Query 032393
Match_columns 142
No_of_seqs 135 out of 1598
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 13:30:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032393.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032393hhsearch_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 99.5 5.1E-13 1.1E-17 85.5 8.4 59 32-91 1-62 (62)
2 KOG1603 Copper chaperone [Inor 99.4 2.4E-12 5.1E-17 86.1 8.5 68 27-96 3-71 (73)
3 COG2608 CopZ Copper chaperone 99.3 1.4E-11 3E-16 82.1 8.8 66 29-95 2-70 (71)
4 KOG4656 Copper chaperone for s 99.1 6.3E-10 1.4E-14 88.3 8.6 71 28-100 6-76 (247)
5 PLN02957 copper, zinc superoxi 98.5 1.3E-06 2.7E-11 70.4 9.8 71 29-101 6-76 (238)
6 PRK10671 copA copper exporting 98.3 2.4E-06 5.2E-11 79.1 8.2 65 29-97 3-68 (834)
7 COG2217 ZntA Cation transport 98.0 1.7E-05 3.6E-10 73.0 7.5 64 29-94 2-69 (713)
8 TIGR00003 copper ion binding p 97.8 0.00035 7.6E-09 40.9 8.4 62 29-91 2-66 (68)
9 PRK10671 copA copper exporting 97.2 0.0011 2.4E-08 61.6 7.8 65 30-96 100-165 (834)
10 PRK11033 zntA zinc/cadmium/mer 96.9 0.0035 7.5E-08 57.9 8.0 67 27-94 51-118 (741)
11 KOG0207 Cation transport ATPas 96.9 0.0027 5.9E-08 59.7 7.0 67 29-96 146-215 (951)
12 KOG0207 Cation transport ATPas 96.6 0.0042 9E-08 58.5 6.0 63 36-99 2-65 (951)
13 COG1888 Uncharacterized protei 92.9 0.96 2.1E-05 31.8 7.6 69 27-96 4-80 (97)
14 TIGR02052 MerP mercuric transp 92.8 1.6 3.5E-05 27.7 9.0 63 30-93 24-89 (92)
15 PF02680 DUF211: Uncharacteriz 92.8 0.61 1.3E-05 32.9 6.5 67 27-95 3-77 (95)
16 PRK13748 putative mercuric red 89.0 3 6.4E-05 36.8 8.7 65 32-97 3-69 (561)
17 PF01883 DUF59: Domain of unkn 84.4 2 4.3E-05 27.7 3.9 33 29-61 34-72 (72)
18 cd00371 HMA Heavy-metal-associ 83.0 4.6 0.0001 20.6 6.9 50 36-85 6-56 (63)
19 PRK14054 methionine sulfoxide 79.0 4 8.6E-05 31.6 4.5 46 40-85 10-76 (172)
20 PF14437 MafB19-deam: MafB19-l 72.3 11 0.00024 28.6 5.2 42 28-70 99-142 (146)
21 PRK05528 methionine sulfoxide 69.6 11 0.00024 28.7 4.7 46 40-85 8-69 (156)
22 PF01206 TusA: Sulfurtransfera 67.8 15 0.00033 23.2 4.6 54 32-95 2-57 (70)
23 PRK00058 methionine sulfoxide 65.3 12 0.00025 30.1 4.3 47 39-85 51-118 (213)
24 PRK13014 methionine sulfoxide 65.1 9 0.0002 30.1 3.6 46 40-85 15-81 (186)
25 PF13732 DUF4162: Domain of un 62.2 26 0.00057 22.7 5.0 44 50-97 26-71 (84)
26 PF14492 EFG_II: Elongation Fa 61.4 43 0.00093 21.9 6.3 62 31-93 6-72 (75)
27 cd04888 ACT_PheB-BS C-terminal 61.2 26 0.00055 21.9 4.7 33 29-61 41-74 (76)
28 cd02410 archeal_CPSF_KH The ar 59.5 43 0.00094 25.4 6.2 72 30-101 38-118 (145)
29 PRK10553 assembly protein for 58.5 41 0.00089 23.1 5.5 49 37-85 12-61 (87)
30 TIGR03406 FeS_long_SufT probab 58.3 14 0.00031 28.5 3.6 34 30-63 114-153 (174)
31 TIGR02945 SUF_assoc FeS assemb 56.2 17 0.00036 24.8 3.3 21 44-64 58-78 (99)
32 PF01625 PMSR: Peptide methion 56.0 29 0.00064 26.2 4.9 46 40-85 7-73 (155)
33 PF03927 NapD: NapD protein; 55.5 58 0.0013 21.7 5.8 44 41-85 15-58 (79)
34 PRK05550 bifunctional methioni 48.0 31 0.00067 28.8 4.2 47 39-85 133-200 (283)
35 PF13291 ACT_4: ACT domain; PD 47.6 54 0.0012 21.0 4.6 34 27-60 46-79 (80)
36 PF08002 DUF1697: Protein of u 45.4 91 0.002 22.8 6.0 48 44-93 22-73 (137)
37 cd03421 SirA_like_N SirA_like_ 39.6 95 0.0021 19.4 4.9 51 34-95 3-55 (67)
38 COG2177 FtsX Cell division pro 38.7 1.2E+02 0.0025 25.4 6.3 45 33-91 65-109 (297)
39 COG2151 PaaD Predicted metal-s 38.5 54 0.0012 23.6 3.7 21 43-63 69-89 (111)
40 PF03927 NapD: NapD protein; 36.2 1.1E+02 0.0024 20.3 4.8 35 29-63 39-73 (79)
41 TIGR00401 msrA methionine-S-su 35.8 28 0.00061 26.2 2.0 46 40-85 7-73 (149)
42 cd06167 LabA_like LabA_like pr 35.6 59 0.0013 23.2 3.6 29 68-98 104-132 (149)
43 PF04972 BON: BON domain; Int 34.2 27 0.00059 21.4 1.5 28 45-73 3-33 (64)
44 PF13462 Thioredoxin_4: Thiore 33.5 44 0.00095 23.7 2.6 20 26-45 11-30 (162)
45 PRK04435 hypothetical protein; 32.1 1.1E+02 0.0024 22.6 4.7 32 30-61 111-143 (147)
46 cd04877 ACT_TyrR N-terminal AC 31.6 1.2E+02 0.0026 19.1 4.3 30 31-60 39-68 (74)
47 PF08777 RRM_3: RNA binding mo 31.5 1.5E+02 0.0033 20.7 5.1 55 31-85 2-58 (105)
48 COG3062 NapD Uncharacterized p 31.2 1.4E+02 0.003 21.0 4.7 48 37-85 13-61 (94)
49 COG3643 Glutamate formiminotra 29.2 52 0.0011 27.4 2.6 44 41-85 18-63 (302)
50 PRK11200 grxA glutaredoxin 1; 27.5 1.7E+02 0.0038 18.8 4.6 29 36-65 8-40 (85)
51 PRK11018 hypothetical protein; 26.9 1.9E+02 0.0041 18.9 6.1 54 31-94 9-64 (78)
52 COG0225 MsrA Peptide methionin 26.7 37 0.00081 26.5 1.3 46 40-85 13-79 (174)
53 TIGR02159 PA_CoA_Oxy4 phenylac 26.6 87 0.0019 23.4 3.3 33 30-63 26-64 (146)
54 KOG3411 40S ribosomal protein 26.2 54 0.0012 24.7 2.0 42 40-85 97-139 (143)
55 cd00291 SirA_YedF_YeeD SirA, Y 24.9 1.7E+02 0.0038 17.9 5.4 50 36-95 6-56 (69)
56 PF08210 APOBEC_N: APOBEC-like 24.5 2.2E+02 0.0048 22.0 5.3 65 28-96 73-146 (188)
57 PRK09577 multidrug efflux prot 24.4 2E+02 0.0043 28.0 6.0 46 43-89 158-210 (1032)
58 cd03023 DsbA_Com1_like DsbA fa 24.2 72 0.0016 22.1 2.4 24 27-51 5-28 (154)
