Query 037689
Match_columns 122
No_of_seqs 224 out of 1097
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 03:27:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037689.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037689hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.4 8.3E-13 1.8E-17 79.1 7.3 53 1-54 7-62 (62)
2 KOG1603 Copper chaperone [Inor 99.3 5.8E-12 1.2E-16 78.3 6.8 58 1-59 13-71 (73)
3 COG2608 CopZ Copper chaperone 99.3 2.5E-11 5.4E-16 75.2 7.2 57 1-58 11-70 (71)
4 KOG4656 Copper chaperone for s 98.9 8.9E-09 1.9E-13 75.3 7.0 60 1-61 15-74 (247)
5 PLN02957 copper, zinc superoxi 98.3 4.8E-06 1E-10 62.4 8.8 61 1-62 14-74 (238)
6 PRK10671 copA copper exporting 98.1 7.2E-06 1.6E-10 70.9 6.6 56 1-59 12-67 (834)
7 COG2217 ZntA Cation transport 97.8 5.5E-05 1.2E-09 64.6 6.5 55 1-57 11-69 (713)
8 TIGR00003 copper ion binding p 97.3 0.0021 4.6E-08 35.6 6.8 54 1-55 11-67 (68)
9 KOG0207 Cation transport ATPas 97.1 0.0012 2.5E-08 57.5 6.3 61 1-62 3-65 (951)
10 PRK10671 copA copper exporting 97.0 0.0022 4.7E-08 55.8 6.8 57 1-58 108-164 (834)
11 KOG0207 Cation transport ATPas 96.5 0.0072 1.6E-07 52.8 6.5 60 1-61 155-217 (951)
12 PRK11033 zntA zinc/cadmium/mer 96.5 0.008 1.7E-07 51.8 6.3 57 1-58 62-119 (741)
13 COG1888 Uncharacterized protei 91.2 1.2 2.6E-05 28.8 5.9 49 10-59 24-80 (97)
14 TIGR02052 MerP mercuric transp 91.1 2.1 4.6E-05 25.5 7.6 56 1-57 32-90 (92)
15 PF02680 DUF211: Uncharacteriz 90.9 1 2.2E-05 29.3 5.4 50 9-59 21-78 (95)
16 PRK13748 putative mercuric red 85.8 4.6 0.0001 33.4 7.5 59 1-60 9-69 (561)
17 cd00371 HMA Heavy-metal-associ 83.8 3.6 7.9E-05 19.9 6.7 52 1-53 7-60 (63)
18 PRK14054 methionine sulfoxide 73.4 8 0.00017 27.8 4.4 45 4-48 10-76 (172)
19 PF14492 EFG_II: Elongation Fa 73.0 12 0.00026 22.7 4.7 49 8-57 19-73 (75)
20 PRK10553 assembly protein for 70.9 24 0.00052 22.4 5.8 41 7-47 19-60 (87)
21 PF01206 TusA: Sulfurtransfera 67.9 20 0.00042 21.1 4.8 50 1-60 8-59 (70)
22 PF13732 DUF4162: Domain of un 65.9 27 0.00058 21.1 5.5 45 13-59 25-70 (84)
23 PF01883 DUF59: Domain of unkn 65.2 8.9 0.00019 22.8 2.9 19 7-25 54-72 (72)
24 PF03927 NapD: NapD protein; 59.0 40 0.00087 20.8 5.7 41 7-48 17-58 (79)
25 PRK13014 methionine sulfoxide 56.6 17 0.00038 26.4 3.5 28 4-31 15-42 (186)
26 cd02410 archeal_CPSF_KH The ar 54.7 53 0.0012 23.0 5.5 55 8-62 56-116 (145)
27 PRK00058 methionine sulfoxide 54.4 30 0.00065 25.8 4.5 45 4-48 52-118 (213)
28 PRK05528 methionine sulfoxide 51.9 12 0.00026 26.4 2.0 45 4-48 8-69 (156)
29 PF04972 BON: BON domain; Int 49.3 12 0.00026 21.5 1.5 30 8-38 2-34 (64)
30 PF09580 Spore_YhcN_YlaJ: Spor 47.5 68 0.0015 22.3 5.4 28 7-34 77-104 (177)
31 PHA01634 hypothetical protein 47.0 5.9 0.00013 27.6 -0.1 13 1-13 98-110 (156)
32 PF04468 PSP1: PSP1 C-terminal 45.2 76 0.0017 19.9 5.3 53 5-58 30-86 (88)
33 COG4004 Uncharacterized protei 44.7 50 0.0011 21.4 3.8 22 15-36 37-58 (96)
34 TIGR02945 SUF_assoc FeS assemb 43.6 25 0.00054 22.2 2.4 21 8-28 58-78 (99)
35 PF08712 Nfu_N: Scaffold prote 43.6 81 0.0018 19.8 5.6 37 10-48 39-77 (87)
36 TIGR00401 msrA methionine-S-su 42.0 21 0.00044 25.0 1.9 28 4-31 7-34 (149)
37 PF01625 PMSR: Peptide methion 40.7 28 0.0006 24.5 2.4 27 4-30 7-33 (155)
38 TIGR02571 ComEB ComE operon pr 40.0 1E+02 0.0022 21.5 5.2 44 2-59 96-139 (151)
39 cd03421 SirA_like_N SirA_like_ 39.1 79 0.0017 18.3 6.0 47 1-58 7-55 (67)
40 PRK05550 bifunctional methioni 38.9 61 0.0013 25.2 4.3 28 4-31 134-161 (283)
41 PRK11023 outer membrane lipopr 38.6 1E+02 0.0022 22.2 5.2 39 7-45 129-169 (191)
42 cd04888 ACT_PheB-BS C-terminal 38.1 42 0.00091 19.5 2.7 19 7-25 56-74 (76)
43 PRK06418 transcription elongat 37.9 1.5E+02 0.0032 21.2 6.4 61 2-62 15-100 (166)
44 PRK09577 multidrug efflux prot 37.8 1.1E+02 0.0023 27.9 6.2 46 7-53 158-211 (1032)
45 COG2151 PaaD Predicted metal-s 37.6 40 0.00087 22.5 2.7 21 7-27 69-89 (111)
46 PRK10555 aminoglycoside/multid 37.6 97 0.0021 28.2 5.9 42 7-48 159-208 (1037)
47 TIGR00489 aEF-1_beta translati 36.9 38 0.00083 21.6 2.4 20 7-26 64-83 (88)
48 TIGR01676 GLDHase galactonolac 36.2 75 0.0016 26.9 4.7 39 14-55 110-148 (541)
49 PRK11023 outer membrane lipopr 35.8 96 0.0021 22.3 4.7 39 7-45 51-92 (191)
50 PF00352 TBP: Transcription fa 35.7 53 0.0011 20.3 3.0 22 27-48 55-76 (86)
51 KOG3411 40S ribosomal protein 35.7 33 0.00071 23.8 2.1 42 4-48 97-139 (143)
52 PF09158 MotCF: Bacteriophage 34.1 1.4E+02 0.003 19.7 4.8 40 16-57 39-78 (103)
53 PRK11200 grxA glutaredoxin 1; 31.7 86 0.0019 18.9 3.4 27 2-29 10-40 (85)
54 cd06167 LabA_like LabA_like pr 31.5 88 0.0019 20.8 3.8 29 32-61 104-132 (149)
55 PF01514 YscJ_FliF: Secretory 30.6 63 0.0014 23.6 3.1 21 7-27 117-137 (206)
56 PF01849 NAC: NAC domain; Int 30.5 74 0.0016 18.2 2.8 27 8-34 2-33 (58)
57 KOG4730 D-arabinono-1, 4-lacto 30.1 62 0.0013 27.1 3.2 34 23-57 105-138 (518)
58 TIGR03527 selenium_YedF seleni 29.3 2.2E+02 0.0049 20.6 6.2 51 1-59 6-56 (194)
59 COG2092 EFB1 Translation elong 29.0 55 0.0012 21.0 2.2 20 7-26 64-83 (88)
60 PRK15127 multidrug efflux syst 29.0 1.7E+02 0.0037 26.7 6.0 43 8-51 160-210 (1049)
61 PRK00435 ef1B elongation facto 28.9 61 0.0013 20.7 2.4 19 8-26 65-83 (88)
62 COG1094 Predicted RNA-binding 28.6 1.7E+02 0.0037 21.5 4.9 27 9-36 28-54 (194)
63 PRK11198 LysM domain/BON super 28.6 1.5E+02 0.0033 20.3 4.6 45 8-52 29-74 (147)
64 TIGR03406 FeS_long_SufT probab 27.8 74 0.0016 22.8 3.0 20 8-27 134-153 (174)
65 COG2177 FtsX Cell division pro 27.6 1.7E+02 0.0038 22.7 5.2 39 4-54 71-109 (297)
66 PHA02588 cd deoxycytidylate de 27.5 2.3E+02 0.0049 20.0 5.4 45 2-59 110-154 (168)
67 COG0225 MsrA Peptide methionin 27.5 41 0.00089 24.3 1.5 28 4-31 13-40 (174)
68 TIGR02830 spore_III_AG stage I 27.5 61 0.0013 23.6 2.5 29 6-34 62-92 (186)
69 PRK11018 hypothetical protein; 27.1 1.5E+02 0.0033 17.9 6.1 51 1-59 16-66 (78)
70 TIGR00915 2A0602 The (Largely 27.1 1.8E+02 0.004 26.5 5.9 41 8-48 160-208 (1044)
71 PRK11670 antiporter inner memb 27.1 2.1E+02 0.0046 22.7 5.7 54 8-62 68-146 (369)
72 PRK05412 putative nucleotide-b 25.9 2.2E+02 0.0047 20.3 4.9 45 6-53 104-150 (161)
73 PF01565 FAD_binding_4: FAD bi 25.6 1E+02 0.0023 20.1 3.3 31 23-54 57-87 (139)
74 PF13193 AMP-binding_C: AMP-bi 25.5 82 0.0018 18.3 2.5 37 10-48 2-45 (73)
75 COG3062 NapD Uncharacterized p 25.2 2E+02 0.0043 18.7 5.2 41 7-48 20-61 (94)
76 PRK11282 glcE glycolate oxidas 25.1 1.4E+02 0.003 23.8 4.3 37 15-54 44-80 (352)
77 COG4669 EscJ Type III secretor 24.4 81 0.0017 24.0 2.7 20 7-26 111-130 (246)
78 PF13216 DUF4024: Protein of u 23.9 26 0.00057 18.0 0.0 12 107-118 8-19 (35)
79 cd03422 YedF YedF is a bacteri 23.6 1.7E+02 0.0036 17.2 6.0 50 2-59 8-57 (69)
80 TIGR03675 arCOG00543 arCOG0054 23.2 2.2E+02 0.0048 24.5 5.4 55 7-62 72-133 (630)
81 TIGR02544 III_secr_YscJ type I 22.8 95 0.0021 22.5 2.8 21 7-27 109-129 (193)
82 PRK07334 threonine dehydratase 22.7 2.2E+02 0.0047 22.8 5.1 51 7-58 340-402 (403)
83 TIGR01679 bact_FAD_ox FAD-link 21.9 1.8E+02 0.0039 23.5 4.4 38 16-56 59-96 (419)
84 PLN02465 L-galactono-1,4-lacto 21.8 1.7E+02 0.0037 25.0 4.4 39 16-57 147-185 (573)
85 PF12685 SpoIIIAH: SpoIIIAH-li 21.6 1.9E+02 0.0041 20.7 4.2 48 7-55 137-190 (196)
86 PF04805 Pox_E10: E10-like pro 21.1 84 0.0018 19.2 1.8 26 1-26 16-41 (70)
87 PF08002 DUF1697: Protein of u 21.1 2.8E+02 0.006 18.8 5.8 48 9-57 23-74 (137)
88 TIGR01677 pln_FAD_oxido plant- 21.1 1.9E+02 0.0041 24.6 4.5 34 23-57 92-125 (557)
89 TIGR00914 2A0601 heavy metal e 21.0 1.5E+02 0.0032 27.0 4.1 42 7-48 700-751 (1051)
90 KOG1635 Peptide methionine sul 20.8 93 0.002 22.7 2.3 28 4-31 31-58 (191)
91 PRK10568 periplasmic protein; 20.8 2.4E+02 0.0052 20.4 4.6 33 7-39 62-96 (203)
92 PF13383 Methyltransf_22: Meth 20.7 1.5E+02 0.0033 22.2 3.6 47 1-58 173-225 (242)
93 cd00292 EF1B Elongation factor 20.7 1.1E+02 0.0024 19.4 2.4 20 8-27 65-84 (88)
94 PF10934 DUF2634: Protein of u 20.5 2E+02 0.0044 18.8 3.8 30 6-35 70-102 (112)
95 PF08210 APOBEC_N: APOBEC-like 20.3 1.7E+02 0.0037 21.0 3.7 55 3-61 85-148 (188)
96 TIGR01678 FAD_lactone_ox sugar 20.3 2E+02 0.0043 23.5 4.4 38 16-56 65-102 (438)
97 KOG3476 Microtubule-associated 20.3 49 0.0011 21.3 0.7 14 1-14 1-14 (100)
98 TIGR00288 conserved hypothetic 20.1 1.8E+02 0.0039 20.6 3.7 29 32-61 110-138 (160)
No 1
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.43 E-value=8.3e-13 Score=79.08 Aligned_cols=53 Identities=30% Similarity=0.601 Sum_probs=49.4
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeec---CCHHHHHHHHHhhcCCc
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGR---IDPQKVLKKLKKKTGKK 54 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~---~~~~~v~~~i~~~~G~~ 54 (122)
|+|++|+++|+++|++++||.++.+|+.+++++|.+. +++++|.++|+ ++||+
T Consensus 7 m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~Gy~ 62 (62)
T PF00403_consen 7 MTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAGYE 62 (62)
T ss_dssp TTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTTSE
T ss_pred cccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhCcC
Confidence 8999999999999999999999999999999999865 46699999998 99985
No 2
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.33 E-value=5.8e-12 Score=78.35 Aligned_cols=58 Identities=50% Similarity=0.871 Sum_probs=54.5
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcC-CceEEec
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTG-KKVEIVD 59 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G-~~~e~~~ 59 (122)
|+|.+|+.+|++.|+.++||.++.+|..+++|+|.|.+++..|++.|+ +.| ++.++|.
