)
T ss_pred eeeEEeccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHH
Confidence 3456677788899999875 5778776 344433332335777652 33 1 12467888
Q ss_pred HHhccCCcEEEcCCC
Q 027936 81 LKEKLKRNVEVVPAK 95 (216)
Q Consensus 81 L~kk~G~~veiV~p~ 95 (216)
|++.+|+++++|.-.
T Consensus 85 l~~~lgk~VevVE~s 99 (166)
T PRK06418 85 LSRKLGKKVRVVEKT 99 (166)
T ss_pred HHHHhCCcEEEEEcC
Confidence 988999999999643
No 27
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=50.98 E-value=59 Score=24.66 Aligned_cols=43 Identities=19% Similarity=0.183 Sum_probs=29.0
Q ss_pred HHHHHHHHHhcCCCccEEEEeCCCCeEEEee-cCCHHHHHHHHH
Q 027936 40 CISKIKKIIYKTKGVDNVTIDGGKDLVTVKG-TMDVKELVPYLK 82 (216)
Q Consensus 40 Ca~kI~KaL~kl~GVesV~vD~~t~kVtV~G-~vd~~~L~~~L~ 82 (216)
=...|.++|..++|++=...|...+++.|+= .-+...+++.|.
T Consensus 18 ~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 18 RISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 3678999999999998555666778877752 234444444443
No 28
>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=49.43 E-value=45 Score=23.08 Aligned_cols=53 Identities=21% Similarity=0.252 Sum_probs=36.8
Q ss_pred EEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeec--CCHHHHHHHHHhccCCcEEEc
Q 027936 30 VLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 30 ~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~--vd~~~L~~~L~kk~G~~veiV 92 (216)
+|.+. +.|+...-+++++|.+++. .+.+.|..+ .....|..+++ ..|+.+..+
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 45554 8999999999999998832 233444433 55688888888 999986554
No 29
>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=47.25 E-value=67 Score=23.61 Aligned_cols=42 Identities=14% Similarity=0.241 Sum_probs=29.0
Q ss_pred HHHHHHHHHhcCCCccEEEEeCCCCeEEEe-ecCCHHHHHHHHH
Q 027936 40 CISKIKKIIYKTKGVDNVTIDGGKDLVTVK-GTMDVKELVPYLK 82 (216)
Q Consensus 40 Ca~kI~KaL~kl~GVesV~vD~~t~kVtV~-G~vd~~~L~~~L~ 82 (216)
=...|..+|..++||+-...+.. +++.|+ =.-+...+.+.|.
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 45689999999999975556655 777665 3345566666665
No 30
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=45.20 E-value=41 Score=28.57 Aligned_cols=46 Identities=17% Similarity=0.295 Sum_probs=35.4
Q ss_pred chhHHHHHHHHHhcCCCccEEEEeCCCCe-------------------EEEe---ecCCHHHHHHHHH
Q 027936 37 CEGCISKIKKIIYKTKGVDNVTIDGGKDL-------------------VTVK---GTMDVKELVPYLK 82 (216)
Q Consensus 37 C~gCa~kI~KaL~kl~GVesV~vD~~t~k-------------------VtV~---G~vd~~~L~~~L~ 82 (216)
-.||-.-++..+.+++||.++.+=.+.+. |.|+ ..++.+.|++..-
T Consensus 9 agGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~ 76 (172)
T PRK14054 9 AGGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF 76 (172)
T ss_pred EcCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence 35788889999999999999998776664 4454 2478888887665
No 31
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=45.18 E-value=52 Score=23.33 Aligned_cols=37 Identities=27% Similarity=0.306 Sum_probs=26.2
Q ss_pred CCceEEEEEEeecchhHHHHHHHHHhcCCCccEEEEeCC
Q 027936 24 DGVVTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGG 62 (216)
Q Consensus 24 ~~~~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~ 62 (216)
.....|+|-..-.|..|. ++++.|..+ ||.-..+|+.
T Consensus 5 ~~~~~V~ly~~~~Cp~C~-~ak~~L~~~-gi~y~~idi~ 41 (79)
T TIGR02190 5 RKPESVVVFTKPGCPFCA-KAKATLKEK-GYDFEEIPLG 41 (79)
T ss_pred CCCCCEEEEECCCCHhHH-HHHHHHHHc-CCCcEEEECC
Confidence 334557777778999998 777878765 7776666653
No 32
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=44.86 E-value=60 Score=22.99 Aligned_cols=42 Identities=19% Similarity=0.286 Sum_probs=30.8
Q ss_pred HhcCCCccEEEEeCCCC--eEEEeecCCHHHHHHHHHhccCCcEEEc
Q 027936 48 IYKTKGVDNVTIDGGKD--LVTVKGTMDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 48 L~kl~GVesV~vD~~t~--kVtV~G~vd~~~L~~~L~kk~G~~veiV 92 (216)
|..++||.++..+- .+ ++.|....+...|+..|. ..|. +.-+
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 88889999998653 44 444555678899999999 6677 6543
No 33
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=44.25 E-value=36 Score=27.05 Aligned_cols=34 Identities=24% Similarity=0.521 Sum_probs=25.9
Q ss_pred EEEEEEeecchhH------HHHHHHHHhcCCCccEEEEeC
Q 027936 28 TVVLKIRLHCEGC------ISKIKKIIYKTKGVDNVTIDG 61 (216)
Q Consensus 28 tv~LKV~MhC~gC------a~kI~KaL~kl~GVesV~vD~ 61 (216)
.+.+++.++-.+| ...|+.+|..++||..|++++
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 3444555666666 678999999999999998875
No 34
>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=42.10 E-value=68 Score=26.81 Aligned_cols=69 Identities=14% Similarity=0.190 Sum_probs=47.5
Q ss_pred EEEEEEe----ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee----c-C-CHHHHHHHHHhccCCcEEEcCCCC
Q 027936 28 TVVLKIR----LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG----T-M-DVKELVPYLKEKLKRNVEVVPAKK 96 (216)
Q Consensus 28 tv~LKV~----MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G----~-v-d~~~L~~~L~kk~G~~veiV~p~k 96 (216)
.++++.+ |.=+--...|++.+=.-.||.++.+|..++.|+|.. . + -....+..|..++|++..++.-+.
T Consensus 38 RIvvR~dps~l~~~e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 38 RIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred eEEEcCChhhcCCHHHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 4556553 334555666777776667999999999999999963 2 1 234455666559999999885443
No 35
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=41.31 E-value=1e+02 Score=24.78 Aligned_cols=50 Identities=22% Similarity=0.276 Sum_probs=34.3
Q ss_pred HHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHH----HHHHhccCCcEEEc
Q 027936 42 SKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELV----PYLKEKLKRNVEVV 92 (216)
Q Consensus 42 ~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~----~~L~kk~G~~veiV 92 (216)
..++.+|..+ |...|++=++++.|.++...++..|. +.|.++.|+.+.++
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 4567778777 89999999999999999777776665 45556788877644
No 36
>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=39.63 E-value=36 Score=24.08 Aligned_cols=14 Identities=14% Similarity=0.394 Sum_probs=9.9
Q ss_pred EEEEEEeecchhHHH
Q 027936 28 TVVLKIRLHCEGCIS 42 (216)
Q Consensus 28 tv~LKV~MhC~gCa~ 42 (216)
+|.+ +...|..|..
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 6677999983
No 37
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=38.46 E-value=77 Score=22.58 Aligned_cols=34 Identities=26% Similarity=0.330 Sum_probs=24.1
Q ss_pred EEEEEeecchhHHHHHHHHHhcC----CCccEEEEeCCC
Q 027936 29 VVLKIRLHCEGCISKIKKIIYKT----KGVDNVTIDGGK 63 (216)
Q Consensus 29 v~LKV~MhC~gCa~kI~KaL~kl----~GVesV~vD~~t 63 (216)
|+|-..-.|..|. ++++.|.++ .||.-..+|...