59 PRK11670 antiporter inner memb 24.2 2.3E+02 0.005 24.1 5.8 69 30-99 48-146 (369)
60 PF03434 DUF276: DUF276 ; Int 23.9 1.2E+02 0.0025 25.3 3.7 30 41-70 87-116 (291)
61 cd03420 SirA_RHOD_Pry_redox Si 23.7 2E+02 0.0044 18.2 4.9 54 33-96 2-57 (69)
62 TIGR00489 aEF-1_beta translati 23.4 85 0.0019 21.6 2.5 24 40-63 61-84 (88)
63 TIGR00288 conserved hypothetic 23.0 1.2E+02 0.0026 23.2 3.5 30 68-99 110-139 (160)
64 PF15235 GRIN_C: G protein-reg 22.9 1.2E+02 0.0027 22.7 3.4 42 52-93 40-81 (137)
65 PF04312 DUF460: Protein of un 22.7 3.4E+02 0.0073 20.4 5.9 38 58-96 45-83 (138)
66 PRK10555 aminoglycoside/multid 22.4 2.2E+02 0.0047 27.7 5.9 44 42-85 158-208 (1037)
67 PF00352 TBP: Transcription fa 21.8 1.1E+02 0.0023 20.4 2.7 22 63-85 55-76 (86)
68 PF01936 NYN: NYN domain; Int 21.6 63 0.0014 22.6 1.6 30 66-97 98-127 (146)
69 PRK00435 ef1B elongation facto 21.6 1.5E+02 0.0033 20.3 3.5 24 40-63 61-84 (88)
70 PRK06418 transcription elongat 20.9 3.9E+02 0.0086 20.5 6.4 71 29-99 6-100 (166)
71 PF13193 AMP-binding_C: AMP-bi 20.5 96 0.0021 19.4 2.2 40 46-86 2-46 (73)
72 PRK15127 multidrug efflux syst 20.2 2.6E+02 0.0057 27.3 5.9 43 43-85 159-208 (1049)
73 PF14424 Toxin-deaminase: The 20.2 2E+02 0.0043 21.1 4.1 29 29-57 97-126 (133)
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=99.46 E-value=5.1e-13 Score=85.52 Aligned_cols=59 Identities=34% Similarity=0.579 Sum_probs=53.8
Q ss_pred EEEE-eccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc--CCCHHHHHHHHHhccCCc
Q 032393 32 VLKV-DMHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRK 91 (142)
Q Consensus 32 ~lkV-~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~--~vd~~~I~~~I~kk~G~~ 91 (142)
+|+| +|+|.+|+++|+++|.+++||.++.+|+.+++++|.++ .+++..|..+|+ ++||.
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhCcC
Confidence 5889 59999999999999999999999999999999999876 246799999999 89984
No 2
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.39 E-value=2.4e-12 Score=86.09 Aligned_cols=68 Identities=47% Similarity=0.851 Sum_probs=62.0
Q ss_pred CCceEEEEEeccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHHhccC-CcEEEcC
Q 032393 27 ETPEIVLKVDMHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSG-RKVELIS 96 (142)
Q Consensus 27 ~~~~i~lkV~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~kk~G-~~aelis 96 (142)
.++..+++++|||.+|..+|.+.|+.+.||.++.+|...++|+|.|. +++..|+..|+ +.| +++.+|.
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~-~~p~~vl~~l~-k~~~k~~~~~~ 71 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGN-VDPVKLLKKLK-KTGGKRAELWK 71 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEe-cCHHHHHHHHH-hcCCCceEEec
Confidence 45678899999999999999999999999999999999999999999 99999999999 466 7777664
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.32 E-value=1.4e-11 Score=82.08 Aligned_cols=66 Identities=30% Similarity=0.497 Sum_probs=58.5
Q ss_pred ceEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc--CCCHHHHHHHHHhccCCcEEEc
Q 032393 29 PEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRKVELI 95 (142)
Q Consensus 29 ~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~--~vd~~~I~~~I~kk~G~~aeli 95 (142)
..+.|+|. |+|.+|+..|+++|..++||.++.+|+..+.+.|+.+ .++...|+.+|. .+||.+..+
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~~~ 70 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVEEI 70 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCeeec
Confidence 46789995 9999999999999999999999999999977777643 379999999999 899988764
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.08 E-value=6.3e-10 Score=88.27 Aligned_cols=71 Identities=28% Similarity=0.470 Sum_probs=66.7
Q ss_pred CceEEEEEeccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHHhccCCcEEEcCCCCC
Q 032393 28 TPEIVLKVDMHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVELISPLPK 100 (142)
Q Consensus 28 ~~~i~lkV~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~kk~G~~aelis~~p~ 100 (142)
...++|.|+|+|++|++.|+.+|..++||.+|.+|+..+.|.|.+. ..++.|.+.|+ .+|++|.+...+-+
T Consensus 6 ~~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts-~p~s~i~~~le-~tGr~Avl~G~G~p 76 (247)
T KOG4656|consen 6 TYEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETS-VPPSEIQNTLE-NTGRDAVLRGAGKP 76 (247)
T ss_pred ceeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEcc-CChHHHHHHHH-hhChheEEecCCch
Confidence 4568899999999999999999999999999999999999999998 89999999999 99999999998764
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.48 E-value=1.3e-06 Score=70.38 Aligned_cols=71 Identities=30% Similarity=0.427 Sum_probs=63.8
Q ss_pred ceEEEEEeccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHHhccCCcEEEcCCCCCC
Q 032393 29 PEIVLKVDMHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVELISPLPKP 101 (142)
Q Consensus 29 ~~i~lkV~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~kk~G~~aelis~~p~~ 101 (142)
..+.|.+.|+|.+|+..|++.|.+++||..+.+|+..++++|.+. .+...|...|. .+||.+.+++..++.