T Consensus 13 ~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~-k~~~k~~~~~~ 71 (73)
T KOG1603|consen 13 MHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLK-KTGGKRAELWK 71 (73)
T ss_pred cccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHH-hcCCCceEEec
Confidence 799999999999999999999999999999999999999999999998 676 8888774
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.27 E-value=2.5e-11 Score=75.16 Aligned_cols=57 Identities=30% Similarity=0.610 Sum_probs=51.2
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEe--e-cCCHHHHHHHHHhhcCCceEEe
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVT--G-RIDPQKVLKKLKKKTGKKVEIV 58 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~--g-~~~~~~v~~~i~~~~G~~~e~~ 58 (122)
|+|++|+.+|+++|.+++||.++++|+..+++.|+ + .++.++|.++|. .+||.+..+
T Consensus 11 MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~~~ 70 (71)
T COG2608 11 MTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVEEI 70 (71)
T ss_pred cCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCeeec
Confidence 89999999999999999999999999999666654 5 589999999998 999998764
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.86 E-value=8.9e-09 Score=75.32 Aligned_cols=60 Identities=20% Similarity=0.477 Sum_probs=57.2
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEEecCC
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVDNN 61 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~~~~~ 61 (122)
|+|++|+..|++.|+.++||.+|+||+.++.|.|.+...+.+|...|+ .+|+++.+....
T Consensus 15 M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le-~tGr~Avl~G~G 74 (247)
T KOG4656|consen 15 MTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLE-NTGRDAVLRGAG 74 (247)
T ss_pred chhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHH-hhChheEEecCC
Confidence 899999999999999999999999999999999999999999999998 999999987654
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.31 E-value=4.8e-06 Score=62.43 Aligned_cols=61 Identities=23% Similarity=0.497 Sum_probs=55.9
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEEecCCC
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVDNNN 62 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~~~~~~ 62 (122)
|+|..|+.+|++.|.+++||..+.+++..++++|........+...|+ ++||.++++...+
T Consensus 14 MsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe-~~Gy~a~~~~~~~ 74 (238)
T PLN02957 14 MKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALE-QTGRKARLIGQGD 74 (238)
T ss_pred ccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHH-HcCCcEEEecCCC
Confidence 789999999999999999999999999999999987778889999998 9999998886644
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.10 E-value=7.2e-06 Score=70.88 Aligned_cols=56 Identities=18% Similarity=0.436 Sum_probs=50.0
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEEec
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~~~ 59 (122)
|+|.+|+.+|+++|++++||..+.+++. +.+|++..+.+.+.++++ ++||+++...
T Consensus 12 mtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~ 67 (834)
T PRK10671 12 LSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIK-QAGYDASVSH 67 (834)
T ss_pred cccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHH-hcCCcccccc
Confidence 8999999999999999999999999994 555666678999999998 9999998754
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.80 E-value=5.5e-05 Score=64.62 Aligned_cols=55 Identities=27% Similarity=0.587 Sum_probs=49.8
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeec---CC-HHHHHHHHHhhcCCceEE
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGR---ID-PQKVLKKLKKKTGKKVEI 57 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~---~~-~~~v~~~i~~~~G~~~e~ 57 (122)
|+|..|+++|| +|.+++||..+.+|+.++++.|... .+ .+.+..+++ +.||.+..
T Consensus 11 m~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~~ 69 (713)
T COG2217 11 MTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSARL 69 (713)
T ss_pred cCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCccccc
Confidence 89999999999 9999999999999999999998742 45 789999998 99998775
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.31 E-value=0.0021 Score=35.56 Aligned_cols=54 Identities=20% Similarity=0.393 Sum_probs=44.7
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEee---cCCHHHHHHHHHhhcCCce
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG---RIDPQKVLKKLKKKTGKKV 55 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g---~~~~~~v~~~i~~~~G~~~ 55 (122)
|+|..|...+++.+..++++..+.+++...++.+.. ..+...+...+. ..|+.+
T Consensus 11 ~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~ 67 (68)
T TIGR00003 11 MTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYEV 67 (68)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCCc
Confidence 579999999999999999999999999999988863 246777777776 777753
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.14 E-value=0.0012 Score=57.51 Aligned_cols=61 Identities=23% Similarity=0.542 Sum_probs=55.5
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEee--cCCHHHHHHHHHhhcCCceEEecCCC
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG--RIDPQKVLKKLKKKTGKKVEIVDNNN 62 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g--~~~~~~v~~~i~~~~G~~~e~~~~~~ 62 (122)
|+|..|.+.|++++.+.+||.++.|++.++..+|.- ..+++.+.+.++ ..|+++++.....
T Consensus 3 mtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~gf~~~~~~~~~ 65 (951)
T KOG0207|consen 3 MTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMGFEASLLSDSE 65 (951)
T ss_pred ccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-cccceeeecccCc
Confidence 899999999999999999999999999999988864 478999999998 9999999886644
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.00 E-value=0.0022 Score=55.77 Aligned_cols=57 Identities=25% Similarity=0.528 Sum_probs=51.0
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEEe
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIV 58 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~~ 58 (122)
|+|..|+..|++.+.+++||..+.+++.++++.+.+..++.++.+.++ +.||.+.++
T Consensus 108 m~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~-~~Gy~a~~~ 164 (834)
T PRK10671 108 MSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVE-KAGYGAEAI 164 (834)
T ss_pred cCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHH-hcCCCcccc
Confidence 789999999999999999999999999999988876677888888998 899987654
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.54 E-value=0.0072 Score=52.79 Aligned_cols=60 Identities=18% Similarity=0.499 Sum_probs=53.6
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEee---cCCHHHHHHHHHhhcCCceEEecCC
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG---RIDPQKVLKKLKKKTGKKVEIVDNN 61 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g---~~~~~~v~~~i~~~~G~~~e~~~~~ 61 (122)
|.|.+|..+|++.|.+++||.++.++..++++.|.. ...+.++.+.|+ .+|+.+......
T Consensus 155 ~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~~~~~~~~~~ 217 (951)
T KOG0207|consen 155 MTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETGFEASVRPYG 217 (951)
T ss_pred ccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhcccceeeecc
Confidence 789999999999999999999999999999999863 368999999998 999987776543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.46 E-value=0.008 Score=51.79 Aligned_cols=57 Identities=23% Similarity=0.373 Sum_probs=47.3
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeec-CCHHHHHHHHHhhcCCceEEe
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGR-IDPQKVLKKLKKKTGKKVEIV 58 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~-~~~~~v~~~i~~~~G~~~e~~ 58 (122)
|+|.+|..++++.+.+++||..+.+++.++++.+... ...+++...++ +.||.+..+
T Consensus 62 m~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~-~~Gy~a~~~ 119 (741)
T PRK11033 62 MDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQ-KAGFSLRDE 119 (741)
T ss_pred CCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHH-hcccccccc
Confidence 7899999999999999999999999999999887632 12267778887 899987654
No 13
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=91.24 E-value=1.2 Score=28.81 Aligned_cols=49 Identities=22% Similarity=0.491 Sum_probs=35.6
Q ss_pred HHHHHhcCCCceEEEE-----EcC--CcEEEEeec-CCHHHHHHHHHhhcCCceEEec
Q 037689 10 VARAISKFKGVEKFTT-----DMN--KHRVVVTGR-IDPQKVLKKLKKKTGKKVEIVD 59 (122)
Q Consensus 10 I~k~l~~~~GV~~v~v-----d~~--~~kv~V~g~-~~~~~v~~~i~~~~G~~~e~~~ 59 (122)
+.+.|++++||+.|.+ |.+ +-+++|.|. ++.++|.+.|+ +.|-.++.+.