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 4444456799998 677888876 677777777654
No 38
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=37.76 E-value=68 Score=24.00 Aligned_cols=40 Identities=33% Similarity=0.588 Sum_probs=30.3
Q ss_pred HHHHHHHhcCCCccEEEEeCCCCeEEEe--ecCCHHHHHHHHHh
Q 027936 42 SKIKKIIYKTKGVDNVTIDGGKDLVTVK--GTMDVKELVPYLKE 83 (216)
Q Consensus 42 ~kI~KaL~kl~GVesV~vD~~t~kVtV~--G~vd~~~L~~~L~k 83 (216)
.-+-++|..++||.+|-+ ..+=|||+ ..++++.|...|..
T Consensus 37 spLA~~Lf~i~gV~~Vf~--~~dfItVtK~~~~~W~~l~~~I~~ 78 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFI--GDDFITVTKNPDADWEDLKPEIRE 78 (87)
T ss_dssp -HHHHHHHTSTTEEEEEE--ETTEEEEEE-TTS-HHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEE--ECCEEEEeeCCCCCHHHHHHHHHH
Confidence 456677889999998765 57889997 45899999988873
No 39
>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=36.73 E-value=1e+02 Score=22.98 Aligned_cols=53 Identities=23% Similarity=0.288 Sum_probs=39.8
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCCCeEEEe----ecCCHHHHHHHHHhccCCcEEE
Q 027936 38 EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK----GTMDVKELVPYLKEKLKRNVEV 91 (216)
Q Consensus 38 ~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~----G~vd~~~L~~~L~kk~G~~vei 91 (216)
.-|...|+..-+.+. |.+|+..+..++++|- +.+|-..|+..|.+..+-+|++
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 457777766655553 5567888899999983 4599999999999777777765
No 40
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=35.47 E-value=33 Score=28.50 Aligned_cols=42 Identities=17% Similarity=0.202 Sum_probs=29.8
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCC-CeEEEeecCCHHHHHHHHH
Q 027936 38 EGCISKIKKIIYKTKGVDNVTIDGGK-DLVTVKGTMDVKELVPYLK 82 (216)
Q Consensus 38 ~gCa~kI~KaL~kl~GVesV~vD~~t-~kVtV~G~vd~~~L~~~L~ 82 (216)
.+|+++|.++|.++ ..|+.+... .++|-.|+-|.+.|...|+
T Consensus 97 ~~i~rkvlQ~Le~~---~~ve~hp~gGR~lt~~GqrdldrIa~~i~ 139 (143)
T KOG3411|consen 97 GGIARKVLQALEKM---GIVEKHPKGGRRLTEQGQRDLDRIAGQIR 139 (143)
T ss_pred cHHHHHHHHHHHhC---CceeeCCCCcceeCcccchhHHHHHHHHH
Confidence 55666666666554 456666654 4666789999999999987
No 41
>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=35.21 E-value=1.9e+02 Score=21.60 Aligned_cols=59 Identities=19% Similarity=0.209 Sum_probs=42.9
Q ss_pred ceEEEEEEeecchhHHHHHHHHHhcCCC-ccEEEEeCCCCeEEEeecCCHHHHHHHHHhccC
Q 027936 26 VVTVVLKIRLHCEGCISKIKKIIYKTKG-VDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLK 86 (216)
Q Consensus 26 ~~tv~LKV~MhC~gCa~kI~KaL~kl~G-VesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G 86 (216)
..|++=+|+=+=..+.+-+...|..... -..+.|+..++.|.|.|.. ...|.++|. ..|
T Consensus 27 ~~T~IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~-~~~Vk~wL~-~~G 86 (87)
T PF05046_consen 27 KITVIRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDH-VEEVKKWLL-EKG 86 (87)
T ss_pred eEEEEEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCcc-HHHHHHHHH-HCc
Confidence 3455566765557788888888865544 1257789999999999986 778888887 444
No 42
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=35.07 E-value=1.2e+02 Score=21.26 Aligned_cols=29 Identities=21% Similarity=0.380 Sum_probs=21.7
Q ss_pred CccEEEEeCCCCeEEEeec-CCHHHHHHHHH
Q 027936 53 GVDNVTIDGGKDLVTVKGT-MDVKELVPYLK 82 (216)
Q Consensus 53 GVesV~vD~~t~kVtV~G~-vd~~~L~~~L~ 82 (216)
.+ .|.+|..++.|.|.|+ -+...|...|+
T Consensus 45 ~~-~i~~d~~tNsliv~g~~~~~~~i~~li~ 74 (82)
T PF03958_consen 45 SG-RIVADERTNSLIVRGTPEDLEQIRELIK 74 (82)
T ss_dssp TT-EEEEECTTTEEEEEEEHHHHHHHHHHHH
T ss_pred Ce-EEEEECCCCEEEEEeCHHHHHHHHHHHH
Confidence 45 7999999999999987 44555555554
No 43
>PRK11670 antiporter inner membrane protein; Provisional
Probab=35.04 E-value=1.1e+02 Score=28.60 Aligned_cols=66 Identities=12% Similarity=0.160 Sum_probs=41.5
Q ss_pred EEEEEEeecchhH------HHHHHHHHhcCCCccEEEEeCCC------------------CeEEEe------ec-CCHHH
Q 027936 28 TVVLKIRLHCEGC------ISKIKKIIYKTKGVDNVTIDGGK------------------DLVTVK------GT-MDVKE 76 (216)
Q Consensus 28 tv~LKV~MhC~gC------a~kI~KaL~kl~GVesV~vD~~t------------------~kVtV~------G~-vd~~~ 76 (216)
++.|.|.+.-..| .+.|+.+|..++||.+|.+.+.. ..+.|. |. .-...
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avN 127 (369)
T PRK11670 48 TLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVN 127 (369)
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHH
Confidence 3455555544444 34689999999999988765532 222342 22 33455
Q ss_pred HHHHHHhccCCcEEEcCC
Q 027936 77 LVPYLKEKLKRNVEVVPA 94 (216)
Q Consensus 77 L~~~L~kk~G~~veiV~p 94 (216)
|...|. +.|++|-+|.-
T Consensus 128 LA~aLA-~~G~rVlLID~ 144 (369)
T PRK11670 128 LALALA-AEGAKVGILDA 144 (369)
T ss_pred HHHHHH-HCCCcEEEEeC
Confidence 666777 78999988844
No 44
>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=34.96 E-value=52 Score=27.17 Aligned_cols=33 Identities=27% Similarity=0.486 Sum_probs=23.8
Q ss_pred EEEEEEeecchhHHH------HHHHHHhcCCCccEEEEeC
Q 027936 28 TVVLKIRLHCEGCIS------KIKKIIYKTKGVDNVTIDG 61 (216)
Q Consensus 28 tv~LKV~MhC~gCa~------kI~KaL~kl~GVesV~vD~ 61 (216)
.|.+.|.++-.+|-. .|+.+|..+ ||.+|.|++
T Consensus 26 ~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~-Gv~~V~V~i 64 (146)
T TIGR02159 26 GVVVKFTPTYSGCPALEVIRQDIRDAVRAL-GVEVVEVST 64 (146)
T ss_pred EEEEEEEeCCCCCchHHHHHHHHHHHHHhc-CCCeEEEeE
Confidence 456666677666654 488888887 998888764
No 45
>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=34.20 E-value=95 Score=25.37 Aligned_cols=34 Identities=21% Similarity=0.218 Sum_probs=28.2
Q ss_pred cchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEe
Q 027936 36 HCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK 69 (216)
Q Consensus 36 hC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~ 69 (216)
.=..=+..|.+.|.+++||.++.|=...+.|.|-
T Consensus 72 ~~~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 72 DRQQLADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred hHHHHHHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 3455688999999999999999988878877764
No 46
>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=34.17 E-value=91 Score=21.73 Aligned_cols=30 Identities=17% Similarity=0.194 Sum_probs=22.2
Q ss_pred EEEEEeecchhHHHHHHHHHhcCCCccEEE
Q 027936 29 VVLKIRLHCEGCISKIKKIIYKTKGVDNVT 58 (216)
Q Consensus 29 v~LKV~MhC~gCa~kI~KaL~kl~GVesV~ 58 (216)
+.|.+...-..--..|.+.|++++||.+|.