T Consensus 6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~-~~~~~I~~aIe-~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS-SPVKAMTAALE-QTGRKARLIGQGDPE 76 (238)
T ss_pred EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec-CCHHHHHHHHH-HcCCcEEEecCCCcc
Confidence 456788899999999999999999999999999999999999886 78889999999 899999999876644
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.29 E-value=2.4e-06 Score=79.15 Aligned_cols=65 Identities=22% Similarity=0.435 Sum_probs=57.6
Q ss_pred ceEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHHhccCCcEEEcCC
Q 032393 29 PEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVELISP 97 (142)
Q Consensus 29 ~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~kk~G~~aelis~ 97 (142)
++++|.|+ |+|.+|+.+|+++|.+++||.++.+|+. +.++.+. .+...+...+. ..||.+...++
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~-~~~~~i~~~i~-~~Gy~~~~~~~ 68 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGT-ASAEALIETIK-QAGYDASVSHP 68 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEec-CCHHHHHHHHH-hcCCccccccc
Confidence 46889996 9999999999999999999999999994 5566676 78999999999 89999998764
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.01 E-value=1.7e-05 Score=72.97 Aligned_cols=64 Identities=28% Similarity=0.542 Sum_probs=56.6
Q ss_pred ceEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc--CCC-HHHHHHHHHhccCCcEEE
Q 032393 29 PEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TAD-PIKVCERLQKKSGRKVEL 94 (142)
Q Consensus 29 ~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~--~vd-~~~I~~~I~kk~G~~ael 94 (142)
..+.|.|. |||..|+++|+ +|.+++||..+.+|+.+++++|.++ ..+ ++.+...+. ..||.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCccccc
Confidence 35679995 99999999999 9999999999999999999999865 245 789999999 89998876
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=97.80 E-value=0.00035 Score=40.92 Aligned_cols=62 Identities=23% Similarity=0.433 Sum_probs=50.5
Q ss_pred ceEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc--CCCHHHHHHHHHhccCCc
Q 032393 29 PEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRK 91 (142)
Q Consensus 29 ~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~--~vd~~~I~~~I~kk~G~~ 91 (142)
....+.|+ ++|..|...+...+....|+..+.+++..+.+.+... ..+...+...+. ..||.
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~ 66 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYE 66 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCC
Confidence 34568885 9999999999999999999999999999999888742 246667777776 67764
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.23 E-value=0.0011 Score=61.58 Aligned_cols=65 Identities=26% Similarity=0.481 Sum_probs=56.8
Q ss_pred eEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHHhccCCcEEEcC
Q 032393 30 EIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVELIS 96 (142)
Q Consensus 30 ~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~kk~G~~aelis 96 (142)
.+.|.+. |+|.+|+..|++.|..++||.++.+++.++++.+.+. .++..+...+. .+||.+.+++
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~-~s~~~I~~~I~-~~Gy~a~~~~ 165 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGS-ASPQDLVQAVE-KAGYGAEAIE 165 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEcc-CCHHHHHHHHH-hcCCCccccc
Confidence 5678895 9999999999999999999999999999999888765 78888888888 8999876543
No 10
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.94 E-value=0.0035 Score=57.91 Aligned_cols=67 Identities=28% Similarity=0.421 Sum_probs=54.1
Q ss_pred CCceEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHHhccCCcEEE
Q 032393 27 ETPEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVEL 94 (142)
Q Consensus 27 ~~~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~kk~G~~ael 94 (142)
...++.|.+. |+|.+|+..++..+..++||.++.+++.++++.+.++......+...+. ..||.+..
T Consensus 51 ~~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~-~~Gy~a~~ 118 (741)
T PRK11033 51 SGTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQ-KAGFSLRD 118 (741)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHH-hccccccc
Confidence 4556778895 9999999999999999999999999999999888754112266777787 78987643
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.90 E-value=0.0027 Score=59.67 Aligned_cols=67 Identities=19% Similarity=0.410 Sum_probs=59.9
Q ss_pred ceEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc--CCCHHHHHHHHHhccCCcEEEcC
Q 032393 29 PEIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRKVELIS 96 (142)
Q Consensus 29 ~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~--~vd~~~I~~~I~kk~G~~aelis 96 (142)
.++.|.|. |+|.+|..+|+..|.+++||.++.++..++++.|..+ .+.+-++++.|. .+|+.+.+..
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~~~~~~~~ 215 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETGFEASVRP 215 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhcccceeee
Confidence 68899995 9999999999999999999999999999999998754 478899999998 8998766554
No 12
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.62 E-value=0.0042 Score=58.47 Aligned_cols=63 Identities=22% Similarity=0.394 Sum_probs=57.1
Q ss_pred eccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc-CCCHHHHHHHHHhccCCcEEEcCCCC
Q 032393 36 DMHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQKKSGRKVELISPLP 99 (142)
Q Consensus 36 ~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-~vd~~~I~~~I~kk~G~~aelis~~p 99 (142)
+|+|..|.+.|+.++++.+||.++.+++.++..+|..+ .++++.|.++|. ..|+.+.+++...