T Consensus 24 ~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSiD 80 (97)
T COG1888 24 LALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSID 80 (97)
T ss_pred HHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeehh
Confidence 4566788888776654 333 445666775 89999999998 9998877653
No 14
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=91.09 E-value=2.1 Score=25.50 Aligned_cols=56 Identities=27% Similarity=0.416 Sum_probs=42.2
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEe--e-cCCHHHHHHHHHhhcCCceEE
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVT--G-RIDPQKVLKKLKKKTGKKVEI 57 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~--g-~~~~~~v~~~i~~~~G~~~e~ 57 (122)
+.|..|...++..+....|+....++....++.+. . ......+...+. ..|+.+++
T Consensus 32 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~ 90 (92)
T TIGR02052 32 MTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSSL 90 (92)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeEe
Confidence 46999999999999999998888888888876654 1 245566666666 77877554
No 15
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=90.89 E-value=1 Score=29.35 Aligned_cols=50 Identities=20% Similarity=0.480 Sum_probs=35.6
Q ss_pred HHHHHHhcCCCceEEEEE-----cCCcE--EEEeec-CCHHHHHHHHHhhcCCceEEec
Q 037689 9 TVARAISKFKGVEKFTTD-----MNKHR--VVVTGR-IDPQKVLKKLKKKTGKKVEIVD 59 (122)
Q Consensus 9 ~I~k~l~~~~GV~~v~vd-----~~~~k--v~V~g~-~~~~~v~~~i~~~~G~~~e~~~ 59 (122)
.+.+.|.+++||..|.+. ..+.. ++|.|. ++.++|.++|+ +.|-.++.+.
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHSID 78 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHSID 78 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEEEE
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEeee
Confidence 356789999998877654 34444 445675 89999999998 9998877654
No 16
>PRK13748 putative mercuric reductase; Provisional
Probab=85.77 E-value=4.6 Score=33.38 Aligned_cols=59 Identities=20% Similarity=0.373 Sum_probs=47.3
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEee--cCCHHHHHHHHHhhcCCceEEecC
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG--RIDPQKVLKKLKKKTGKKVEIVDN 60 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g--~~~~~~v~~~i~~~~G~~~e~~~~ 60 (122)
|.|..|..+++..+..++++....+++..+.+.+.. ......+...+. ..|+..++...
T Consensus 9 ~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g~~~~~~~~ 69 (561)
T PRK13748 9 MTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLGYRATLADA 69 (561)
T ss_pred eecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcCCeeeccCc
Confidence 579999999999999999998899999888877653 245666767776 78888776655
No 17
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=83.80 E-value=3.6 Score=19.94 Aligned_cols=52 Identities=25% Similarity=0.592 Sum_probs=35.1
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeec--CCHHHHHHHHHhhcCC
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGR--IDPQKVLKKLKKKTGK 53 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~--~~~~~v~~~i~~~~G~ 53 (122)
+.|..|...++..+....|+.....++....+.+... .....+...+. ..|+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 60 (63)
T cd00371 7 MTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE-DAGY 60 (63)
T ss_pred eEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH-HcCC
Confidence 4589999999998888899877777877776555432 24444444444 4443
No 18
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=73.37 E-value=8 Score=27.76 Aligned_cols=45 Identities=18% Similarity=0.234 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCcE-------------------EEEe---ecCCHHHHHHHHH
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKHR-------------------VVVT---GRIDPQKVLKKLK 48 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~k-------------------v~V~---g~~~~~~v~~~i~ 48 (122)
.||=+-++..+.+++||.++.+-...+. |.|+ ..++.++|++..-
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~ 76 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF 76 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence 5899999999999999999999887765 4454 2367778877654
No 19
>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=72.95 E-value=12 Score=22.73 Aligned_cols=49 Identities=20% Similarity=0.478 Sum_probs=35.7
Q ss_pred HHHHHHHhcC----CCceEEEEEcCCcEEEEe--ecCCHHHHHHHHHhhcCCceEE
Q 037689 8 RTVARAISKF----KGVEKFTTDMNKHRVVVT--GRIDPQKVLKKLKKKTGKKVEI 57 (122)
Q Consensus 8 ~~I~k~l~~~----~GV~~v~vd~~~~kv~V~--g~~~~~~v~~~i~~~~G~~~e~ 57 (122)
.++..+|.++ +++ .+..|-.++.+.|. |.+..+-+++.|+++.|..+++
T Consensus 19 ~kl~~aL~~l~~eDP~l-~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~~ 73 (75)
T PF14492_consen 19 PKLSEALQKLSEEDPSL-RVERDEETGELILSGMGELHLEVLLERLKRRFGVEVEF 73 (75)
T ss_dssp HHHHHHHHHHHHH-TTS-EEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEEE
T ss_pred HHHHHHHHHHHhcCCeE-EEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeEe
Confidence 4555565555 455 78899999998887 5578888999998666766554
No 20
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=70.95 E-value=24 Score=22.45 Aligned_cols=41 Identities=17% Similarity=0.350 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCcEEEEe-ecCCHHHHHHHH
Q 037689 7 ERTVARAISKFKGVEKFTTDMNKHRVVVT-GRIDPQKVLKKL 47 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~~~~kv~V~-g~~~~~~v~~~i 47 (122)
...+.+.|..++|++-...|...+|+.|+ ...+...+++.+
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i 60 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTI 60 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHH
Confidence 45788999999999766677778887775 223444444444
No 21
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=67.88 E-value=20 Score=21.08 Aligned_cols=50 Identities=12% Similarity=0.135 Sum_probs=35.6
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEe--ecCCHHHHHHHHHhhcCCceEEecC
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVT--GRIDPQKVLKKLKKKTGKKVEIVDN 60 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~--g~~~~~~v~~~i~~~~G~~~e~~~~ 60 (122)
+.|+....++.++|.+++.= +.+.|. .......|...++ ..|+++..+..
T Consensus 8 ~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~-~~g~~~~~~~~ 59 (70)
T PF01206_consen 8 LSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCE-ENGYEVVEVEE 59 (70)
T ss_dssp -STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHH-HHTEEEEEEEE
T ss_pred CCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHH-HCCCEEEEEEE
Confidence 36999999999999998542 234443 3355678999997 99998666544
No 22
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=65.90 E-value=27 Score=21.06 Aligned_cols=45 Identities=18% Similarity=0.358 Sum_probs=31.8
Q ss_pred HHhcCCCceEEEEEcCC-cEEEEeecCCHHHHHHHHHhhcCCceEEec
Q 037689 13 AISKFKGVEKFTTDMNK-HRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (122)
Q Consensus 13 ~l~~~~GV~~v~vd~~~-~kv~V~g~~~~~~v~~~i~~~~G~~~e~~~ 59 (122)
.|..++||..+...-.. -.+.+....+..+|+..|. ..|. +.-+.
T Consensus 25 ~l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~-~~g~-I~~f~ 70 (84)
T PF13732_consen 25 ELEELPGVESVEQDGDGKLRIKLEDEETANELLQELI-EKGI-IRSFE 70 (84)
T ss_pred HHhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHH-hCCC-eeEEE
Confidence 37788999988765333 3444555567889999998 8888 66543
No 23
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=65.22 E-value=8.9 Score=22.79 Aligned_cols=19 Identities=16% Similarity=0.377 Sum_probs=15.3
Q ss_pred HHHHHHHHhcCCCceEEEE
Q 037689 7 ERTVARAISKFKGVEKFTT 25 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~v 25 (122)
...|+++|+.++||.+|+|
T Consensus 54 ~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 54 REEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHhCCCCceEeC
Confidence 4678999999999998875
No 24
>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=59.01 E-value=40 Score=20.78 Aligned_cols=41 Identities=24% Similarity=0.345 Sum_probs=27.7
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCcEEEEe-ecCCHHHHHHHHH
Q 037689 7 ERTVARAISKFKGVEKFTTDMNKHRVVVT-GRIDPQKVLKKLK 48 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~~~~kv~V~-g~~~~~~v~~~i~ 48 (122)
...+.++|..++|++-...+-. +|+.|+ ...+...+.+.+.
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 3568899999999965556655 787765 3345555555554
No 25
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=56.59 E-value=17 Score=26.39 Aligned_cols=28 Identities=14% Similarity=0.220 Sum_probs=24.7
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCcE
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~k 31 (122)
.||-+-++..+.+++||.++++-+..+.
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~ 42 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGH 42 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCC
Confidence 5788999999999999999999887664
No 26
>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=54.65 E-value=53 Score=22.99 Aligned_cols=55 Identities=15% Similarity=0.324 Sum_probs=38.2
Q ss_pred HHHHHHHhcCCCceEEEEEcCCcEEEEe----ecC--CHHHHHHHHHhhcCCceEEecCCC
Q 037689 8 RTVARAISKFKGVEKFTTDMNKHRVVVT----GRI--DPQKVLKKLKKKTGKKVEIVDNNN 62 (122)
Q Consensus 8 ~~I~k~l~~~~GV~~v~vd~~~~kv~V~----g~~--~~~~v~~~i~~~~G~~~e~~~~~~ 62 (122)
..|++.+-.-.||.++.+|..++.|.|. |.+ -....+..|..++|+...+....+
T Consensus 56 ~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 56 KIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 4555555555799999999999999995 221 223444444459999998886655
No 27
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=54.45 E-value=30 Score=25.75 Aligned_cols=45 Identities=18% Similarity=0.121 Sum_probs=34.5
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCcE-------------------EEEee---cCCHHHHHHHHH
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKHR-------------------VVVTG---RIDPQKVLKKLK 48 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~k-------------------v~V~g---~~~~~~v~~~i~ 48 (122)
.||-+-++..+.+++||.++.+-+..+. |.|+- .++.++|+...-
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff 118 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFW 118 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 5899999999999999999999887542 44442 367788877664
No 28
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=51.94 E-value=12 Score=26.44 Aligned_cols=45 Identities=16% Similarity=0.154 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCcE--------------EEEe---ecCCHHHHHHHHH
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKHR--------------VVVT---GRIDPQKVLKKLK 48 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~k--------------v~V~---g~~~~~~v~~~i~ 48 (122)
.||=+-++..+.+++||.++.+-...+. |.|+ ..++.++|++..-
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~ 69 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLF 69 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHH
Confidence 5899999999999999999999876643 3333 2367777777664
No 29
>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=49.35 E-value=12 Score=21.47 Aligned_cols=30 Identities=13% Similarity=0.309 Sum_probs=16.1
Q ss_pred HHHHHHHhc---CCCceEEEEEcCCcEEEEeecC
Q 037689 8 RTVARAISK---FKGVEKFTTDMNKHRVVVTGRI 38 (122)
Q Consensus 8 ~~I~k~l~~---~~GV~~v~vd~~~~kv~V~g~~ 38 (122)
.+|+.+|.. +++- .+.+....+.|+++|.+
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v 34 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEV 34 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEE
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeC
Confidence 356666666 4444 67888889999999975
No 30
>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=47.53 E-value=68 Score=22.34 Aligned_cols=28 Identities=25% Similarity=0.331 Sum_probs=24.6
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCcEEEE
Q 037689 7 ERTVARAISKFKGVEKFTTDMNKHRVVV 34 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~~~~kv~V 34 (122)
+..|.+.+.+++||..+.|=.....+.|
T Consensus 77 a~~i~~~v~~~~~V~~A~vvv~~~~a~V 104 (177)
T PF09580_consen 77 ADRIANRVKKVPGVEDATVVVTDDNAYV 104 (177)
T ss_pred HHHHHHHHhcCCCceEEEEEEECCEEEE
Confidence 5678999999999999998888888776
No 31
>PHA01634 hypothetical protein
Probab=47.04 E-value=5.9 Score=27.60 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=10.6
Q ss_pred CCchhHHHHHHHH
Q 037689 1 MYCNACERTVARA 13 (122)
Q Consensus 1 m~C~~C~~~I~k~ 13 (122)
|+|+||+++|.-.