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 555555544445678889999999999886
No 47
>PRK04435 hypothetical protein; Provisional
Probab=33.48 E-value=92 Score=25.36 Aligned_cols=33 Identities=24% Similarity=0.418 Sum_probs=24.9
Q ss_pred eEEEEEEeec-chhHHHHHHHHHhcCCCccEEEE
Q 027936 27 VTVVLKIRLH-CEGCISKIKKIIYKTKGVDNVTI 59 (216)
Q Consensus 27 ~tv~LKV~Mh-C~gCa~kI~KaL~kl~GVesV~v 59 (216)
..+.|.|+.. .......|...|+.++||.+|++
T Consensus 110 a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 110 ANVTISIDTSSMEGDIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred EEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEEE
Confidence 4456666643 34588999999999999998875
No 48
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=33.13 E-value=94 Score=26.01 Aligned_cols=46 Identities=17% Similarity=0.337 Sum_probs=34.1
Q ss_pred chhHHHHHHHHHhcCCCccEEEEeCCCCe--------------EEEe---ecCCHHHHHHHHH
Q 027936 37 CEGCISKIKKIIYKTKGVDNVTIDGGKDL--------------VTVK---GTMDVKELVPYLK 82 (216)
Q Consensus 37 C~gCa~kI~KaL~kl~GVesV~vD~~t~k--------------VtV~---G~vd~~~L~~~L~ 82 (216)
-.||-.-++..+.+++||.++.+=.+.+. |.|+ ..++.+.|++..-
T Consensus 7 agGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~ 69 (156)
T PRK05528 7 AGGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLF 69 (156)
T ss_pred ecCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHH
Confidence 35788889999999999999998765433 3333 2377888888665
No 49
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.72 E-value=93 Score=30.72 Aligned_cols=10 Identities=20% Similarity=0.248 Sum_probs=5.8
Q ss_pred ccCCcEEEcC
Q 027936 84 KLKRNVEVVP 93 (216)
Q Consensus 84 k~G~~veiV~ 93 (216)
++|..|-+++
T Consensus 278 ~ig~~vy~ap 287 (483)
T KOG2236|consen 278 CIGEKVYYAP 287 (483)
T ss_pred ccCCeeEecC
Confidence 4666665555
No 50
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=31.12 E-value=1.1e+02 Score=22.44 Aligned_cols=36 Identities=22% Similarity=0.233 Sum_probs=29.2
Q ss_pred CCCceEEEEEEeecchhHHHHHHHHHhcCCCccEEEEe
Q 027936 23 DDGVVTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTID 60 (216)
Q Consensus 23 ~~~~~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD 60 (216)
++....++|-|. -+.+...|.+-|.+|..|..|+++
T Consensus 41 ~~~~sriti~v~--~~~~i~ql~kQL~KL~dV~~V~~~ 76 (76)
T PRK11152 41 DAQNINIELTVA--SERPIDLLSSQLNKLVDVAHVEIL 76 (76)
T ss_pred CCCEEEEEEEEC--CCchHHHHHHHHhcCcCeEEEEEC
Confidence 556777777774 688999999999999999888763
No 51
>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=29.86 E-value=1.6e+02 Score=19.88 Aligned_cols=35 Identities=9% Similarity=0.059 Sum_probs=24.2
Q ss_pred CceEEEEEEeecchhHHHHHHHHHhcCCCccEEEE
Q 027936 25 GVVTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTI 59 (216)
Q Consensus 25 ~~~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~v 59 (216)
....+.|.|...-..-...|...|.+++||...++
T Consensus 38 ~~~~~~~~vev~~~~~l~~i~~~L~~i~gV~~~~~ 72 (74)
T cd04887 38 DYTVRDITVDAPSEEHAETIVAAVRALPEVKVLSV 72 (74)
T ss_pred CEEEEEEEEEcCCHHHHHHHHHHHhcCCCeEEEEe
Confidence 34445566666556666778899999999876554
No 52
>PF08210 APOBEC_N: APOBEC-like N-terminal domain; InterPro: IPR013158 This domain is found at the N terminus of the Apolipoprotein B mRNA editing enzyme. Apobec-1 catalyzes C to U editing of apolipoprotein B (apoB) mRNA in the mammalian intestine. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination. APOBEC-3 like members contain two copies of this domain. This family also includes the functionally homologous activation induced deaminase, which is essential for the development of antibody diversity in B lymphocytes. RNA editing by APOBEC-1 requires homodimerisation and this complex interacts with RNA binding proteins to from the editosome [] (and references therein).; GO: 0008270 zinc ion binding, 0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines; PDB: 3IQS_A 3IR2_A 3V4J_B 2KEM_A 2KBO_A 3V4K_A 3E1U_A 2JYW_A 2RPZ_A.
Probab=29.76 E-value=69 Score=27.32 Aligned_cols=66 Identities=17% Similarity=0.239 Sum_probs=39.7
Q ss_pred CceEEEEEEeec-chh----HHHHHHHHHhcC--CCccEEEEeCCCCeEEEeecCC---HHHHHHHHHhccCCcEEEcCC
Q 027936 25 GVVTVVLKIRLH-CEG----CISKIKKIIYKT--KGVDNVTIDGGKDLVTVKGTMD---VKELVPYLKEKLKRNVEVVPA 94 (216)
Q Consensus 25 ~~~tv~LKV~Mh-C~g----Ca~kI~KaL~kl--~GVesV~vD~~t~kVtV~G~vd---~~~L~~~L~kk~G~~veiV~p 94 (216)
..-+|++-|.++ |.. |+.+|...|.+. ++|. +.|=.+ . +=-...-. ..+=+..|. .+|-+++++..