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~gf~~~~~~~~~ 65 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMGFEASLLSDSE 65 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-cccceeeecccCc
Confidence 49999999999999999999999999999998888754 579999999999 9999999888644
No 13
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=92.92 E-value=0.96 Score=31.84 Aligned_cols=69 Identities=22% Similarity=0.306 Sum_probs=46.8
Q ss_pred CCceEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEec-------CCCEEEEeccCCCHHHHHHHHHhccCCcEEEcC
Q 032393 27 ETPEIVLKVD-MHCEACARKVARALKGFEGVDDITADS-------KASKVVVKGKTADPIKVCERLQKKSGRKVELIS 96 (142)
Q Consensus 27 ~~~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~-------~~~kVtV~g~~vd~~~I~~~I~kk~G~~aelis 96 (142)
....++|.|. -|-.--.--+-..|++++||.-|++.. .+-+++|.|..+|..+|...|. .+|..++.+.
T Consensus 4 ~iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSiD 80 (97)
T COG1888 4 GIRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSID 80 (97)
T ss_pred cceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeehh
Confidence 4455667763 332223335566778888877665543 4556677887799999999999 8998877554
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=92.78 E-value=1.6 Score=27.69 Aligned_cols=63 Identities=25% Similarity=0.357 Sum_probs=46.4
Q ss_pred eEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc--CCCHHHHHHHHHhccCCcEE
Q 032393 30 EIVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK--TADPIKVCERLQKKSGRKVE 93 (142)
Q Consensus 30 ~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~--~vd~~~I~~~I~kk~G~~ae 93 (142)
.+.+.++ ++|.+|...+...+....|+....++.....+.+... ..+...+...+. ..|+.++
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~ 89 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSS 89 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeE
Confidence 3456675 9999999999999999999888888888887666521 135555556666 6777654
No 15
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=92.78 E-value=0.61 Score=32.93 Aligned_cols=67 Identities=25% Similarity=0.388 Sum_probs=46.0
Q ss_pred CCceEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEec-----CCC--EEEEeccCCCHHHHHHHHHhccCCcEEEc
Q 032393 27 ETPEIVLKVD-MHCEACARKVARALKGFEGVDDITADS-----KAS--KVVVKGKTADPIKVCERLQKKSGRKVELI 95 (142)
Q Consensus 27 ~~~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~-----~~~--kVtV~g~~vd~~~I~~~I~kk~G~~aeli 95 (142)
...+++|.|- -|-+.-. .+-..|+.++||..|++.. .+. +++|.|+.+|.+.|..+|. .+|-.++-+
T Consensus 3 ~irRlVLDVlKP~~p~i~-e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHSI 77 (95)
T PF02680_consen 3 GIRRLVLDVLKPHEPSIV-ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHSI 77 (95)
T ss_dssp SEEEEEEEEEEESSS-HH-HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEEE
T ss_pred ceeEEEEEeecCCCCCHH-HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEee
Confidence 4456778874 4444433 6778899999988776644 444 4455687799999999999 899777644
No 16
>PRK13748 putative mercuric reductase; Provisional
Probab=88.97 E-value=3 Score=36.79 Aligned_cols=65 Identities=22% Similarity=0.370 Sum_probs=50.3
Q ss_pred EEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc-CCCHHHHHHHHHhccCCcEEEcCC
Q 032393 32 VLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQKKSGRKVELISP 97 (142)
Q Consensus 32 ~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-~vd~~~I~~~I~kk~G~~aelis~ 97 (142)
.+.+. |+|.+|...++..+..++|+....+++..+.+.+... ..+...+...+. ..|+..+..+.
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g~~~~~~~~ 69 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLGYRATLADA 69 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcCCeeeccCc
Confidence 35674 9999999999999999999999999998888777632 245566666666 68877666555
No 17
>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=84.36 E-value=2 Score=27.67 Aligned_cols=33 Identities=21% Similarity=0.540 Sum_probs=22.6
Q ss_pred ceEEEEEeccchhHH------HHHHHHhhCCCCccEEEE
Q 032393 29 PEIVLKVDMHCEACA------RKVARALKGFEGVDDITA 61 (142)
Q Consensus 29 ~~i~lkV~M~C~~Ca------~kIekaL~~i~GV~~V~v 61 (142)
.++.|.+.+.+++|. ..|+.+|+.++||.+|.|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 456666666666664 678889999999998875
No 18
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=82.98 E-value=4.6 Score=20.56 Aligned_cols=50 Identities=26% Similarity=0.563 Sum_probs=34.9
Q ss_pred eccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc-CCCHHHHHHHHH
Q 032393 36 DMHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQ 85 (142)
Q Consensus 36 ~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-~vd~~~I~~~I~ 85 (142)
.++|..|...+...+....|+....+++....+.+... ..+...+...+.
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE 56 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH
Confidence 38899999999999999999877777777766666542 124444434444
No 19
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=78.96 E-value=4 Score=31.60 Aligned_cols=46 Identities=11% Similarity=0.102 Sum_probs=37.2
Q ss_pred hhHHHHHHHHhhCCCCccEEEEecCCCE-------------------EEEecc--CCCHHHHHHHHH
Q 032393 40 EACARKVARALKGFEGVDDITADSKASK-------------------VVVKGK--TADPIKVCERLQ 85 (142)
Q Consensus 40 ~~Ca~kIekaL~~i~GV~~V~vd~~~~k-------------------VtV~g~--~vd~~~I~~~I~ 85 (142)
.||-+-++..+.+++||.++.+-..+|. |.|+.+ .++...|++...
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 5777888889999999999999987775 556544 578888888776
No 20
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=72.27 E-value=11 Score=28.61 Aligned_cols=42 Identities=19% Similarity=0.380 Sum_probs=34.8
Q ss_pred CceEEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecC-CCEEEE
Q 032393 28 TPEIVLKVD-MHCEACARKVARALKGFEGVDDITADSK-ASKVVV 70 (142)
Q Consensus 28 ~~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~-~~kVtV 70 (142)
...+++.|+ -.|..|..-|....+++ |+.++.|... +|++.+
T Consensus 99 g~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~~ 142 (146)
T PF14437_consen 99 GRSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVYY 142 (146)
T ss_pred CCeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEEE
Confidence 456788897 88999999998888776 9999999887 776654
No 21
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=69.56 E-value=11 Score=28.72 Aligned_cols=46 Identities=17% Similarity=0.135 Sum_probs=35.4
Q ss_pred hhHHHHHHHHhhCCCCccEEEEecCCCE--------------EEEecc--CCCHHHHHHHHH
Q 032393 40 EACARKVARALKGFEGVDDITADSKASK--------------VVVKGK--TADPIKVCERLQ 85 (142)
Q Consensus 40 ~~Ca~kIekaL~~i~GV~~V~vd~~~~k--------------VtV~g~--~vd~~~I~~~I~ 85 (142)
.||-+-++..+.+++||.++.+-+.+|. |.|+.+ .++.+.|++...