T Consensus 98 iDCeGCE~~l~v~ 110 (156)
T PHA01634 98 MDCEGCEEKLNVS 110 (156)
T ss_pred EEccchHHhcCHH
Confidence 7899999988543
No 32
>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=45.19 E-value=76 Score=19.89 Aligned_cols=53 Identities=13% Similarity=0.290 Sum_probs=36.0
Q ss_pred hHHHHHHHHHhcCCCceEEEEEcCCcEEEEe----ecCCHHHHHHHHHhhcCCceEEe
Q 037689 5 ACERTVARAISKFKGVEKFTTDMNKHRVVVT----GRIDPQKVLKKLKKKTGKKVEIV 58 (122)
Q Consensus 5 ~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~----g~~~~~~v~~~i~~~~G~~~e~~ 58 (122)
-|...++..-..|+ +..++..+..+++++- +.+|...|++.|.+..+-++++.
T Consensus 30 ~c~~~~~~~~L~m~-lvd~e~~~D~~k~~fyy~a~~rvDFR~Lvr~L~~~f~~RIem~ 86 (88)
T PF04468_consen 30 FCRELVKELGLPMK-LVDVEYQFDGSKLTFYYTAESRVDFRELVRDLAREFKTRIEMR 86 (88)
T ss_pred HHHHHHHHcCCCeE-EEEEEEEcCCCEEEEEEEeCCcCcHHHHHHHHHHHhCceEEEE
Confidence 35555554422222 4578888999999983 45899999999986666666553
No 33
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=44.65 E-value=50 Score=21.39 Aligned_cols=22 Identities=9% Similarity=0.308 Sum_probs=19.2
Q ss_pred hcCCCceEEEEEcCCcEEEEee
Q 037689 15 SKFKGVEKFTTDMNKHRVVVTG 36 (122)
Q Consensus 15 ~~~~GV~~v~vd~~~~kv~V~g 36 (122)
...+|++.++++++++++.|++
T Consensus 37 as~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 37 ASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EecCCceEEEEecccceEEEec
Confidence 3468999999999999999975
No 34
>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=43.65 E-value=25 Score=22.24 Aligned_cols=21 Identities=24% Similarity=0.354 Sum_probs=17.4
Q ss_pred HHHHHHHhcCCCceEEEEEcC
Q 037689 8 RTVARAISKFKGVEKFTTDMN 28 (122)
Q Consensus 8 ~~I~k~l~~~~GV~~v~vd~~ 28 (122)
..++.+|..++|+.++.+++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 457888999999999988864
No 35
>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=43.61 E-value=81 Score=19.77 Aligned_cols=37 Identities=19% Similarity=0.258 Sum_probs=27.6
Q ss_pred HHHHHhcCCCceEEEEEcCCcEEEEe--ecCCHHHHHHHHH
Q 037689 10 VARAISKFKGVEKFTTDMNKHRVVVT--GRIDPQKVLKKLK 48 (122)
Q Consensus 10 I~k~l~~~~GV~~v~vd~~~~kv~V~--g~~~~~~v~~~i~ 48 (122)
+-+.|-.++||.+|-+. ..=|+|+ ...+++.|...|.
T Consensus 39 LA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~ 77 (87)
T PF08712_consen 39 LAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIR 77 (87)
T ss_dssp HHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHH
T ss_pred HHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHH
Confidence 44567799999887766 6778886 4588999888776
No 36
>TIGR00401 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens.
Probab=42.02 E-value=21 Score=25.01 Aligned_cols=28 Identities=14% Similarity=0.093 Sum_probs=24.1
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCcE
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~k 31 (122)
.||=+-++..+.+++||.++.+-+..+.
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~ 34 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGY 34 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCC
Confidence 5899999999999999999998776553
No 37
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=40.74 E-value=28 Score=24.49 Aligned_cols=27 Identities=19% Similarity=0.224 Sum_probs=24.1
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCc
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKH 30 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~ 30 (122)
.||=+.++..+.+++||.++.+-+..+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG 33 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGG 33 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESS
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCC
Confidence 489999999999999999999987665
No 38
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=40.03 E-value=1e+02 Score=21.46 Aligned_cols=44 Identities=16% Similarity=0.379 Sum_probs=29.3
Q ss_pred CchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEEec
Q 037689 2 YCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (122)
Q Consensus 2 ~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~~~ 59 (122)
-|..|+..|..+ ||..|-+- ..+.+...-.+.++ ++|..++-++
T Consensus 96 PC~~Ca~ai~~a-----gI~~Vvy~--------~~~~~~~~~~~~l~-~~gi~v~~~~ 139 (151)
T TIGR02571 96 PCLQCTKSIIQA-----GIKKIYYA--------QDYHNHPYAIELFE-QAGVELKKVP 139 (151)
T ss_pred CcHHHHHHHHHh-----CCCEEEEc--------cCCCCcHHHHHHHH-HCCCEEEEeC
Confidence 488999988875 77766442 12222334567787 8998888775
No 39
>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=39.07 E-value=79 Score=18.30 Aligned_cols=47 Identities=13% Similarity=0.227 Sum_probs=31.9
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEe--ecCCHHHHHHHHHhhcCCceEEe
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVT--GRIDPQKVLKKLKKKTGKKVEIV 58 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~--g~~~~~~v~~~i~~~~G~~~e~~ 58 (122)
+.|+.-.-+++++| ++..- +.+.|. .......|..-++ +.|++++..
T Consensus 7 ~~CP~P~l~~k~al-~~~~g---------~~l~v~~d~~~s~~~i~~~~~-~~G~~~~~~ 55 (67)
T cd03421 7 LACPQPVIKTKKAL-ELEAG---------GEIEVLVDNEVAKENVSRFAE-SRGYEVSVE 55 (67)
T ss_pred CCCCHHHHHHHHHH-hcCCC---------CEEEEEEcChhHHHHHHHHHH-HcCCEEEEE
Confidence 46888889999999 65432 233332 3345578888887 999998544
No 40
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=38.87 E-value=61 Score=25.16 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=24.4
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCcE
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~k 31 (122)
.||=+-++..+.+++||.++.+-+..+.
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~ 161 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGD 161 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCC
Confidence 5899999999999999999999876653
No 41
>PRK11023 outer membrane lipoprotein; Provisional
Probab=38.58 E-value=1e+02 Score=22.16 Aligned_cols=39 Identities=10% Similarity=0.159 Sum_probs=25.7
Q ss_pred HHHHHHHHhcCCCce--EEEEEcCCcEEEEeecCCHHHHHH
Q 037689 7 ERTVARAISKFKGVE--KFTTDMNKHRVVVTGRIDPQKVLK 45 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~--~v~vd~~~~kv~V~g~~~~~~v~~ 45 (122)
..+|+.+|..-+++. .++|.-..+.|++.|.++.++...
T Consensus 129 t~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~~ 169 (191)
T PRK11023 129 TTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAKA 169 (191)
T ss_pred HHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHHH
Confidence 457777777666655 444555688888888876655433
No 42
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=38.14 E-value=42 Score=19.48 Aligned_cols=19 Identities=21% Similarity=0.330 Sum_probs=15.1
Q ss_pred HHHHHHHHhcCCCceEEEE
Q 037689 7 ERTVARAISKFKGVEKFTT 25 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~v 25 (122)
-..+-+.|++++||.+|.+
T Consensus 56 l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 56 IDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHhcCCCeEEEEE
Confidence 3567788999999988864
No 43
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=37.94 E-value=1.5e+02 Score=21.17 Aligned_cols=61 Identities=31% Similarity=0.508 Sum_probs=36.0
Q ss_pred CchhHHHHHH------------HHHhcC------CCceEEEEEcCCcEEE-Ee--ec---C-CHHHHHHHHHhhcCCceE
Q 037689 2 YCNACERTVA------------RAISKF------KGVEKFTTDMNKHRVV-VT--GR---I-DPQKVLKKLKKKTGKKVE 56 (122)
Q Consensus 2 ~C~~C~~~I~------------k~l~~~------~GV~~v~vd~~~~kv~-V~--g~---~-~~~~v~~~i~~~~G~~~e 56 (122)
-|+.|.++++ ++|.++ .++.-.+.=....++. |. |. + ..-+..++++++.|++++
T Consensus 15 lC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l~~~lgk~Ve 94 (166)
T PRK06418 15 LCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKALSRKLGKKVR 94 (166)
T ss_pred cChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHHHHHhCCcEE
Confidence 4899988764 555555 3433222222235544 32 33 1 123567778778999999
Q ss_pred EecCCC
Q 037689 57 IVDNNN 62 (122)
Q Consensus 57 ~~~~~~ 62 (122)
++++.+
T Consensus 95 vVE~s~ 100 (166)
T PRK06418 95 VVEKTN 100 (166)
T ss_pred EEEcCC
Confidence 998755
No 44
>PRK09577 multidrug efflux protein; Reviewed
Probab=37.75 E-value=1.1e+02 Score=27.90 Aligned_cols=46 Identities=11% Similarity=0.115 Sum_probs=35.5
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCcEEEEe--------ecCCHHHHHHHHHhhcCC
Q 037689 7 ERTVARAISKFKGVEKFTTDMNKHRVVVT--------GRIDPQKVLKKLKKKTGK 53 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~~~~kv~V~--------g~~~~~~v~~~i~~~~G~ 53 (122)
+..|+..|++++||.+|++.-....+.|. -.++..+|.++|+ ..+.
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~-~~n~ 211 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVR-AHNA 211 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHH-HhCC
Confidence 35789999999999999998765556663 2378889999997 6543
No 45
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=37.64 E-value=40 Score=22.45 Aligned_cols=21 Identities=24% Similarity=0.463 Sum_probs=17.6
Q ss_pred HHHHHHHHhcCCCceEEEEEc
Q 037689 7 ERTVARAISKFKGVEKFTTDM 27 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~ 27 (122)
...++.+|..++||..++|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 467899999999999887764
No 46
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=37.61 E-value=97 Score=28.18 Aligned_cols=42 Identities=10% Similarity=0.185 Sum_probs=33.3
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCcEEEEe--------ecCCHHHHHHHHH
Q 037689 7 ERTVARAISKFKGVEKFTTDMNKHRVVVT--------GRIDPQKVLKKLK 48 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~~~~kv~V~--------g~~~~~~v~~~i~ 48 (122)
+..++..|++++||.+|++.-....+.|. -.++..+|..+|+
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~ 208 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIE 208 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 46788999999999999998765556664 1378888999997
No 47
>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=36.93 E-value=38 Score=21.59 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=17.2
Q ss_pred HHHHHHHHhcCCCceEEEEE
Q 037689 7 ERTVARAISKFKGVEKFTTD 26 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd 26 (122)
...|+.+|++++||+++++-
T Consensus 64 td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 64 TEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred hHHHHHHHhcCCCccEEEEE
Confidence 45789999999999999875
No 48
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=36.15 E-value=75 Score=26.94 Aligned_cols=39 Identities=26% Similarity=0.394 Sum_probs=31.8
Q ss_pred HhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCce
Q 037689 14 ISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKV 55 (122)
Q Consensus 14 l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~ 55 (122)
|..|.+| +.+|..+++|+|.+-+...+|.+.|. +.|+..