T Consensus 72 ~~y~ITwy~SwSPC~~~~~~Ca~~i~~FL~~~~~~~v~-L~I~~a-r-LY~~~~~~~~~~~eGLr~L~-~aGv~v~iM~~ 147 (188)
T PF08210_consen 72 QIYRITWYLSWSPCPESDHCCAEKIAEFLKKHLKPNVS-LSIFAA-R-LYYHWEPEPLWNQEGLRRLA-SAGVQVEIMSY 147 (188)
T ss_dssp SEEEEEEEESSS--CC----HHHHHHHHHCCC--TTEE-EEEEES-S---STTSTT---HHHHHHHHH-HCTEEEEE-SH
T ss_pred ceEEEEEEEecCCCcchhhHHHHHHHHHHHHhCCCCCe-EEEEEE-e-eeeecCCcchhHHHHHHHHH-HcCCEEEEcCH
Confidence 445788888854 999 999999999999 8884 544332 1 11011112 234455555 56888877643
No 53
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=29.35 E-value=51 Score=30.26 Aligned_cols=55 Identities=16% Similarity=0.125 Sum_probs=37.4
Q ss_pred hhHHHHHHHHHhcCCCccEEEE--eCCCCeEEEeecCCHHHHHHHHHhccCCcEEEc
Q 027936 38 EGCISKIKKIIYKTKGVDNVTI--DGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 38 ~gCa~kI~KaL~kl~GVesV~v--D~~t~kVtV~G~vd~~~L~~~L~kk~G~~veiV 92 (216)
-.-+.+|..++..+++|.-+.+ |...++-.|+-.-|++.++.++-+-+++-++++
T Consensus 17 ~~~ie~i~a~~~~~~~v~ildve~danhNRsViT~vgdp~~~~~A~f~~ik~AaelI 73 (302)
T COG3643 17 LEKIEKIVAAAKSIPTVKILDVEMDANHNRSVITLVGDPSKVVNAAFALIKKAAELI 73 (302)
T ss_pred HHHHHHHHHHHhcCCceEEEEeccCCCCCceEEEEecChHHHHHHHHHHHHHHHHhh
Confidence 3456778888888898765554 445677677777889888887764555544433
No 54
>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=29.33 E-value=1.7e+02 Score=21.29 Aligned_cols=48 Identities=23% Similarity=0.316 Sum_probs=31.4
Q ss_pred hhHHHHHHHHHhcCCC-ccEEEEeCCCCeEEEeecCCHHHH---HHHHHhccC
Q 027936 38 EGCISKIKKIIYKTKG-VDNVTIDGGKDLVTVKGTMDVKEL---VPYLKEKLK 86 (216)
Q Consensus 38 ~gCa~kI~KaL~kl~G-VesV~vD~~t~kVtV~G~vd~~~L---~~~L~kk~G 86 (216)
..+..+|...|.+..| |.++..+ .++.++|.+.+....+ ...|+.-+.
T Consensus 15 ~~~~g~v~~~l~~r~g~i~~~~~~-~~~~~~i~~~iP~~~~~gf~~~Lr~~T~ 66 (89)
T PF00679_consen 15 EEYLGKVISDLSKRRGEILSMDPI-GGDRVVIEAEIPVRELFGFRSELRSLTS 66 (89)
T ss_dssp GGGHHHHHHHHHHTT-EEEEEEEE-STTEEEEEEEEEGGGHTTHHHHHHHHTT
T ss_pred HHHHHHHHHHhcccccEEEechhh-hhhheeEEEEEChhhhhhHHHHhhccCC
Confidence 6788899999999888 4444443 5789999987554444 445543333
No 55
>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=28.42 E-value=1.4e+02 Score=20.41 Aligned_cols=32 Identities=28% Similarity=0.560 Sum_probs=21.9
Q ss_pred EEEEEeecchhHHHHHHHHHhcCCCccEEEEeCC
Q 027936 29 VVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGG 62 (216)
Q Consensus 29 v~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~ 62 (216)
|+|-..-.|..|. ++++.|..+ ||.-..+|+.
T Consensus 3 v~ly~~~~C~~C~-ka~~~L~~~-gi~~~~~di~ 34 (73)
T cd03027 3 VTIYSRLGCEDCT-AVRLFLREK-GLPYVEINID 34 (73)
T ss_pred EEEEecCCChhHH-HHHHHHHHC-CCceEEEECC
Confidence 4444446799998 777778764 7776666654
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=28.39 E-value=73 Score=24.79 Aligned_cols=29 Identities=38% Similarity=0.428 Sum_probs=25.0
Q ss_pred EEEeecCCHHHHHHHHHhccCCcEEEcCCC
Q 027936 66 VTVKGTMDVKELVPYLKEKLKRNVEVVPAK 95 (216)
Q Consensus 66 VtV~G~vd~~~L~~~L~kk~G~~veiV~p~ 95 (216)
|.|+|.-|-..+++.|+ ..|++|.++++.
T Consensus 104 vLvSgD~Df~~~i~~lr-~~G~~V~v~~~~ 132 (149)
T cd06167 104 VLVSGDSDFVPLVERLR-ELGKRVIVVGFE 132 (149)
T ss_pred EEEECCccHHHHHHHHH-HcCCEEEEEccC
Confidence 44578899999999999 779999999875
No 57
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=28.30 E-value=1.1e+02 Score=23.40 Aligned_cols=23 Identities=22% Similarity=0.401 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHhcCCCccEEEEe
Q 027936 38 EGCISKIKKIIYKTKGVDNVTID 60 (216)
Q Consensus 38 ~gCa~kI~KaL~kl~GVesV~vD 60 (216)
.+-...|+.+|..++||++|++-
T Consensus 61 ~g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 61 EGGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred CcChHHHHHHHhcCCCccEEEEE
Confidence 36679999999999999999875
No 58
>PRK11018 hypothetical protein; Provisional
Probab=28.16 E-value=2.3e+02 Score=20.43 Aligned_cols=57 Identities=7% Similarity=-0.013 Sum_probs=39.2
Q ss_pred EEEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHHhccCCcEEEc
Q 027936 28 TVVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 28 tv~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G~~veiV 92 (216)
+.+|-+. +.|+.-.-+.+++|.+++.=+.+.| .++.......|...++ ..|+.+..+
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~~G~~L~V-------~~d~~~a~~di~~~~~-~~G~~v~~~ 65 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLKKGEILEV-------VSDCPQSINNIPLDAR-NHGYTVLDI 65 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCCCCCEEEE-------EeCCccHHHHHHHHHH-HcCCEEEEE
Confidence 4567774 9999999999999998852222222 1222355677788888 999988654
No 59
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=28.07 E-value=1e+02 Score=23.52 Aligned_cols=33 Identities=18% Similarity=0.377 Sum_probs=24.4
Q ss_pred EEEEEEeecc-hhHHHHHHHHHhcCCCccEEEEe
Q 027936 28 TVVLKIRLHC-EGCISKIKKIIYKTKGVDNVTID 60 (216)
Q Consensus 28 tv~LKV~MhC-~gCa~kI~KaL~kl~GVesV~vD 60 (216)
.+.+.+-|-+ .+-...|+.+|..++||++|++-
T Consensus 50 aL~i~~vv~D~~~~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 50 ALKLYVIMPDEEGGTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred eEEEEEEEEcCCcCcHHHHHHHhccCCCcEEEEE
Confidence 3333333433 47789999999999999999875
No 60
>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=27.91 E-value=1.8e+02 Score=21.81 Aligned_cols=51 Identities=20% Similarity=0.214 Sum_probs=32.2
Q ss_pred EEEEEEeecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHHhccCC
Q 027936 28 TVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKR 87 (216)
Q Consensus 28 tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G~ 87 (216)
.|++-..-.|..|. ++++.|.++ ||.-..+|+. -..+...+++.|.+.+|.
T Consensus 9 ~Vvvysk~~Cp~C~-~ak~~L~~~-~i~~~~vdid-------~~~~~~~~~~~l~~~tg~ 59 (99)
T TIGR02189 9 AVVIFSRSSCCMCH-VVKRLLLTL-GVNPAVHEID-------KEPAGKDIENALSRLGCS 59 (99)
T ss_pred CEEEEECCCCHHHH-HHHHHHHHc-CCCCEEEEcC-------CCccHHHHHHHHHHhcCC
Confidence 45555568899999 777778766 6654444433 223445677777755665
No 61
>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=27.63 E-value=1.6e+02 Score=21.56 Aligned_cols=33 Identities=15% Similarity=0.144 Sum_probs=27.3
Q ss_pred eEEEEEEeecchhHHHHHHHHHhcCCCccEEEE
Q 027936 27 VTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTI 59 (216)
Q Consensus 27 ~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~v 59 (216)
.++++-|.-....-...+-++|..|+||-++.+
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 567777777777888888899999999988764
No 62
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=27.42 E-value=84 Score=27.13 Aligned_cols=46 Identities=15% Similarity=0.258 Sum_probs=34.3
Q ss_pred chhHHHHHHHHHhcCCCccEEEEeCCCCe-------------------EEEe---ecCCHHHHHHHHH
Q 027936 37 CEGCISKIKKIIYKTKGVDNVTIDGGKDL-------------------VTVK---GTMDVKELVPYLK 82 (216)
Q Consensus 37 C~gCa~kI~KaL~kl~GVesV~vD~~t~k-------------------VtV~---G~vd~~~L~~~L~ 82 (216)
-.||-.-++..+.+++||.++.+=.+.+. |.|+ ..++...|++..-
T Consensus 14 agGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff 81 (186)
T PRK13014 14 AGGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFF 81 (186)
T ss_pred ecCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHH
Confidence 35788888888999999999998776654 4443 2377888888665
No 63
>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=27.21 E-value=1.5e+02 Score=20.25 Aligned_cols=32 Identities=25% Similarity=0.387 Sum_probs=22.0
Q ss_pred EEEEEeecchhHHHHHHHHHhcCCCccEEEEeCC
Q 027936 29 VVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGG 62 (216)
Q Consensus 29 v~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~ 62 (216)
|+|-..-.|..|. ++++.|... ||.-..+|..