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 5777778889999999999999886654 444443 578888888776
No 22
>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=67.80 E-value=15 Score=23.19 Aligned_cols=54 Identities=19% Similarity=0.174 Sum_probs=37.5
Q ss_pred EEEE-eccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc-CCCHHHHHHHHHhccCCcEEEc
Q 032393 32 VLKV-DMHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQKKSGRKVELI 95 (142)
Q Consensus 32 ~lkV-~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-~vd~~~I~~~I~kk~G~~aeli 95 (142)
++.+ ++.|+...-.+.++|..++.- +.+.|..+ ..+...|...+. ..||.+.-+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~-~~g~~~~~~ 57 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCE-ENGYEVVEV 57 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHH-HHTEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHH-HCCCEEEEE
Confidence 4556 489999999999999997443 33444332 256678999998 899875544
No 23
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=65.35 E-value=12 Score=30.08 Aligned_cols=47 Identities=13% Similarity=0.033 Sum_probs=36.8
Q ss_pred chhHHHHHHHHhhCCCCccEEEEecCCCE-------------------EEEecc--CCCHHHHHHHHH
Q 032393 39 CEACARKVARALKGFEGVDDITADSKASK-------------------VVVKGK--TADPIKVCERLQ 85 (142)
Q Consensus 39 C~~Ca~kIekaL~~i~GV~~V~vd~~~~k-------------------VtV~g~--~vd~~~I~~~I~ 85 (142)
-.||-+-++..+.+++||.++.+-+.+|. |.|+.+ .++...|++...
T Consensus 51 agGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff 118 (213)
T PRK00058 51 GMGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFW 118 (213)
T ss_pred EccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 46778888888999999999999987552 455544 578889988876
No 24
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=65.12 E-value=9 Score=30.07 Aligned_cols=46 Identities=11% Similarity=0.134 Sum_probs=35.5
Q ss_pred hhHHHHHHHHhhCCCCccEEEEecCCCE-------------------EEEecc--CCCHHHHHHHHH
Q 032393 40 EACARKVARALKGFEGVDDITADSKASK-------------------VVVKGK--TADPIKVCERLQ 85 (142)
Q Consensus 40 ~~Ca~kIekaL~~i~GV~~V~vd~~~~k-------------------VtV~g~--~vd~~~I~~~I~ 85 (142)
.||-+-++..+.+++||.++.+-+.+|. |.|+.+ .++...|++...
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff 81 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFF 81 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHH
Confidence 4666677888889999999999987774 455543 478888888776
No 25
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=62.23 E-value=26 Score=22.66 Aligned_cols=44 Identities=16% Similarity=0.344 Sum_probs=31.6
Q ss_pred hhCCCCccEEEEecCCCEEE--EeccCCCHHHHHHHHHhccCCcEEEcCC
Q 032393 50 LKGFEGVDDITADSKASKVV--VKGKTADPIKVCERLQKKSGRKVELISP 97 (142)
Q Consensus 50 L~~i~GV~~V~vd~~~~kVt--V~g~~vd~~~I~~~I~kk~G~~aelis~ 97 (142)
|..++||.++..+- .+.+. +... .+...|+..|. ..|. +.-++.
T Consensus 26 l~~~~~v~~v~~~~-~~~~~i~l~~~-~~~~~ll~~l~-~~g~-I~~f~~ 71 (84)
T PF13732_consen 26 LEELPGVESVEQDG-DGKLRIKLEDE-ETANELLQELI-EKGI-IRSFEE 71 (84)
T ss_pred HhhCCCeEEEEEeC-CcEEEEEECCc-ccHHHHHHHHH-hCCC-eeEEEE
Confidence 88889999887643 44344 4454 68889999998 7887 665543
No 26
>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=61.42 E-value=43 Score=21.86 Aligned_cols=62 Identities=18% Similarity=0.344 Sum_probs=40.7
Q ss_pred EEEEEeccchhHHHHHHHHhhCC----CCccEEEEecCCCEEEEecc-CCCHHHHHHHHHhccCCcEE
Q 032393 31 IVLKVDMHCEACARKVARALKGF----EGVDDITADSKASKVVVKGK-TADPIKVCERLQKKSGRKVE 93 (142)
Q Consensus 31 i~lkV~M~C~~Ca~kIekaL~~i----~GV~~V~vd~~~~kVtV~g~-~vd~~~I~~~I~kk~G~~ae 93 (142)
+.+.|.-.-.+=..++..+|..+ +++ .+..|..++.+.|.|- .+..+-++..|+..+|..++
T Consensus 6 ~~~~i~p~~~~d~~kl~~aL~~l~~eDP~l-~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 6 LSVAIEPKNKEDEPKLSEALQKLSEEDPSL-RVERDEETGELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHH-TTS-EEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred EEEEEEECCHhHHHHHHHHHHHHHhcCCeE-EEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 44555444445555666665555 444 7889999999998743 16777788888866665554
No 27
>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=61.25 E-value=26 Score=21.93 Aligned_cols=33 Identities=12% Similarity=0.344 Sum_probs=25.1
Q ss_pred ceEEEEEeccchh-HHHHHHHHhhCCCCccEEEE
Q 032393 29 PEIVLKVDMHCEA-CARKVARALKGFEGVDDITA 61 (142)
Q Consensus 29 ~~i~lkV~M~C~~-Ca~kIekaL~~i~GV~~V~v 61 (142)
..+.|.+..+-.. --..|...|++++||.+|.+
T Consensus 41 ~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 41 ANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 3455666656665 78899999999999988864
No 28
>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=59.51 E-value=43 Score=25.35 Aligned_cols=72 Identities=15% Similarity=0.280 Sum_probs=48.7
Q ss_pred eEEEEEe----ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc----CC-CHHHHHHHHHhccCCcEEEcCCCCC
Q 032393 30 EIVLKVD----MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK----TA-DPIKVCERLQKKSGRKVELISPLPK 100 (142)
Q Consensus 30 ~i~lkV~----M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~----~v-d~~~I~~~I~kk~G~~aelis~~p~ 100 (142)
.++++.+ |.-..-...|.+.+-.-.||.++.+|..+|.|.|... .+ -....++.|..++|+.+.++..+|.