T Consensus 110 L~~ln~V--l~vD~~~~tVtV~AG~~l~~L~~~L~-~~Glal 148 (541)
T TIGR01676 110 LALMDKV--LEVDEEKKRVRVQAGIRVQQLVDAIK-EYGITL 148 (541)
T ss_pred hhhCCCC--EEEcCCCCEEEEcCCCCHHHHHHHHH-HcCCEe
Confidence 4456666 46788899999998899999999998 899765
No 49
>PRK11023 outer membrane lipoprotein; Provisional
Probab=35.84 E-value=96 Score=22.28 Aligned_cols=39 Identities=21% Similarity=0.311 Sum_probs=28.2
Q ss_pred HHHHHHHHhcCCCce---EEEEEcCCcEEEEeecCCHHHHHH
Q 037689 7 ERTVARAISKFKGVE---KFTTDMNKHRVVVTGRIDPQKVLK 45 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~---~v~vd~~~~kv~V~g~~~~~~v~~ 45 (122)
+.+|+.+|..-+++. .+.|....+.|+++|.++.+....
T Consensus 51 ~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~ 92 (191)
T PRK11023 51 ELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSE 92 (191)
T ss_pred HHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHH
Confidence 567888887766663 577778899999999876544433
No 50
>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=35.73 E-value=53 Score=20.34 Aligned_cols=22 Identities=18% Similarity=0.419 Sum_probs=17.2
Q ss_pred cCCcEEEEeecCCHHHHHHHHH
Q 037689 27 MNKHRVVVTGRIDPQKVLKKLK 48 (122)
Q Consensus 27 ~~~~kv~V~g~~~~~~v~~~i~ 48 (122)
+.+++++++|.-+.+++..+++
T Consensus 55 F~sGki~itGaks~~~~~~a~~ 76 (86)
T PF00352_consen 55 FSSGKIVITGAKSEEEAKKAIE 76 (86)
T ss_dssp ETTSEEEEEEESSHHHHHHHHH
T ss_pred EcCCEEEEEecCCHHHHHHHHH
Confidence 5789999999877777766664
No 51
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=35.69 E-value=33 Score=23.78 Aligned_cols=42 Identities=17% Similarity=0.288 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCc-EEEEeecCCHHHHHHHHH
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKH-RVVVTGRIDPQKVLKKLK 48 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~-kv~V~g~~~~~~v~~~i~ 48 (122)
++|.+++-++|+++ .-|+-+...+ +++-.|..+.++|...|.
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 45666666666555 3455666554 455678889999988886
No 52
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=34.08 E-value=1.4e+02 Score=19.70 Aligned_cols=40 Identities=25% Similarity=0.431 Sum_probs=28.8
Q ss_pred cCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEE
Q 037689 16 KFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEI 57 (122)
Q Consensus 16 ~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~ 57 (122)
+..|+..+++. ..+.++|-|+--.+++++.+. ++|..+..
T Consensus 39 Rt~GirqfEi~-n~G~~RI~gYk~se~~~~~f~-slG~~~K~ 78 (103)
T PF09158_consen 39 RTKGIRQFEIR-NKGEFRIFGYKMSEEIIKKFT-SLGMEVKQ 78 (103)
T ss_dssp EETTEEEEEEE-TTSEEEEEEES--HHHHHHHH-HTT-EEEE
T ss_pred ccCceeEEEEe-cCCcEEEEEEcCCHHHHHHHH-hcCcEEEE
Confidence 34677777775 467788888888899999998 99988766
No 53
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=31.74 E-value=86 Score=18.87 Aligned_cols=27 Identities=15% Similarity=0.267 Sum_probs=18.1
Q ss_pred CchhHHHHHHHHHhcC----CCceEEEEEcCC
Q 037689 2 YCNACERTVARAISKF----KGVEKFTTDMNK 29 (122)
Q Consensus 2 ~C~~C~~~I~k~l~~~----~GV~~v~vd~~~ 29 (122)
.|+.|. ++.+.|..+ .||.-..+|...
T Consensus 10 ~C~~C~-~a~~~L~~l~~~~~~i~~~~idi~~ 40 (85)
T PRK11200 10 GCPYCV-RAKELAEKLSEERDDFDYRYVDIHA 40 (85)
T ss_pred CChhHH-HHHHHHHhhcccccCCcEEEEECCC
Confidence 599998 556667765 577666666543
No 54
>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=31.45 E-value=88 Score=20.76 Aligned_cols=29 Identities=31% Similarity=0.519 Sum_probs=24.6
Q ss_pred EEEeecCCHHHHHHHHHhhcCCceEEecCC
Q 037689 32 VVVTGRIDPQKVLKKLKKKTGKKVEIVDNN 61 (122)
Q Consensus 32 v~V~g~~~~~~v~~~i~~~~G~~~e~~~~~ 61 (122)
|.|+|+.+...+++.++ +.|+++.++...
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 44578889999999998 899999998776
No 55
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=30.64 E-value=63 Score=23.58 Aligned_cols=21 Identities=29% Similarity=0.474 Sum_probs=17.9
Q ss_pred HHHHHHHHhcCCCceEEEEEc
Q 037689 7 ERTVARAISKFKGVEKFTTDM 27 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~ 27 (122)
+..+++.|+.++||..++|.+
T Consensus 117 e~eL~~tI~~i~gV~~A~V~l 137 (206)
T PF01514_consen 117 EGELERTIESIDGVESARVHL 137 (206)
T ss_dssp HHHHHHHHTTSTTEEEEEEEE
T ss_pred HHHHHHHHHcCCCeeEEEEEE
Confidence 456889999999999998874
No 56
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=30.45 E-value=74 Score=18.24 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=15.6
Q ss_pred HHHHHHHhc-----CCCceEEEEEcCCcEEEE
Q 037689 8 RTVARAISK-----FKGVEKFTTDMNKHRVVV 34 (122)
Q Consensus 8 ~~I~k~l~~-----~~GV~~v~vd~~~~kv~V 34 (122)
+++++.|.+ ++||..|.+-...+++.+
T Consensus 2 kk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~ 33 (58)
T PF01849_consen 2 KKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFV 33 (58)
T ss_dssp ------GHHCT-EEETTEEEEEEEETTTEEEE
T ss_pred HHHHHHHHHcCCcccCCcEEEEEEECCceEEE
Confidence 345555544 478999998888877655
No 57
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=30.13 E-value=62 Score=27.09 Aligned_cols=34 Identities=21% Similarity=0.253 Sum_probs=29.3
Q ss_pred EEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEE
Q 037689 23 FTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEI 57 (122)
Q Consensus 23 v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~ 57 (122)
+++|.+..+|||..-+...+|.+.++ +.|+.+..
T Consensus 105 v~~dpe~~tvTV~aGirlrQLie~~~-~~GlsL~~ 138 (518)
T KOG4730|consen 105 VEFDPELKTVTVQAGIRLRQLIEELA-KLGLSLPN 138 (518)
T ss_pred eeeCchhceEEeccCcCHHHHHHHHH-hcCccccC
Confidence 56688889999998899999999998 99997654
No 58
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=29.26 E-value=2.2e+02 Score=20.58 Aligned_cols=51 Identities=18% Similarity=0.237 Sum_probs=35.2
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEEec
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~~~ 59 (122)
+.|+.-.-+.+++|.+++.-+.+ +|.+......+.|.+-++ ..||+++...
T Consensus 6 l~CP~Pvi~tKkal~~l~~g~~L-------~VlvD~~~a~~nV~~~~~-~~G~~v~~~e 56 (194)
T TIGR03527 6 LACPQPVILTKKALDELGEEGVL-------TVIVDNEAAKENVSKFAT-SLGYEVEVEE 56 (194)
T ss_pred CCCCHHHHHHHHHHHcCCCCCEE-------EEEECCccHHHHHHHHHH-HcCCEEEEEE
Confidence 36999999999999998621111 222333456677888887 9999987543
No 59
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=29.00 E-value=55 Score=20.98 Aligned_cols=20 Identities=20% Similarity=0.446 Sum_probs=16.9
Q ss_pred HHHHHHHHhcCCCceEEEEE
Q 037689 7 ERTVARAISKFKGVEKFTTD 26 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd 26 (122)
-..++++|+++.||.++++-
T Consensus 64 td~~ee~l~~vegV~sveve 83 (88)
T COG2092 64 TDALEEALEEVEGVESVEVE 83 (88)
T ss_pred cHHHHHHHhhccCcceEEEE
Confidence 35789999999999998864
No 60
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=28.99 E-value=1.7e+02 Score=26.73 Aligned_cols=43 Identities=16% Similarity=0.196 Sum_probs=33.6
Q ss_pred HHHHHHHhcCCCceEEEEEcCCcEEEEe--------ecCCHHHHHHHHHhhc
Q 037689 8 RTVARAISKFKGVEKFTTDMNKHRVVVT--------GRIDPQKVLKKLKKKT 51 (122)
Q Consensus 8 ~~I~k~l~~~~GV~~v~vd~~~~kv~V~--------g~~~~~~v~~~i~~~~ 51 (122)
+.++..|++++||.+|++.-....+.|. -.++..+|..+|+ ..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~-~~ 210 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIK-AQ 210 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHH-Hh
Confidence 5688999999999999988665556664 1378888888887 44
No 61
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=28.88 E-value=61 Score=20.65 Aligned_cols=19 Identities=26% Similarity=0.480 Sum_probs=16.4
Q ss_pred HHHHHHHhcCCCceEEEEE
Q 037689 8 RTVARAISKFKGVEKFTTD 26 (122)
Q Consensus 8 ~~I~k~l~~~~GV~~v~vd 26 (122)
..++.++++++||+++++-
T Consensus 65 d~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 65 EPVEEAFANVEGVESVEVE 83 (88)
T ss_pred HHHHHHHhccCCCcEEEEE
Confidence 4688899999999999875
No 62
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=28.65 E-value=1.7e+02 Score=21.50 Aligned_cols=27 Identities=30% Similarity=0.401 Sum_probs=22.5
Q ss_pred HHHHHHhcCCCceEEEEEcCCcEEEEee
Q 037689 9 TVARAISKFKGVEKFTTDMNKHRVVVTG 36 (122)
Q Consensus 9 ~I~k~l~~~~GV~~v~vd~~~~kv~V~g 36 (122)
.+.+.|....|+ .+.+|..++.|+|..