T Consensus 3 v~lys~~~Cp~C~-~ak~~L~~~-~i~~~~~~v~ 34 (72)
T cd03029 3 VSLFTKPGCPFCA-RAKAALQEN-GISYEEIPLG 34 (72)
T ss_pred EEEEECCCCHHHH-HHHHHHHHc-CCCcEEEECC
Confidence 4555557899999 567777765 7776666654
No 64
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=27.19 E-value=1.1e+02 Score=24.79 Aligned_cols=45 Identities=22% Similarity=0.229 Sum_probs=30.4
Q ss_pred hhHHHHHHHHHhcC-CCccEEEEeCCCCeEEEeecCCHHHHHHHHH
Q 027936 38 EGCISKIKKIIYKT-KGVDNVTIDGGKDLVTVKGTMDVKELVPYLK 82 (216)
Q Consensus 38 ~gCa~kI~KaL~kl-~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~ 82 (216)
+.=+..|.++|.+. -++..+.|....+.||+.|++.-...+.+|.
T Consensus 25 ~~~~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~ 70 (147)
T PRK11198 25 EDAADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKIL 70 (147)
T ss_pred HHHHHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHH
Confidence 33456677777653 2344456666799999999987666666666
No 65
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=27.10 E-value=83 Score=28.89 Aligned_cols=48 Identities=23% Similarity=0.214 Sum_probs=35.9
Q ss_pred eEEEEEEeecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHHhccCC
Q 027936 27 VTVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKR 87 (216)
Q Consensus 27 ~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G~ 87 (216)
.++.|+++.+ +.|.+.|+..|..++||.++.+- |.++-.+.|++.+|.
T Consensus 61 i~vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~~------------sre~~l~~L~~~lg~ 108 (297)
T COG2177 61 ITVYLQIDAD-QDDAALVREKIEGIPGVKSVRFI------------SREEALKELQPWLGF 108 (297)
T ss_pred EEEEEecCCC-hHHHHHHHHHHhcCCCcceEEEe------------CHHHHHHHHHHHcCc
Confidence 4555666666 89999999999999999988653 556666666656664
No 66
>PRK10638 glutaredoxin 3; Provisional
Probab=27.05 E-value=1.3e+02 Score=21.27 Aligned_cols=33 Identities=21% Similarity=0.327 Sum_probs=22.9
Q ss_pred EEEEEEeecchhHHHHHHHHHhcCCCccEEEEeCC
Q 027936 28 TVVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDGG 62 (216)
Q Consensus 28 tv~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~ 62 (216)
+|+|-..-.|..|. +++..|... ||.-..+|..
T Consensus 3 ~v~ly~~~~Cp~C~-~a~~~L~~~-gi~y~~~dv~ 35 (83)
T PRK10638 3 NVEIYTKATCPFCH-RAKALLNSK-GVSFQEIPID 35 (83)
T ss_pred cEEEEECCCChhHH-HHHHHHHHc-CCCcEEEECC
Confidence 56666567899998 777777754 7765555553
No 67
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=26.97 E-value=1.3e+02 Score=26.38 Aligned_cols=36 Identities=33% Similarity=0.454 Sum_probs=28.5
Q ss_pred HHHHHHHhcCCCccEEEEeCCCCeEEEeec---CCHHHHH
Q 027936 42 SKIKKIIYKTKGVDNVTIDGGKDLVTVKGT---MDVKELV 78 (216)
Q Consensus 42 ~kI~KaL~kl~GVesV~vD~~t~kVtV~G~---vd~~~L~ 78 (216)
..|.+.|....||+ +.+|..++.|+|..+ .||-.++
T Consensus 27 g~v~k~ie~~~~~~-~~iD~~~~~V~i~~~~~t~Dp~~~~ 65 (194)
T COG1094 27 GEVKKAIEEKTGVK-LRIDSKTGSVTIRTTRKTEDPLALL 65 (194)
T ss_pred ccchHHHHhhcCeE-EEEECCCCeEEEEecCCCCChHHHH
Confidence 46788899888895 999999999999754 5665543
No 68
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=26.93 E-value=1.1e+02 Score=26.94 Aligned_cols=46 Identities=15% Similarity=0.305 Sum_probs=34.7
Q ss_pred chhHHHHHHHHHhcCCCccEEEEeCCCCe-------------------EEEe---ecCCHHHHHHHHH
Q 027936 37 CEGCISKIKKIIYKTKGVDNVTIDGGKDL-------------------VTVK---GTMDVKELVPYLK 82 (216)
Q Consensus 37 C~gCa~kI~KaL~kl~GVesV~vD~~t~k-------------------VtV~---G~vd~~~L~~~L~ 82 (216)
=.||-.-++..+.+++||.++.+=.+.+. |.|+ ..++.++|++..-
T Consensus 51 agGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff 118 (213)
T PRK00058 51 GMGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFW 118 (213)
T ss_pred EccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 46788889999999999999998776442 3443 2477788887775
No 69
>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=26.65 E-value=1.7e+02 Score=23.45 Aligned_cols=45 Identities=13% Similarity=0.108 Sum_probs=28.2
Q ss_pred chhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHH
Q 027936 37 CEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLK 82 (216)
Q Consensus 37 C~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~ 82 (216)
-.+|.+.+ +.|.+|+=--..+--.-.-++||...+..+++...+.
T Consensus 46 nqhclrtm-rhleklkipyefqygwlgvkitiksnvpndevtkkvs 90 (138)
T PF05663_consen 46 NQHCLRTM-RHLEKLKIPYEFQYGWLGVKITIKSNVPNDEVTKKVS 90 (138)
T ss_pred cHHHHHHH-HHHHhcCCCeeeeecceeEEEEEecCCCchHhhhccC
Confidence 35676554 4466665444445555566778888888887776665
No 70
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=26.62 E-value=1.9e+02 Score=22.55 Aligned_cols=45 Identities=20% Similarity=0.243 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHH
Q 027936 38 EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLK 82 (216)
Q Consensus 38 ~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~ 82 (216)
+.-...|..+|+.|+|++--.-|...+.|.|.-.-+...|++.|.
T Consensus 17 pe~l~av~~~L~~ip~~EV~~~d~~GKlVVVie~~~~~~l~~tie 61 (94)
T COG3062 17 PERLSAVKTALLAIPGCEVYGEDAEGKLVVVIEAEDSETLLETIE 61 (94)
T ss_pred HHHHHHHHHHHhcCCCcEeeccCCCceEEEEEEcCchHHHHHHHH
Confidence 455678999999999997444454434444444567777777776
No 71
>PRK11023 outer membrane lipoprotein; Provisional
Probab=26.56 E-value=1.4e+02 Score=25.30 Aligned_cols=42 Identities=12% Similarity=0.175 Sum_probs=29.8
Q ss_pred hhHHHHHHHHHhcCCCccEEE--EeCCCCeEEEeecCCHHHHHH
Q 027936 38 EGCISKIKKIIYKTKGVDNVT--IDGGKDLVTVKGTMDVKELVP 79 (216)
Q Consensus 38 ~gCa~kI~KaL~kl~GVesV~--vD~~t~kVtV~G~vd~~~L~~ 79 (216)
..=..+|+.+|..-+.|.... |...++.|++.|.++..+...