T Consensus 38 RIvvR~dps~l~~~e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpPi 117 (145)
T cd02410 38 RIVIRPDPSVLKPPEEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPPI 117 (145)
T ss_pred eEEEcCChhhcCCHHHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCCC
Confidence 4555553 3345556667776766679999999999999998522 11 1233444554589999999988775
Q ss_pred C
Q 032393 101 P 101 (142)
Q Consensus 101 ~ 101 (142)
+
T Consensus 118 ~ 118 (145)
T cd02410 118 Q 118 (145)
T ss_pred C
Confidence 5
No 29
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=58.53 E-value=41 Score=23.12 Aligned_cols=49 Identities=12% Similarity=0.309 Sum_probs=33.0
Q ss_pred ccc-hhHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHH
Q 032393 37 MHC-EACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQ 85 (142)
Q Consensus 37 M~C-~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~ 85 (142)
.+| +.=...+...|..++|+.-...|...|++.|+=...+...+.+.|.
T Consensus 12 V~~~Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 12 VQAKSERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred EEeChHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 445 4447789999999999977777778888887522124444444443
No 30
>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=58.30 E-value=14 Score=28.52 Aligned_cols=34 Identities=12% Similarity=0.389 Sum_probs=24.4
Q ss_pred eEEEEEeccchhHH------HHHHHHhhCCCCccEEEEec
Q 032393 30 EIVLKVDMHCEACA------RKVARALKGFEGVDDITADS 63 (142)
Q Consensus 30 ~i~lkV~M~C~~Ca------~kIekaL~~i~GV~~V~vd~ 63 (142)
++.+.+.++.++|. ..|+.+|..++||.+|.|++
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 45555555555554 44888999999999888865
No 31
>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=56.20 E-value=17 Score=24.77 Aligned_cols=21 Identities=24% Similarity=0.415 Sum_probs=17.3
Q ss_pred HHHHHHhhCCCCccEEEEecC
Q 032393 44 RKVARALKGFEGVDDITADSK 64 (142)
Q Consensus 44 ~kIekaL~~i~GV~~V~vd~~ 64 (142)
..+..+|..++|+.++.+++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 357888999999999988874
No 32
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=55.98 E-value=29 Score=26.23 Aligned_cols=46 Identities=15% Similarity=0.131 Sum_probs=34.2
Q ss_pred hhHHHHHHHHhhCCCCccEEEEecCCC-------------------EEEEecc--CCCHHHHHHHHH
Q 032393 40 EACARKVARALKGFEGVDDITADSKAS-------------------KVVVKGK--TADPIKVCERLQ 85 (142)
Q Consensus 40 ~~Ca~kIekaL~~i~GV~~V~vd~~~~-------------------kVtV~g~--~vd~~~I~~~I~ 85 (142)
.||-+.++..+.+++||.++.+-+.+| .|.|+.+ .++...|++...
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~ 73 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFF 73 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHH
Confidence 467788889999999999999988665 3344432 578888888776
No 33
>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=55.46 E-value=58 Score=21.70 Aligned_cols=44 Identities=23% Similarity=0.287 Sum_probs=29.9
Q ss_pred hHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHH
Q 032393 41 ACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQ 85 (142)
Q Consensus 41 ~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~ 85 (142)
.=...+..+|..++|+.-...+.. |++.|+-...+...+.+.+.
T Consensus 15 ~~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 15 ERLEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp CCHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred hhHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 445688999999999965566665 88877532135555655554
No 34
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=48.03 E-value=31 Score=28.84 Aligned_cols=47 Identities=15% Similarity=0.118 Sum_probs=36.0
Q ss_pred chhHHHHHHHHhhCCCCccEEEEecCCCE-------------------EEEecc--CCCHHHHHHHHH
Q 032393 39 CEACARKVARALKGFEGVDDITADSKASK-------------------VVVKGK--TADPIKVCERLQ 85 (142)
Q Consensus 39 C~~Ca~kIekaL~~i~GV~~V~vd~~~~k-------------------VtV~g~--~vd~~~I~~~I~ 85 (142)
-.||-+-++..+.+++||.++.+-+.++. |.|+.+ .++...|++...
T Consensus 133 agGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F~ 200 (283)
T PRK05550 133 AGGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVFF 200 (283)
T ss_pred ecCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 46777888889999999999999886664 445543 478888888775
No 35
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=47.56 E-value=54 Score=20.97 Aligned_cols=34 Identities=24% Similarity=0.341 Sum_probs=26.8
Q ss_pred CCceEEEEEeccchhHHHHHHHHhhCCCCccEEE
Q 032393 27 ETPEIVLKVDMHCEACARKVARALKGFEGVDDIT 60 (142)
Q Consensus 27 ~~~~i~lkV~M~C~~Ca~kIekaL~~i~GV~~V~ 60 (142)
....+.|.|......=-..|...|++++||.+|.
T Consensus 46 ~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 46 GTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp TEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred CEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 4456667777777777789999999999998763
No 36
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=45.44 E-value=91 Score=22.84 Aligned_cols=48 Identities=21% Similarity=0.440 Sum_probs=31.6
Q ss_pred HHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHH----HHhccCCcEE
Q 032393 44 RKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCER----LQKKSGRKVE 93 (142)
Q Consensus 44 ~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~----I~kk~G~~ae 93 (142)
..+...|..+ |..+|..-+.+|.|.++.. .++..|... |...+|+.+.