T Consensus 28 ~v~k~ie~~~~~-~~~iD~~~~~V~i~~ 54 (194)
T COG1094 28 EVKKAIEEKTGV-KLRIDSKTGSVTIRT 54 (194)
T ss_pred cchHHHHhhcCe-EEEEECCCCeEEEEe
Confidence 466778888888 799999999999963
No 63
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=28.56 E-value=1.5e+02 Score=20.27 Aligned_cols=45 Identities=20% Similarity=0.288 Sum_probs=26.3
Q ss_pred HHHHHHHhcCC-CceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcC
Q 037689 8 RTVARAISKFK-GVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTG 52 (122)
Q Consensus 8 ~~I~k~l~~~~-GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G 52 (122)
..|.+.|.+.. +...+.|....+.|++.|.+.......++...+|
T Consensus 29 ~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~~aa~ 74 (147)
T PRK11198 29 DALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKILLAVG 74 (147)
T ss_pred HHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHHHHhc
Confidence 45666665531 3444566667999999998654433333332444
No 64
>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=27.80 E-value=74 Score=22.78 Aligned_cols=20 Identities=10% Similarity=0.275 Sum_probs=16.8
Q ss_pred HHHHHHHhcCCCceEEEEEc
Q 037689 8 RTVARAISKFKGVEKFTTDM 27 (122)
Q Consensus 8 ~~I~k~l~~~~GV~~v~vd~ 27 (122)
..|+.+|..++||.+|.|++
T Consensus 134 ~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 134 EDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred HHHHHHHHhCCCceeEEEEE
Confidence 55889999999999888775
No 65
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=27.63 E-value=1.7e+02 Score=22.71 Aligned_cols=39 Identities=21% Similarity=0.174 Sum_probs=30.3
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCc
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKK 54 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~ 54 (122)
..|...+++.+.+++||.++++- +.++-++.+++..|+.
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~~------------sre~~l~~L~~~lg~~ 109 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRFI------------SREEALKELQPWLGFG 109 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEEe------------CHHHHHHHHHHHcCch
Confidence 46788899999999999877654 6677777777677764
No 66
>PHA02588 cd deoxycytidylate deaminase; Provisional
Probab=27.51 E-value=2.3e+02 Score=20.04 Aligned_cols=45 Identities=20% Similarity=0.317 Sum_probs=27.9
Q ss_pred CchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEEec
Q 037689 2 YCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (122)
Q Consensus 2 ~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~~~ 59 (122)
-|..|+..|..+ ||..|.+-.. ...........|+ +.|.+++.++
T Consensus 110 PC~~Ca~aI~~~-----gI~rVvy~~~-------~~~~~~~~~~~L~-~~Gi~v~~~~ 154 (168)
T PHA02588 110 PCPDCAKAIAQS-----GIKKLVYCEK-------YDRNGPGWDDILR-KSGIEVIQIP 154 (168)
T ss_pred CcHHHHHHHHHh-----CCCEEEEeec-------cCCCcHHHHHHHH-HCCCEEEEeC
Confidence 388899888664 7766544321 0112334677887 8898877653
No 67
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=27.49 E-value=41 Score=24.29 Aligned_cols=28 Identities=14% Similarity=0.166 Sum_probs=24.2
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCcE
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~k 31 (122)
.||=+-+++.+.+++||.++.+-...+.
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG~ 40 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGGH 40 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCCC
Confidence 5788999999999999999998776654
No 68
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=27.49 E-value=61 Score=23.59 Aligned_cols=29 Identities=21% Similarity=0.373 Sum_probs=20.6
Q ss_pred HHHHHHHHHhcCCCceEEE--EEcCCcEEEE
Q 037689 6 CERTVARAISKFKGVEKFT--TDMNKHRVVV 34 (122)
Q Consensus 6 C~~~I~k~l~~~~GV~~v~--vd~~~~kv~V 34 (122)
=+.+++..|+++.||..|+ |.+.++.-.|
T Consensus 62 lE~~L~~iL~~I~GvG~V~VmItl~s~~e~v 92 (186)
T TIGR02830 62 YENELKEILEKIEGVGDVTVMVNLDSSEEKV 92 (186)
T ss_pred HHHHHHHHHHhccCcceeEEEEEECCCceEE
Confidence 3678899999999988665 4455555444
No 69
>PRK11018 hypothetical protein; Provisional
Probab=27.15 E-value=1.5e+02 Score=17.95 Aligned_cols=51 Identities=16% Similarity=0.112 Sum_probs=34.2
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEEec
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~~~ 59 (122)
+.|+.-.-+.+++|.+++.-+.+ .|.++.......|..-++ +.|+++....
T Consensus 16 ~~CP~Pvl~~kk~l~~l~~G~~L-------~V~~d~~~a~~di~~~~~-~~G~~v~~~~ 66 (78)
T PRK11018 16 EPCPYPAVATLEALPQLKKGEIL-------EVVSDCPQSINNIPLDAR-NHGYTVLDIQ 66 (78)
T ss_pred CcCCHHHHHHHHHHHhCCCCCEE-------EEEeCCccHHHHHHHHHH-HcCCEEEEEE
Confidence 35888999999999998632222 122223345677888887 9999886543
No 70
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=27.14 E-value=1.8e+02 Score=26.46 Aligned_cols=41 Identities=15% Similarity=0.260 Sum_probs=33.1
Q ss_pred HHHHHHHhcCCCceEEEEEcCCcEEEEe--------ecCCHHHHHHHHH
Q 037689 8 RTVARAISKFKGVEKFTTDMNKHRVVVT--------GRIDPQKVLKKLK 48 (122)
Q Consensus 8 ~~I~k~l~~~~GV~~v~vd~~~~kv~V~--------g~~~~~~v~~~i~ 48 (122)
..++..|++++||.+|++.-....+.|. -.+++.+|..+|+
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~ 208 (1044)
T TIGR00915 160 SNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQ 208 (1044)
T ss_pred HHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 5688999999999999998775556664 1378889999997
No 71
>PRK11670 antiporter inner membrane protein; Provisional
Probab=27.10 E-value=2.1e+02 Score=22.72 Aligned_cols=54 Identities=17% Similarity=0.322 Sum_probs=36.5
Q ss_pred HHHHHHHhcCCCceEEEEEcCC------------------cEEEEe---e---c-CCHHHHHHHHHhhcCCceEEecCCC
Q 037689 8 RTVARAISKFKGVEKFTTDMNK------------------HRVVVT---G---R-IDPQKVLKKLKKKTGKKVEIVDNNN 62 (122)
Q Consensus 8 ~~I~k~l~~~~GV~~v~vd~~~------------------~kv~V~---g---~-~~~~~v~~~i~~~~G~~~e~~~~~~ 62 (122)
..++++|+.++||..+.+.+.. +.+.|. | . ....-|...+. +.|+++-++....
T Consensus 68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avNLA~aLA-~~G~rVlLID~D~ 146 (369)
T PRK11670 68 EQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVNLALALA-AEGAKVGILDADI 146 (369)
T ss_pred HHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHHHHHHHH-HCCCcEEEEeCCC
Confidence 5688899999999877765432 223343 2 2 23456777887 8999998886654
No 72
>PRK05412 putative nucleotide-binding protein; Reviewed
Probab=25.90 E-value=2.2e+02 Score=20.34 Aligned_cols=45 Identities=27% Similarity=0.381 Sum_probs=30.9
Q ss_pred HHHHHHHHHhcCCCceEEEEEcCCcEEEEeec--CCHHHHHHHHHhhcCC
Q 037689 6 CERTVARAISKFKGVEKFTTDMNKHRVVVTGR--IDPQKVLKKLKKKTGK 53 (122)
Q Consensus 6 C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~--~~~~~v~~~i~~~~G~ 53 (122)
-+++|-+.+...+ . .|.+.....+|+|+|. .+.+++...|+ ...+
T Consensus 104 ~AKkIvK~IKd~k-l-KVqa~IQGd~vRVtgKkrDDLQ~viallk-~~d~ 150 (161)
T PRK05412 104 LAKKIVKLIKDSK-L-KVQAQIQGDQVRVTGKKRDDLQAVIALLR-KADL 150 (161)
T ss_pred HHHHHHHHHHhcC-C-ceeEEecCcEEEEecCCHhHHHHHHHHHH-hccC
Confidence 3566777765543 3 3777788889999884 56788888886 5543
No 73
>PF01565 FAD_binding_4: FAD binding domain This is only a subset of the Pfam family; InterPro: IPR006094 Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. One of the enzymes Vanillyl-alcohol oxidase (VAO, 1.1.3.38 from EC) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 []. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging from aromatic amines to 4-alkylphenols. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZR6_A 3HSU_A 2AXR_A 3D2J_A 3D2H_A 3FW9_A 3FW8_A 3FW7_A 3GSY_A 3FWA_A ....
Probab=25.56 E-value=1e+02 Score=20.12 Aligned_cols=31 Identities=16% Similarity=0.153 Sum_probs=26.0
Q ss_pred EEEEcCCcEEEEeecCCHHHHHHHHHhhcCCc
Q 037689 23 FTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKK 54 (122)
Q Consensus 23 v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~ 54 (122)
+++|.....++|..-+...+|.+.+. +.|+.
T Consensus 57 ~~id~~~~~v~v~aG~~~~~l~~~l~-~~g~~ 87 (139)
T PF01565_consen 57 IEIDPENGTVTVGAGVTWGDLYEALA-PRGLM 87 (139)
T ss_dssp EEEETTTTEEEEETTSBHHHHHHHHH-HHTEE
T ss_pred ccccccceeEEEeccccchhcccccc-ccccc
Confidence 67888899999998899999999997 66653
No 74
>PF13193 AMP-binding_C: AMP-binding enzyme C-terminal domain; PDB: 3L8C_B 2VSQ_A 3R44_A 3RG2_B 3A9U_A 3A9V_A 3NI2_A 1V26_B 1ULT_B 1V25_B ....
Probab=25.55 E-value=82 Score=18.33 Aligned_cols=37 Identities=19% Similarity=0.246 Sum_probs=22.8
Q ss_pred HHHHHhcCCCceEEEEEcC----Cc-EEE--EeecCCHHHHHHHHH
Q 037689 10 VARAISKFKGVEKFTTDMN----KH-RVV--VTGRIDPQKVLKKLK 48 (122)
Q Consensus 10 I~k~l~~~~GV~~v~vd~~----~~-kv~--V~g~~~~~~v~~~i~ 48 (122)
|+.+|.+.+||.++.|=.. .+ .+. |.. +.++|.+.++
T Consensus 2 IE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv~--~~~~i~~~~~ 45 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAVVGVPDEDWGERLVAFVVL--DEEEIRDHLR 45 (73)
T ss_dssp HHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEEE--HHHHHHHHHH
T ss_pred HHHHHhcCCCccEEEEEEEEcccccccceeEEEe--eecccccchh
Confidence 7899999999887665321 12 221 123 4467777776
No 75
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=25.24 E-value=2e+02 Score=18.66 Aligned_cols=41 Identities=22% Similarity=0.359 Sum_probs=27.7
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCcEEEE-eecCCHHHHHHHHH
Q 037689 7 ERTVARAISKFKGVEKFTTDMNKHRVVV-TGRIDPQKVLKKLK 48 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~~~~kv~V-~g~~~~~~v~~~i~ 48 (122)
-..|.++|..++|++--.-+.. +|+.| ....+.+.++..++
T Consensus 20 l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie 61 (94)
T COG3062 20 LSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIE 61 (94)
T ss_pred HHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHH
Confidence 3578899999999965555555 66655 34456666766665
No 76
>PRK11282 glcE glycolate oxidase FAD binding subunit; Provisional
Probab=25.06 E-value=1.4e+02 Score=23.82 Aligned_cols=37 Identities=11% Similarity=0.197 Sum_probs=29.5
Q ss_pred hcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCc
Q 037689 15 SKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKK 54 (122)
Q Consensus 15 ~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~ 54 (122)
+++.+| +++|.....|+|..-+...+|.+.+. +.|+.