T Consensus 126 ~~It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~~ 169 (191)
T PRK11023 126 TWITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAKA 169 (191)
T ss_pred HHHHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHHH
Confidence 346678889998777766544 444689999999888655433
No 72
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=26.12 E-value=1.9e+02 Score=18.98 Aligned_cols=32 Identities=22% Similarity=0.415 Sum_probs=20.2
Q ss_pred EEEeecchhHHHHHHHHHhcCCCccEEEEeCCCC
Q 027936 31 LKIRLHCEGCISKIKKIIYKTKGVDNVTIDGGKD 64 (216)
Q Consensus 31 LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~~t~ 64 (216)
|-..-.|..|. ++++.|.+. ||.=..+|+...
T Consensus 3 vy~~~~C~~C~-~~~~~L~~~-~i~y~~~dv~~~ 34 (60)
T PF00462_consen 3 VYTKPGCPYCK-KAKEFLDEK-GIPYEEVDVDED 34 (60)
T ss_dssp EEESTTSHHHH-HHHHHHHHT-TBEEEEEEGGGS
T ss_pred EEEcCCCcCHH-HHHHHHHHc-CCeeeEcccccc
Confidence 33346899998 566667554 777555665433
No 73
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.02 E-value=2.1e+02 Score=19.16 Aligned_cols=60 Identities=15% Similarity=0.254 Sum_probs=36.4
Q ss_pred EEEEeec-chhHHHHHHHHHhcCCC-ccEEEEeCC----CCeEEEee-cCCHHHHHHHHHhccCCcEE
Q 027936 30 VLKIRLH-CEGCISKIKKIIYKTKG-VDNVTIDGG----KDLVTVKG-TMDVKELVPYLKEKLKRNVE 90 (216)
Q Consensus 30 ~LKV~Mh-C~gCa~kI~KaL~kl~G-VesV~vD~~----t~kVtV~G-~vd~~~L~~~L~kk~G~~ve 90 (216)
+|.|.|. ..+...+|...|.+..- |.++..... ...++|.- ..+.+.|++.|+ +.|+.+.
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~~~~~~~~~~L~-~~G~~v~ 69 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQTMNPRPIIEDLR-RAGYEVL 69 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEecCCHHHHHHHHH-HCCCeee
Confidence 4455543 44788888888876632 555543332 22234432 267789999999 7888653
No 74
>PRK11023 outer membrane lipoprotein; Provisional
Probab=25.89 E-value=1.2e+02 Score=25.70 Aligned_cols=48 Identities=13% Similarity=0.144 Sum_probs=36.6
Q ss_pred ecchhHHHHHHHHHhcCCCcc---EEEEeCCCCeEEEeecCCHHHHHHHHH
Q 027936 35 LHCEGCISKIKKIIYKTKGVD---NVTIDGGKDLVTVKGTMDVKELVPYLK 82 (216)
Q Consensus 35 MhC~gCa~kI~KaL~kl~GVe---sV~vD~~t~kVtV~G~vd~~~L~~~L~ 82 (216)
+....=..+|+.+|..-+.+. .+.+....+.|+++|.++...+.....
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 455566788999998877774 577888899999999988766655554
No 75
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=25.62 E-value=1.4e+02 Score=25.33 Aligned_cols=44 Identities=25% Similarity=0.323 Sum_probs=34.6
Q ss_pred chhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeec--CCHHHHHHHHH
Q 027936 37 CEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLK 82 (216)
Q Consensus 37 C~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~--vd~~~L~~~L~ 82 (216)
-...+.+|.+.|... ... |++.....+|+|+|. -|.+.+++.|+
T Consensus 101 ~~e~AKkIvK~IKd~-klK-Vqa~IQGd~vRVtgKkrDDLQ~viallk 146 (161)
T PRK05412 101 DQELAKKIVKLIKDS-KLK-VQAQIQGDQVRVTGKKRDDLQAVIALLR 146 (161)
T ss_pred CHHHHHHHHHHHHhc-CCc-eeEEecCcEEEEecCCHhHHHHHHHHHH
Confidence 345778999998744 343 788889999999995 56888888887
No 76
>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=25.30 E-value=1.9e+02 Score=18.53 Aligned_cols=31 Identities=23% Similarity=0.361 Sum_probs=19.6
Q ss_pred EEEEEeecchhHHHHHHHHHhcCCCccEEEEeC
Q 027936 29 VVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDG 61 (216)
Q Consensus 29 v~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~ 61 (216)
|+|-..-.|..|. +++..|.++. |.-..+|.
T Consensus 2 v~ly~~~~Cp~C~-~~~~~L~~~~-i~~~~~di 32 (72)
T cd02066 2 VVVFSKSTCPYCK-RAKRLLESLG-IEFEEIDI 32 (72)
T ss_pred EEEEECCCCHHHH-HHHHHHHHcC-CcEEEEEC
Confidence 3344446699998 7788887774 54444444
No 77
>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=24.87 E-value=2.3e+02 Score=19.73 Aligned_cols=48 Identities=25% Similarity=0.308 Sum_probs=35.1
Q ss_pred ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee--cCCHHHHHHHHHhccCCcEEEc
Q 027936 35 LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 35 MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G--~vd~~~L~~~L~kk~G~~veiV 92 (216)
+.|..=.-+++++|.++.. .+.+.|.. ......|..+.+ ..|+.+..+
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 8899999999999998852 22333332 355678888888 999988754
No 78
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=24.65 E-value=3.2e+02 Score=21.00 Aligned_cols=54 Identities=20% Similarity=0.169 Sum_probs=31.0
Q ss_pred EEEEEe-ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEe--ecCCHHHHHHHHH
Q 027936 29 VVLKIR-LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVK--GTMDVKELVPYLK 82 (216)
Q Consensus 29 v~LKV~-MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~--G~vd~~~L~~~L~ 82 (216)
++|+|. ++=+-+...|+.+|..+..|.-|.+......-.|- ..-+...++.++.
T Consensus 2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~ 58 (105)
T PF08777_consen 2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLK 58 (105)
T ss_dssp -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHH
T ss_pred eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHH
Confidence 357775 77666799999999999989877776655555554 4455888888888
No 79
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=24.44 E-value=1.3e+02 Score=23.27 Aligned_cols=35 Identities=17% Similarity=0.387 Sum_probs=26.7
Q ss_pred ceEEEEEEeec-chhHHHHHHHHHhcCCCccEEEEe
Q 027936 26 VVTVVLKIRLH-CEGCISKIKKIIYKTKGVDNVTID 60 (216)
Q Consensus 26 ~~tv~LKV~Mh-C~gCa~kI~KaL~kl~GVesV~vD 60 (216)
+..+.|.|-|. -++-...|+.+|..+.||+++++-
T Consensus 48 Lkal~l~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 48 LKALKLYVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred eeeEEEEEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 34555666553 466688999999999999999874
No 80
>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=23.97 E-value=2.8e+02 Score=19.86 Aligned_cols=40 Identities=8% Similarity=0.122 Sum_probs=28.3
Q ss_pred hHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHH
Q 027936 39 GCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVP 79 (216)
Q Consensus 39 gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~ 79 (216)
.+...|...|.+..|.- +.++..+..++|.+.+....+..