T Consensus 22 aeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~-~~~~~l~~~ie~~l~~~fG~~v~ 73 (137)
T PF08002_consen 22 AELREALEDL-GFTNVRTYIQSGNVVFESD-RDPAELAAKIEKALEERFGFDVP 73 (137)
T ss_dssp HHHHHHHHHC-T-EEEEEETTTTEEEEEES-S-HHHHHHHHHHHHHHH-TT---
T ss_pred HHHHHHHHHc-CCCCceEEEeeCCEEEecC-CChHHHHHHHHHHHHHhcCCCeE
Confidence 3456667666 8999999999999999965 677666544 4457888764
No 37
>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=39.55 E-value=95 Score=19.36 Aligned_cols=51 Identities=18% Similarity=0.200 Sum_probs=34.6
Q ss_pred EE-eccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc-CCCHHHHHHHHHhccCCcEEEc
Q 032393 34 KV-DMHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQKKSGRKVELI 95 (142)
Q Consensus 34 kV-~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-~vd~~~I~~~I~kk~G~~aeli 95 (142)
.+ ++.|+.-.-.+.++| .+..- +.+.|..+ ..+...|...++ ..||.+...
T Consensus 3 D~rG~~CP~P~l~~k~al-~~~~g---------~~l~v~~d~~~s~~~i~~~~~-~~G~~~~~~ 55 (67)
T cd03421 3 DARGLACPQPVIKTKKAL-ELEAG---------GEIEVLVDNEVAKENVSRFAE-SRGYEVSVE 55 (67)
T ss_pred ccCCCCCCHHHHHHHHHH-hcCCC---------CEEEEEEcChhHHHHHHHHHH-HcCCEEEEE
Confidence 44 489999999999999 55332 23333322 255678888888 899988543
No 38
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=38.68 E-value=1.2e+02 Score=25.45 Aligned_cols=45 Identities=22% Similarity=0.274 Sum_probs=34.5
Q ss_pred EEEeccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHHhccCCc
Q 032393 33 LKVDMHCEACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRK 91 (142)
Q Consensus 33 lkV~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~kk~G~~ 91 (142)
++.+.+ ..|...+...|.+++||.++++ .+.++-.+.+++.+|+.
T Consensus 65 L~~~~~-~~~~~~v~~~i~~~~gV~~v~~-------------~sre~~l~~L~~~lg~~ 109 (297)
T COG2177 65 LQIDAD-QDDAALVREKIEGIPGVKSVRF-------------ISREEALKELQPWLGFG 109 (297)
T ss_pred EecCCC-hHHHHHHHHHHhcCCCcceEEE-------------eCHHHHHHHHHHHcCch
Confidence 333455 8999999999999999988866 56667777777677763
No 39
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=38.47 E-value=54 Score=23.61 Aligned_cols=21 Identities=33% Similarity=0.553 Sum_probs=18.2
Q ss_pred HHHHHHHhhCCCCccEEEEec
Q 032393 43 ARKVARALKGFEGVDDITADS 63 (142)
Q Consensus 43 a~kIekaL~~i~GV~~V~vd~ 63 (142)
...++.+|..++||.++.+++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 578999999999999988865
No 40
>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=36.22 E-value=1.1e+02 Score=20.28 Aligned_cols=35 Identities=14% Similarity=0.193 Sum_probs=28.5
Q ss_pred ceEEEEEeccchhHHHHHHHHhhCCCCccEEEEec
Q 032393 29 PEIVLKVDMHCEACARKVARALKGFEGVDDITADS 63 (142)
Q Consensus 29 ~~i~lkV~M~C~~Ca~kIekaL~~i~GV~~V~vd~ 63 (142)
.++++-+.-...+.....-..|..++||.++..=+
T Consensus 39 GKiVVtiE~~~~~~~~~~~~~i~~l~GVlsa~lvY 73 (79)
T PF03927_consen 39 GKIVVTIEAESSEEEVDLIDAINALPGVLSASLVY 73 (79)
T ss_dssp TEEEEEEEESSHHHHHHHHHHHCCSTTEEEEEESS
T ss_pred CeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEE
Confidence 66777787777888888889999999998886543
No 41
>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=35.81 E-value=28 Score=26.21 Aligned_cols=46 Identities=11% Similarity=0.028 Sum_probs=33.7
Q ss_pred hhHHHHHHHHhhCCCCccEEEEecCCCEE-------------------EEecc--CCCHHHHHHHHH
Q 032393 40 EACARKVARALKGFEGVDDITADSKASKV-------------------VVKGK--TADPIKVCERLQ 85 (142)
Q Consensus 40 ~~Ca~kIekaL~~i~GV~~V~vd~~~~kV-------------------tV~g~--~vd~~~I~~~I~ 85 (142)
.||-+-++..+..++||.++.+-+.+|.. .|..+ .++...|++...
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~g~tgh~E~V~V~yDp~~is~~~Ll~~f~ 73 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGYTPNPTYEEVCSGDTGHAEAVQVTYDPKVISYEELLDVFW 73 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCCCCCCChhhcccCCCCceEEEEEEECCCcCcHHHHHHHHH
Confidence 46777788889999999999998765532 23332 467788888776
No 42
>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=35.57 E-value=59 Score=23.16 Aligned_cols=29 Identities=31% Similarity=0.534 Sum_probs=24.9
Q ss_pred EEEeccCCCHHHHHHHHHhccCCcEEEcCCC
Q 032393 68 VVVKGKTADPIKVCERLQKKSGRKVELISPL 98 (142)
Q Consensus 68 VtV~g~~vd~~~I~~~I~kk~G~~aelis~~ 98 (142)
+.|+|+ .|...++..++ ..|+++.++++.
T Consensus 104 vLvSgD-~Df~~~i~~lr-~~G~~V~v~~~~ 132 (149)
T cd06167 104 VLVSGD-SDFVPLVERLR-ELGKRVIVVGFE 132 (149)
T ss_pred EEEECC-ccHHHHHHHHH-HcCCEEEEEccC
Confidence 445787 89999999999 789999999986
No 43
>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=34.20 E-value=27 Score=21.43 Aligned_cols=28 Identities=25% Similarity=0.425 Sum_probs=14.9
Q ss_pred HHHHHhhC---CCCccEEEEecCCCEEEEecc
Q 032393 45 KVARALKG---FEGVDDITADSKASKVVVKGK 73 (142)
Q Consensus 45 kIekaL~~---i~GV~~V~vd~~~~kVtV~g~ 73 (142)
+|..+|.. +++- ++.+...++.|+++|.