T Consensus 44 ~~ln~I--le~d~~~~~vtV~AG~~l~el~~~L~-~~G~~ 80 (352)
T PRK11282 44 RAHRGI--VSYDPTELVITARAGTPLAELEAALA-EAGQM 80 (352)
T ss_pred ccCCCc--EEEcCCCCEEEECCCCCHHHHHHHHH-HcCCe
Confidence 445555 36788889999988899999999998 88864
No 77
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=24.45 E-value=81 Score=24.03 Aligned_cols=20 Identities=25% Similarity=0.411 Sum_probs=16.2
Q ss_pred HHHHHHHHhcCCCceEEEEE
Q 037689 7 ERTVARAISKFKGVEKFTTD 26 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd 26 (122)
+..+++.|++|+||.+++|-
T Consensus 111 eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 111 EQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HHHHHHHHHhcCceEEEEEE
Confidence 56889999999998766554
No 78
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=23.91 E-value=26 Score=18.00 Aligned_cols=12 Identities=33% Similarity=0.465 Sum_probs=9.4
Q ss_pred ccCCCCCCCCCc
Q 037689 107 VVMMFSDENPNA 118 (122)
Q Consensus 107 ~~~~FsDeNpna 118 (122)
..++|-|||+|-
T Consensus 8 ~lhlfrde~vnf 19 (35)
T PF13216_consen 8 NLHLFRDEKVNF 19 (35)
T ss_pred EEEEeecCCccE
Confidence 357899999884
No 79
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=23.63 E-value=1.7e+02 Score=17.20 Aligned_cols=50 Identities=16% Similarity=0.163 Sum_probs=34.3
Q ss_pred CchhHHHHHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEEec
Q 037689 2 YCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (122)
Q Consensus 2 ~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~~~ 59 (122)
.|+.=.-+.+++|++++.-+.+ .|.++.......|..-++ ..|+++....
T Consensus 8 ~CP~Pvi~~kkal~~l~~G~~l-------~V~~d~~~s~~ni~~~~~-~~g~~v~~~~ 57 (69)
T cd03422 8 PCPYPAIATLEALPSLKPGEIL-------EVISDCPQSINNIPIDAR-NHGYKVLAIE 57 (69)
T ss_pred cCCHHHHHHHHHHHcCCCCCEE-------EEEecCchHHHHHHHHHH-HcCCEEEEEE
Confidence 5888888999999998632222 122233456777888887 9999986553
No 80
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=23.20 E-value=2.2e+02 Score=24.54 Aligned_cols=55 Identities=11% Similarity=0.148 Sum_probs=39.1
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCcEEEEee----cC---CHHHHHHHHHhhcCCceEEecCCC
Q 037689 7 ERTVARAISKFKGVEKFTTDMNKHRVVVTG----RI---DPQKVLKKLKKKTGKKVEIVDNNN 62 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~~~~kv~V~g----~~---~~~~v~~~i~~~~G~~~e~~~~~~ 62 (122)
...|++.+-.-.||.++.++..++.|.|.. .+ .-..+.+.. +++|++.+++...+
T Consensus 72 ~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~-~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 72 IEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREIT-AETGWTPKVVRTPP 133 (630)
T ss_pred HHHHHHhCCCcCCceeEEecCCCceEEEEEcCCeEEEecCcchHHHHH-HHhCCeeeEEecCC
Confidence 356666666668999999999999999862 22 233344445 49999998876655
No 81
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=22.85 E-value=95 Score=22.49 Aligned_cols=21 Identities=19% Similarity=0.377 Sum_probs=17.4
Q ss_pred HHHHHHHHhcCCCceEEEEEc
Q 037689 7 ERTVARAISKFKGVEKFTTDM 27 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~ 27 (122)
+..+++.|+.++||..++|.+
T Consensus 109 e~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 109 EQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHhcCCeeeeEEEE
Confidence 456788999999999888864
No 82
>PRK07334 threonine dehydratase; Provisional
Probab=22.72 E-value=2.2e+02 Score=22.77 Aligned_cols=51 Identities=14% Similarity=0.157 Sum_probs=30.7
Q ss_pred HHHHHHHHhcCCC-ceEEEEEcC-----CcEEEEe------ecCCHHHHHHHHHhhcCCceEEe
Q 037689 7 ERTVARAISKFKG-VEKFTTDMN-----KHRVVVT------GRIDPQKVLKKLKKKTGKKVEIV 58 (122)
Q Consensus 7 ~~~I~k~l~~~~G-V~~v~vd~~-----~~kv~V~------g~~~~~~v~~~i~~~~G~~~e~~ 58 (122)
-..|-+.|+..+. |.++..... .+...+. .....+.|+++|+ +.||+++++
T Consensus 340 L~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr-~~g~~~~~~ 402 (403)
T PRK07334 340 LARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALR-AAGFEARLV 402 (403)
T ss_pred HHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHH-HcCCeeEeC
Confidence 3456667766532 555554422 3443332 1234568899998 999999876
No 83
>TIGR01679 bact_FAD_ox FAD-linked oxidoreductase. This model represents a family of bacterial oxidoreductases with covalently linked FAD, closely related to two different eukaryotic oxidases, L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae.
Probab=21.86 E-value=1.8e+02 Score=23.51 Aligned_cols=38 Identities=18% Similarity=0.196 Sum_probs=29.8
Q ss_pred cCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceE
Q 037689 16 KFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVE 56 (122)
Q Consensus 16 ~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e 56 (122)
.+.+| +.+|..+++|+|.+-+...+|.+.+. +.|+...
T Consensus 59 ~l~~i--~~~d~~~~~v~v~aG~~l~~l~~~L~-~~G~~l~ 96 (419)
T TIGR01679 59 GLQGV--VDVDQPTGLATVEAGTRLGALGPQLA-QRGLGLE 96 (419)
T ss_pred HcCCc--eeecCCCCEEEEcCCCCHHHHHHHHH-HcCCccc
Confidence 34444 35777889999988899999999998 8998554
No 84
>PLN02465 L-galactono-1,4-lactone dehydrogenase
Probab=21.76 E-value=1.7e+02 Score=25.02 Aligned_cols=39 Identities=26% Similarity=0.357 Sum_probs=30.5
Q ss_pred cCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEE
Q 037689 16 KFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEI 57 (122)
Q Consensus 16 ~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~ 57 (122)
.+.+| +.+|...++|+|.+-+...+|.+.+. +.|.....
T Consensus 147 ~l~~I--l~vD~e~~~VtV~AG~~l~~L~~~L~-~~GLal~n 185 (573)
T PLN02465 147 LMDKV--LEVDKEKKRVTVQAGARVQQVVEALR-PHGLTLQN 185 (573)
T ss_pred CCCCc--EEEeCCCCEEEEccCCCHHHHHHHHH-HcCCEecc
Confidence 34444 36788888999998899999999998 89976554
No 85
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=21.56 E-value=1.9e+02 Score=20.74 Aligned_cols=48 Identities=17% Similarity=0.313 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCCceEEEEEcCCcEEEEe---ecCC---HHHHHHHHHhhcCCce
Q 037689 7 ERTVARAISKFKGVEKFTTDMNKHRVVVT---GRID---PQKVLKKLKKKTGKKV 55 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~~~~kv~V~---g~~~---~~~v~~~i~~~~G~~~ 55 (122)
+..|+..|+. +|-..+-|.+...++.|. ..++ ..+|...+.+.+|..+
T Consensus 137 E~~iE~llka-kGf~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~ 190 (196)
T PF12685_consen 137 EMEIENLLKA-KGFEDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPA 190 (196)
T ss_dssp HHHHHHHHHT-TS-SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-ST
T ss_pred HHHHHHHHHh-CCCCceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCc
Confidence 3456666655 699999999999998874 2343 4566777776777543
No 86
>PF04805 Pox_E10: E10-like protein conserved region; InterPro: IPR006890 This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process
Probab=21.13 E-value=84 Score=19.18 Aligned_cols=26 Identities=19% Similarity=0.296 Sum_probs=18.5
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEE
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTD 26 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd 26 (122)
|-|+.|.....+++++-.=..+-++|
T Consensus 16 LPC~~Cr~HA~~ai~kNNiMSs~DiN 41 (70)
T PF04805_consen 16 LPCPECRIHAKEAIQKNNIMSSNDIN 41 (70)
T ss_pred CCCHHHHHHHHHHHHhcCccccCCcc
Confidence 46999999999998876544444443
No 87
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=21.09 E-value=2.8e+02 Score=18.79 Aligned_cols=48 Identities=23% Similarity=0.394 Sum_probs=30.8
Q ss_pred HHHHHHhcCCCceEEEEEcCCcEEEEeecCCHHHHH----HHHHhhcCCceEE
Q 037689 9 TVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVL----KKLKKKTGKKVEI 57 (122)
Q Consensus 9 ~I~k~l~~~~GV~~v~vd~~~~kv~V~g~~~~~~v~----~~i~~~~G~~~e~ 57 (122)
.++..|..+ |...|+.=+.++-|.++...+++.|. +.|++..|+.+..
T Consensus 23 eLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v 74 (137)
T PF08002_consen 23 ELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPV 74 (137)
T ss_dssp HHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---E
T ss_pred HHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEE
Confidence 345666665 88999999999999998666766655 4555577887654
No 88
>TIGR01677 pln_FAD_oxido plant-specific FAD-dependent oxidoreductase. This model represents an uncharacterized plant-specific family of FAD-dependent oxidoreductases. At least seven distinct members are found in Arabidopsis thaliana. The family shows considerable sequence similarity to three different enzymes of ascorbic acid biosynthesis: L-galactono-1,4-lactone dehydrogenase (EC 1.3.2.3) from higher plants, D-arabinono-1,4-lactone oxidase (EC 1.1.3.37 from Saccharomyces cerevisiae, and L-gulonolactone oxidase (EC 1.1.3.8) from mouse, as well as to a bacterial sorbitol oxidase. The class of compound acted on by members of this family is unknown.
Probab=21.08 E-value=1.9e+02 Score=24.59 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=27.4
Q ss_pred EEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceEE
Q 037689 23 FTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEI 57 (122)
Q Consensus 23 v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e~ 57 (122)
+.+|..+.+|+|.+-+...+|.+.|. +.|+....