T Consensus 15 ~~~g~v~~~l~~rrG~i-~~~~~~~~~~~i~~~iP~~~~~~ 54 (85)
T smart00838 15 EYMGDVIGDLNSRRGKI-EGMEQRGGAQVIKAKVPLSEMFG 54 (85)
T ss_pred HHHHHHHHHHHHcCCEE-ECeeccCCcEEEEEECCHHHHhc
Confidence 46678888888888854 34444556888999877766643
No 81
>PRK07334 threonine dehydratase; Provisional
Probab=23.34 E-value=5e+02 Score=24.29 Aligned_cols=64 Identities=13% Similarity=0.186 Sum_probs=41.3
Q ss_pred EEEEEEe-ecchhHHHHHHHHHhcCCC-ccEEEEeCC-----CCeEEEeec---CC---HHHHHHHHHhccCCcEEEc
Q 027936 28 TVVLKIR-LHCEGCISKIKKIIYKTKG-VDNVTIDGG-----KDLVTVKGT---MD---VKELVPYLKEKLKRNVEVV 92 (216)
Q Consensus 28 tv~LKV~-MhC~gCa~kI~KaL~kl~G-VesV~vD~~-----t~kVtV~G~---vd---~~~L~~~L~kk~G~~veiV 92 (216)
++.|.|. ..=.+=...|...|..... |.++.+... .+.++|.-+ -| ...|+..|+ +.|+.+++|
T Consensus 326 ~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr-~~g~~~~~~ 402 (403)
T PRK07334 326 LARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALR-AAGFEARLV 402 (403)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHH-HcCCeeEeC
Confidence 3667776 4445567888888876632 555655432 345444322 24 468899999 999999887
No 82
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=23.11 E-value=1.8e+02 Score=18.81 Aligned_cols=32 Identities=22% Similarity=0.272 Sum_probs=21.4
Q ss_pred CceEEEEEEeecchhHHHHHHHHHhcCCCccEE
Q 027936 25 GVVTVVLKIRLHCEGCISKIKKIIYKTKGVDNV 57 (216)
Q Consensus 25 ~~~tv~LKV~MhC~gCa~kI~KaL~kl~GVesV 57 (216)
....+.|.+.. +..=...+...|.++++|.+|
T Consensus 40 ~~~~~~~~~~~-~~~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 40 GISRITIVVEG-DDDVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred CeEEEEEEEEC-CHHHHHHHHHHHhCCccEEEe
Confidence 34456666664 224466777888899998876
No 83
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=23.00 E-value=1.2e+02 Score=32.38 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=34.0
Q ss_pred HHHHHHHHHhcCCCccEEEEeCCCCeEEEee--------cCCHHHHHHHHH
Q 027936 40 CISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--------TMDVKELVPYLK 82 (216)
Q Consensus 40 Ca~kI~KaL~kl~GVesV~vD~~t~kVtV~G--------~vd~~~L~~~L~ 82 (216)
=++.|+..|.+++||.+|.+......+.|.- -+++..|..+|+
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 4577999999999999999987655566642 277888888998
No 84
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=22.94 E-value=2.1e+02 Score=19.53 Aligned_cols=46 Identities=17% Similarity=0.224 Sum_probs=32.7
Q ss_pred ecchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEee--cCCHHHHHHHHHhccCCcEEE
Q 027936 35 LHCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKG--TMDVKELVPYLKEKLKRNVEV 91 (216)
Q Consensus 35 MhC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G--~vd~~~L~~~L~kk~G~~vei 91 (216)
+.|+.-.-+++++| ++.. .+.+.|.. ......|...++ +.|+.+.+
T Consensus 7 ~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~-~~G~~~~~ 54 (67)
T cd03421 7 LACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAE-SRGYEVSV 54 (67)
T ss_pred CCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHH-HcCCEEEE
Confidence 89999999999999 6532 22333332 345578888888 99998854
No 85
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=22.13 E-value=1.7e+02 Score=20.13 Aligned_cols=27 Identities=22% Similarity=0.367 Sum_probs=19.5
Q ss_pred eecchhHHHHHHHHHhcCCCccEEEEeCC
Q 027936 34 RLHCEGCISKIKKIIYKTKGVDNVTIDGG 62 (216)
Q Consensus 34 ~MhC~gCa~kI~KaL~kl~GVesV~vD~~ 62 (216)
.-.|..|. ++++.|.+. ||.-..+|..
T Consensus 6 ~~~Cp~C~-~ak~~L~~~-~i~~~~~di~ 32 (72)
T TIGR02194 6 KNNCVQCK-MTKKALEEH-GIAFEEINID 32 (72)
T ss_pred CCCCHHHH-HHHHHHHHC-CCceEEEECC
Confidence 46799998 777878764 7766666654
No 86
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=21.97 E-value=1.6e+02 Score=23.88 Aligned_cols=30 Identities=20% Similarity=0.267 Sum_probs=24.9
Q ss_pred eEEEEEEe-ecchhHHHHHHHHHhcCCCccE
Q 027936 27 VTVVLKIR-LHCEGCISKIKKIIYKTKGVDN 56 (216)
Q Consensus 27 ~tv~LKV~-MhC~gCa~kI~KaL~kl~GVes 56 (216)
-+|.|-.. -.|.+|...|.+.....+.|.-
T Consensus 97 G~i~l~te~~pC~SC~~vi~qF~~~~pni~~ 127 (133)
T PF14424_consen 97 GTIDLFTELPPCESCSNVIEQFKKDFPNIKV 127 (133)
T ss_pred ceEEEEecCCcChhHHHHHHHHHHHCCCcEE
Confidence 46767666 4699999999999999999863
No 87
>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=21.88 E-value=2e+02 Score=24.79 Aligned_cols=45 Identities=16% Similarity=0.107 Sum_probs=30.5
Q ss_pred hhHHHHHHHHHhcCCCcc--EEEEeCCCCeEEEeecCCHHHHHHHHH
Q 027936 38 EGCISKIKKIIYKTKGVD--NVTIDGGKDLVTVKGTMDVKELVPYLK 82 (216)
Q Consensus 38 ~gCa~kI~KaL~kl~GVe--sV~vD~~t~kVtV~G~vd~~~L~~~L~ 82 (216)
..=+..|.++++..+||. ++..|...++..||-.-+++.|.+++-
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 345678888998899865 455667888888875555666655543
No 88
>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=21.87 E-value=2e+02 Score=19.33 Aligned_cols=31 Identities=32% Similarity=0.563 Sum_probs=20.3
Q ss_pred EEEEEeecchhHHHHHHHHHhcCCCccEEEEeC
Q 027936 29 VVLKIRLHCEGCISKIKKIIYKTKGVDNVTIDG 61 (216)
Q Consensus 29 v~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD~ 61 (216)
|+|-..-.|..|. ++++.|.+. ||.-..+|.