T Consensus 92 l~iD~~~~tVtV~AG~~l~~L~~~L~-~~Glal~~ 125 (557)
T TIGR01677 92 VAVDATAMTVTVESGMSLRELIVEAE-KAGLALPY 125 (557)
T ss_pred EEEeCCCCEEEECCCCcHHHHHHHHH-HcCCEecc
Confidence 56677778888888889999999998 88976544
No 89
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=20.99 E-value=1.5e+02 Score=27.03 Aligned_cols=42 Identities=7% Similarity=0.135 Sum_probs=31.8
Q ss_pred HHHHHHHHhcCCCceEEEEEcCC--cEEEEe--------ecCCHHHHHHHHH
Q 037689 7 ERTVARAISKFKGVEKFTTDMNK--HRVVVT--------GRIDPQKVLKKLK 48 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~~v~vd~~~--~kv~V~--------g~~~~~~v~~~i~ 48 (122)
+..|++.|.+++||..|+.+... ..+.|. -.+++++|...++
T Consensus 700 a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~~~~Glt~~~v~~~l~ 751 (1051)
T TIGR00914 700 AEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKAARYGLTVGDVQDTVA 751 (1051)
T ss_pred HHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 46789999999999999988654 344443 1278888888886
No 90
>KOG1635 consensus Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=20.79 E-value=93 Score=22.65 Aligned_cols=28 Identities=18% Similarity=0.186 Sum_probs=24.5
Q ss_pred hhHHHHHHHHHhcCCCceEEEEEcCCcE
Q 037689 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (122)
Q Consensus 4 ~~C~~~I~k~l~~~~GV~~v~vd~~~~k 31 (122)
.+|-+.++.+..+++||...+|-++.++
T Consensus 31 ~GCFWg~E~a~~~l~gV~~T~vGYagG~ 58 (191)
T KOG1635|consen 31 AGCFWGVELAYQRLPGVVRTEVGYAGGI 58 (191)
T ss_pred ccchhhHHHHHhhcCCeEEEeecccCCc
Confidence 4799999999999999999999887664
No 91
>PRK10568 periplasmic protein; Provisional
Probab=20.76 E-value=2.4e+02 Score=20.41 Aligned_cols=33 Identities=12% Similarity=0.322 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCCce--EEEEEcCCcEEEEeecCC
Q 037689 7 ERTVARAISKFKGVE--KFTTDMNKHRVVVTGRID 39 (122)
Q Consensus 7 ~~~I~k~l~~~~GV~--~v~vd~~~~kv~V~g~~~ 39 (122)
..+|+.+|..-+++. .+.|....+.|++.|.+.
T Consensus 62 ~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~V~ 96 (203)
T PRK10568 62 TAKVKAALVDHDNIKSTDISVKTHQKVVTLSGFVE 96 (203)
T ss_pred HHHHHHHHHhCCCCCCCceEEEEECCEEEEEEEeC
Confidence 467778877666654 566777899999999865
No 92
>PF13383 Methyltransf_22: Methyltransferase domain
Probab=20.71 E-value=1.5e+02 Score=22.25 Aligned_cols=47 Identities=26% Similarity=0.366 Sum_probs=30.2
Q ss_pred CCchhHHHHHHHHHhcCCCceEEEEEcCCcEEEE--eecC----CHHHHHHHHHhhcCCceEEe
Q 037689 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVV--TGRI----DPQKVLKKLKKKTGKKVEIV 58 (122)
Q Consensus 1 m~C~~C~~~I~k~l~~~~GV~~v~vd~~~~kv~V--~g~~----~~~~v~~~i~~~~G~~~e~~ 58 (122)
|+|++|+..+-..+.. .|+ .++.| .+.. ...++++.|+ +.||+.--.
T Consensus 173 iDIEG~Ew~~L~~~l~-~~~---------~Qi~iEiH~~~~~~~~~~~~l~~l~-~~gfr~F~~ 225 (242)
T PF13383_consen 173 IDIEGAEWTVLEPLLE-SGV---------CQILIEIHGWPSEHREWYKLLQELE-KAGFRLFNV 225 (242)
T ss_pred EEcCccHHHHHHHHHh-cCC---------cEEEEEEEeCccchhHHHHHHHHHH-HCCcEEEEe
Confidence 6889999888776643 244 34443 3321 2346899998 999875444
No 93
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=20.68 E-value=1.1e+02 Score=19.36 Aligned_cols=20 Identities=25% Similarity=0.370 Sum_probs=16.5
Q ss_pred HHHHHHHhcCCCceEEEEEc
Q 037689 8 RTVARAISKFKGVEKFTTDM 27 (122)
Q Consensus 8 ~~I~k~l~~~~GV~~v~vd~ 27 (122)
..++.++++.+||+++++--
T Consensus 65 d~lee~i~~~d~VqsveI~~ 84 (88)
T cd00292 65 DELEEAISEEDGVQSVDVEA 84 (88)
T ss_pred HHHHHHHhccCCceEEEEEE
Confidence 46788899999999998753
No 94
>PF10934 DUF2634: Protein of unknown function (DUF2634); InterPro: IPR020288 This entry is represented by the Bacteriophage EJ-1, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Bacteriophage EJ-1, Orf60 function has not been characterised. It has been shown to be simialr to XkdS (P54331 from SWISSPROT), which is encoded on a phage-like element (prophage) of PSBX found in Bacillus subtilis.
Probab=20.53 E-value=2e+02 Score=18.80 Aligned_cols=30 Identities=23% Similarity=0.465 Sum_probs=23.4
Q ss_pred HHHHHHHHH---hcCCCceEEEEEcCCcEEEEe
Q 037689 6 CERTVARAI---SKFKGVEKFTTDMNKHRVVVT 35 (122)
Q Consensus 6 C~~~I~k~l---~~~~GV~~v~vd~~~~kv~V~ 35 (122)
-.+.|+.+| ..+.+|.++.+.....++.|+
T Consensus 70 i~r~I~EaL~~d~rI~~V~~f~f~~~~~~l~v~ 102 (112)
T PF10934_consen 70 IEREIEEALLQDPRITSVENFSFEWEGDSLYVS 102 (112)
T ss_pred HHHHHHHHHhcCCCcceEEEEEEEEECCEEEEE
Confidence 356788888 455778888899988888875
No 95
>PF08210 APOBEC_N: APOBEC-like N-terminal domain; InterPro: IPR013158 This domain is found at the N terminus of the Apolipoprotein B mRNA editing enzyme. Apobec-1 catalyzes C to U editing of apolipoprotein B (apoB) mRNA in the mammalian intestine. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination. APOBEC-3 like members contain two copies of this domain. This family also includes the functionally homologous activation induced deaminase, which is essential for the development of antibody diversity in B lymphocytes. RNA editing by APOBEC-1 requires homodimerisation and this complex interacts with RNA binding proteins to from the editosome [] (and references therein).; GO: 0008270 zinc ion binding, 0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines; PDB: 3IQS_A 3IR2_A 3V4J_B 2KEM_A 2KBO_A 3V4K_A 3E1U_A 2JYW_A 2RPZ_A.
Probab=20.32 E-value=1.7e+02 Score=21.01 Aligned_cols=55 Identities=24% Similarity=0.399 Sum_probs=33.3
Q ss_pred chh----HHHHHHHHHhcC--CCceEEEEEcCCcEEEEeecCC---HHHHHHHHHhhcCCceEEecCC
Q 037689 3 CNA----CERTVARAISKF--KGVEKFTTDMNKHRVVVTGRID---PQKVLKKLKKKTGKKVEIVDNN 61 (122)
Q Consensus 3 C~~----C~~~I~k~l~~~--~GV~~v~vd~~~~kv~V~g~~~---~~~v~~~i~~~~G~~~e~~~~~ 61 (122)
|.. |+.+|-..|.+. ++| ++.+-.+ ++--...-. ..+=+..|. ++|-++++....
T Consensus 85 C~~~~~~Ca~~i~~FL~~~~~~~v-~L~I~~a--rLY~~~~~~~~~~~eGLr~L~-~aGv~v~iM~~~ 148 (188)
T PF08210_consen 85 CPESDHCCAEKIAEFLKKHLKPNV-SLSIFAA--RLYYHWEPEPLWNQEGLRRLA-SAGVQVEIMSYK 148 (188)
T ss_dssp -CC----HHHHHHHHHCCC--TTE-EEEEEES--S--STTSTT---HHHHHHHHH-HCTEEEEE-SHH
T ss_pred CcchhhHHHHHHHHHHHHhCCCCC-eEEEEEE--eeeeecCCcchhHHHHHHHHH-HcCCEEEEcCHH
Confidence 777 999999999999 887 2333221 111111122 456677776 789999987543
No 96
>TIGR01678 FAD_lactone_ox sugar 1,4-lactone oxidases. This model represents a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesizing ascorbic acid or a derivative. These include L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by Prosite motif PS00862; OX2_COVAL_FAD; 1.
Probab=20.29 E-value=2e+02 Score=23.54 Aligned_cols=38 Identities=21% Similarity=0.341 Sum_probs=29.6
Q ss_pred cCCCceEEEEEcCCcEEEEeecCCHHHHHHHHHhhcCCceE
Q 037689 16 KFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVE 56 (122)
Q Consensus 16 ~~~GV~~v~vd~~~~kv~V~g~~~~~~v~~~i~~~~G~~~e 56 (122)
++.+| +.+|..++.|+|.+-+...+|.+.|. +.|+...
T Consensus 65 ~l~~i--~~id~~~~~vtV~aG~~l~~L~~~L~-~~Gl~l~ 102 (438)
T TIGR01678 65 KMNKV--LQFDKEKKQITVEAGIRLYQLHEQLD-EHGYSMS 102 (438)
T ss_pred hcCCc--eEEcCCCCEEEEcCCCCHHHHHHHHH-HcCCEec
Confidence 34444 35677788899988889999999998 8998754
No 97
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=20.29 E-value=49 Score=21.29 Aligned_cols=14 Identities=36% Similarity=1.018 Sum_probs=10.9
Q ss_pred CCchhHHHHHHHHH
Q 037689 1 MYCNACERTVARAI 14 (122)
Q Consensus 1 m~C~~C~~~I~k~l 14 (122)
|-|+.|+.++.+++
T Consensus 1 MVC~kCEkKLskvi 14 (100)
T KOG3476|consen 1 MVCEKCEKKLSKVI 14 (100)
T ss_pred CchhHHHHHhcccc
Confidence 77999988876654
No 98
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=20.13 E-value=1.8e+02 Score=20.60 Aligned_cols=29 Identities=28% Similarity=0.386 Sum_probs=24.3
Q ss_pred EEEeecCCHHHHHHHHHhhcCCceEEecCC
Q 037689 32 VVVTGRIDPQKVLKKLKKKTGKKVEIVDNN 61 (122)
Q Consensus 32 v~V~g~~~~~~v~~~i~~~~G~~~e~~~~~ 61 (122)
+.|+|+-|...|+.+|+ +.|.++..++.+
T Consensus 110 vLvSgD~DF~~Lv~~lr-e~G~~V~v~g~~ 138 (160)
T TIGR00288 110 ALVTRDADFLPVINKAK-ENGKETIVIGAE 138 (160)
T ss_pred EEEeccHhHHHHHHHHH-HCCCEEEEEeCC
Confidence 45678889999999998 889999998753
Done!