T Consensus 2 i~ly~~~~Cp~C~-~ak~~L~~~-~i~~~~i~i 32 (75)
T cd03418 2 VEIYTKPNCPYCV-RAKALLDKK-GVDYEEIDV 32 (75)
T ss_pred EEEEeCCCChHHH-HHHHHHHHC-CCcEEEEEC
Confidence 4444456799998 677777765 775554544
No 89
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=21.50 E-value=2e+02 Score=19.17 Aligned_cols=30 Identities=17% Similarity=0.309 Sum_probs=18.7
Q ss_pred EEEEEeecchhHHHHHHHHHhcCCCccEEEEe
Q 027936 29 VVLKIRLHCEGCISKIKKIIYKTKGVDNVTID 60 (216)
Q Consensus 29 v~LKV~MhC~gCa~kI~KaL~kl~GVesV~vD 60 (216)
|+|--.-+|..|. +++..|.++ ||.-..+|
T Consensus 2 v~ly~~~~C~~C~-~~~~~L~~~-~~~~~~id 31 (77)
T TIGR02200 2 ITVYGTTWCGYCA-QLMRTLDKL-GAAYEWVD 31 (77)
T ss_pred EEEEECCCChhHH-HHHHHHHHc-CCceEEEe
Confidence 3333347899998 577777766 66543344
No 90
>COG1666 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.48 E-value=1.7e+02 Score=24.88 Aligned_cols=44 Identities=23% Similarity=0.283 Sum_probs=34.5
Q ss_pred chhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeec--CCHHHHHHHHH
Q 027936 37 CEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLK 82 (216)
Q Consensus 37 C~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~--vd~~~L~~~L~ 82 (216)
-.--+.+|.+.|.. .++. |+.......|+|+|. -|.+.+++.|+
T Consensus 105 ~~e~AKKI~KlIkD-sklK-VqaqIQGdqVRVtgK~rDDLQaVialvr 150 (165)
T COG1666 105 ESENAKKIVKLIKD-SKLK-VQAQIQGDQVRVTGKKRDDLQAVIALVR 150 (165)
T ss_pred hHHHHHHHHHHHHh-cccc-eeeeeccceEEEeccchhhHHHHHHHHH
Confidence 34467889888753 3454 888899999999986 67899999888
No 91
>PF04461 DUF520: Protein of unknown function (DUF520); InterPro: IPR007551 This entry represents the UPF0234 family of uncharacterised proteins.; PDB: 1IN0_A.
Probab=21.11 E-value=1e+02 Score=26.24 Aligned_cols=44 Identities=30% Similarity=0.368 Sum_probs=32.9
Q ss_pred chhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeec--CCHHHHHHHHH
Q 027936 37 CEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGT--MDVKELVPYLK 82 (216)
Q Consensus 37 C~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~--vd~~~L~~~L~ 82 (216)
-...+.+|.+.|... ++. |++.....+|+|+|. -|.+.+++.|+
T Consensus 101 ~~d~AKkIvK~IKd~-klK-Vqa~IQgd~vRVtgKkrDDLQ~viallk 146 (160)
T PF04461_consen 101 DQDTAKKIVKLIKDS-KLK-VQAQIQGDQVRVTGKKRDDLQEVIALLK 146 (160)
T ss_dssp -HHHHHHHHHHHHHH---S-EEEEEETTEEEEEES-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhc-CCc-eeEEecCcEEEEecCCHHHHHHHHHHHH
Confidence 345677898888744 443 778889999999996 66788888887
No 92
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=20.94 E-value=1e+02 Score=22.54 Aligned_cols=54 Identities=15% Similarity=0.175 Sum_probs=31.3
Q ss_pred EEEEEEeecchhHHHHHHHHHh-------cCCCcc--------EEEEeCCCCeEEEeecCCHHHHHHHHH
Q 027936 28 TVVLKIRLHCEGCISKIKKIIY-------KTKGVD--------NVTIDGGKDLVTVKGTMDVKELVPYLK 82 (216)
Q Consensus 28 tv~LKV~MhC~gCa~kI~KaL~-------kl~GVe--------sV~vD~~t~kVtV~G~vd~~~L~~~L~ 82 (216)
.|+-..+|.|.---..|-..+. +++||. ++.+ +.+++|+|+|.-+.+.+..+++
T Consensus 8 NIva~~~l~~~idL~~la~~~~~~~YePe~fpgl~~r~~~p~~t~~I-F~sGki~itGaks~~~~~~a~~ 76 (86)
T PF00352_consen 8 NIVASFDLPFEIDLEELAEELENVEYEPERFPGLIYRLRNPKATVLI-FSSGKIVITGAKSEEEAKKAIE 76 (86)
T ss_dssp EEEEEEE-SSEB-HHHHHHHSTTEEEETTTESSEEEEETTTTEEEEE-ETTSEEEEEEESSHHHHHHHHH
T ss_pred EEEEEEECCCccCHHHHHhhccCcEEeeccCCeEEEeecCCcEEEEE-EcCCEEEEEecCCHHHHHHHHH
Confidence 3444445666555555555442 234432 1222 4799999999988888877776
No 93
>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=20.80 E-value=2.4e+02 Score=20.48 Aligned_cols=41 Identities=32% Similarity=0.281 Sum_probs=27.0
Q ss_pred cchhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHHHHHHhccCCc
Q 027936 36 HCEGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELVPYLKEKLKRN 88 (216)
Q Consensus 36 hC~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~~~L~kk~G~~ 88 (216)
.|..|. ++++.|..+ ||.-..+|... + ..+.+.|.+.+|.+
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 677778766 67766666532 2 45677777566653
No 94
>PF14535 AMP-binding_C_2: AMP-binding enzyme C-terminal domain; PDB: 2Y27_A 2Y4N_A 3QOV_B 3S89_D 3LAX_A 2Y4O_B.
Probab=20.55 E-value=3.2e+02 Score=20.15 Aligned_cols=55 Identities=29% Similarity=0.423 Sum_probs=31.9
Q ss_pred HHHHHHHhcCCCcc-EEE--Ee--CCCCeEEEe--e---cCC--------HHHHHHHHHhccCCcE--EEcCCCC
Q 027936 42 SKIKKIIYKTKGVD-NVT--ID--GGKDLVTVK--G---TMD--------VKELVPYLKEKLKRNV--EVVPAKK 96 (216)
Q Consensus 42 ~kI~KaL~kl~GVe-sV~--vD--~~t~kVtV~--G---~vd--------~~~L~~~L~kk~G~~v--eiV~p~k 96 (216)
..|+.+|.++++|. ... ++ -..+.++|. . ..+ ...|...|+..+|-++ ++|++..
T Consensus 7 ~~Ie~vl~~~~~~~~~y~i~v~~~~~~D~l~v~vE~~~~~~~~~~~~~~l~~~i~~~lk~~lgv~~~V~lv~~gt 81 (96)
T PF14535_consen 7 SQIEEVLREFPEVSPEYQIVVTREGGLDELTVRVELRPGFSDDAEDLEALAERIAERLKERLGVRPEVELVPPGT 81 (96)
T ss_dssp HHHHHHHCTSTTEEEEEEEEEEEETTEEEEEEEEEESTTCCTTHHHHHHHHHHHHHHHHHHHSS-EEEEEE-TT-
T ss_pred HHHHHHHHhCcCCCCcEEEEEEcCCCCcEEEEEEEECCccCcchHHHHHHHHHHHHHHHhhcCceEEEEEECCCC
Confidence 46899999999987 322 22 245556653 1 122 3466667777777755 5677654
No 95
>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=20.23 E-value=3.1e+02 Score=19.11 Aligned_cols=46 Identities=11% Similarity=0.213 Sum_probs=29.8
Q ss_pred EEeecc-hhHHHHHHHHHhcCCCccEEEEeCCCCeEEEeecCCHHHHH
Q 027936 32 KIRLHC-EGCISKIKKIIYKTKGVDNVTIDGGKDLVTVKGTMDVKELV 78 (216)
Q Consensus 32 KV~MhC-~gCa~kI~KaL~kl~GVesV~vD~~t~kVtV~G~vd~~~L~ 78 (216)
+|.++| ..+..+|...|.+..|.- +..+..++.++|.+.+....+.
T Consensus 5 ~~~I~~p~~~~g~v~~~l~~rrg~i-~~~~~~~~~~~i~~~iP~~e~~ 51 (78)
T cd03713 5 KVEVTVPEEYMGDVIGDLSSRRGQI-LGTESRGGWKVIKAEVPLAEMF 51 (78)
T ss_pred EEEEEcCHHHHHHHHHHHHHcCCce-EceeccCCcEEEEEEcCHHHHh
Confidence 344444 346668888888888843 2334446678899987766653
Done!