T Consensus 3 ~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~ 33 (64)
T PF04972_consen 3 KVRAALRADPWLPDS-NISVSVENGVVTLSGE 33 (64)
T ss_dssp ----------CTT-T-TEEEEEECTEEEEEEE
T ss_pred ccccccccccccCCC-eEEEEEECCEEEEEee
Confidence 45556655 4444 6788888999999986
No 44
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=33.47 E-value=44 Score=23.74 Aligned_cols=20 Identities=20% Similarity=0.471 Sum_probs=13.6
Q ss_pred CCCceEEEEEeccchhHHHH
Q 032393 26 EETPEIVLKVDMHCEACARK 45 (142)
Q Consensus 26 ~~~~~i~lkV~M~C~~Ca~k 45 (142)
++..++++-.+..|++|+.-
T Consensus 11 ~a~~~v~~f~d~~Cp~C~~~ 30 (162)
T PF13462_consen 11 DAPITVTEFFDFQCPHCAKF 30 (162)
T ss_dssp TTSEEEEEEE-TTSHHHHHH
T ss_pred CCCeEEEEEECCCCHhHHHH
Confidence 34555666668999999964
No 45
>PRK04435 hypothetical protein; Provisional
Probab=32.13 E-value=1.1e+02 Score=22.57 Aligned_cols=32 Identities=13% Similarity=0.385 Sum_probs=23.6
Q ss_pred eEEEEEeccch-hHHHHHHHHhhCCCCccEEEE
Q 032393 30 EIVLKVDMHCE-ACARKVARALKGFEGVDDITA 61 (142)
Q Consensus 30 ~i~lkV~M~C~-~Ca~kIekaL~~i~GV~~V~v 61 (142)
.+.|.|+.+-. .....+...|++++||.+|.+
T Consensus 111 ~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 111 NVTISIDTSSMEGDIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred EEEEEEEeCChHHHHHHHHHHHHcCCCcEEEEE
Confidence 35566654433 478899999999999988765
No 46
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=31.61 E-value=1.2e+02 Score=19.12 Aligned_cols=30 Identities=17% Similarity=0.268 Sum_probs=21.8
Q ss_pred EEEEEeccchhHHHHHHHHhhCCCCccEEE
Q 032393 31 IVLKVDMHCEACARKVARALKGFEGVDDIT 60 (142)
Q Consensus 31 i~lkV~M~C~~Ca~kIekaL~~i~GV~~V~ 60 (142)
+.|.+......=-..+...|++++||.+|.
T Consensus 39 i~l~i~v~~~~~L~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 39 IYLNFPTIEFEKLQTLMPEIRRIDGVEDVK 68 (74)
T ss_pred EEEEeEecCHHHHHHHHHHHhCCCCceEEE
Confidence 455555555445678999999999998775
No 47
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=31.49 E-value=1.5e+02 Score=20.65 Aligned_cols=55 Identities=18% Similarity=0.213 Sum_probs=30.9
Q ss_pred EEEEEe-ccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc-CCCHHHHHHHHH
Q 032393 31 IVLKVD-MHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQ 85 (142)
Q Consensus 31 i~lkV~-M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-~vd~~~I~~~I~ 85 (142)
++|+|. ++-.-+...|...|+.+..|..|++........|-.. .-+...++..+.
T Consensus 2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~ 58 (105)
T PF08777_consen 2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLK 58 (105)
T ss_dssp -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHH
T ss_pred eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHH
Confidence 356775 7766679999999999999988888886666666433 135667777776
No 48
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=31.23 E-value=1.4e+02 Score=21.03 Aligned_cols=48 Identities=21% Similarity=0.259 Sum_probs=33.8
Q ss_pred ccc-hhHHHHHHHHhhCCCCccEEEEecCCCEEEEeccCCCHHHHHHHHH
Q 032393 37 MHC-EACARKVARALKGFEGVDDITADSKASKVVVKGKTADPIKVCERLQ 85 (142)
Q Consensus 37 M~C-~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~ 85 (142)
++| +.-...|..+|..++|+.-..-|.. |++.|.-...+...|.+.|.
T Consensus 13 v~~~pe~l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie 61 (94)
T COG3062 13 VQAKPERLSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIE 61 (94)
T ss_pred eecCHHHHHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHH
Confidence 444 5667789999999999976666666 77766422146677777765
No 49
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=29.20 E-value=52 Score=27.40 Aligned_cols=44 Identities=20% Similarity=0.216 Sum_probs=29.3
Q ss_pred hHHHHHHHHhhCCCCccEEEEec--CCCEEEEeccCCCHHHHHHHHH
Q 032393 41 ACARKVARALKGFEGVDDITADS--KASKVVVKGKTADPIKVCERLQ 85 (142)
Q Consensus 41 ~Ca~kIekaL~~i~GV~~V~vd~--~~~kVtV~g~~vd~~~I~~~I~ 85 (142)
.-..+|..+...+++|.-++++. ..++-.++.. .|++.++++..
T Consensus 18 ~~ie~i~a~~~~~~~v~ildve~danhNRsViT~v-gdp~~~~~A~f 63 (302)
T COG3643 18 EKIEKIVAAAKSIPTVKILDVEMDANHNRSVITLV-GDPSKVVNAAF 63 (302)
T ss_pred HHHHHHHHHHhcCCceEEEEeccCCCCCceEEEEe-cChHHHHHHHH
Confidence 34567778888999976555544 6666666655 56777766553
No 50
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=27.55 E-value=1.7e+02 Score=18.77 Aligned_cols=29 Identities=17% Similarity=0.292 Sum_probs=20.5
Q ss_pred eccchhHHHHHHHHhhCC----CCccEEEEecCC
Q 032393 36 DMHCEACARKVARALKGF----EGVDDITADSKA 65 (142)
Q Consensus 36 ~M~C~~Ca~kIekaL~~i----~GV~~V~vd~~~ 65 (142)
.-.|+.|. ++.+.|..+ .||.-..+|...
T Consensus 8 ~~~C~~C~-~a~~~L~~l~~~~~~i~~~~idi~~ 40 (85)
T PRK11200 8 RPGCPYCV-RAKELAEKLSEERDDFDYRYVDIHA 40 (85)
T ss_pred CCCChhHH-HHHHHHHhhcccccCCcEEEEECCC
Confidence 36799998 667777775 577666666643
No 51
>PRK11018 hypothetical protein; Provisional
Probab=26.88 E-value=1.9e+02 Score=18.93 Aligned_cols=54 Identities=15% Similarity=0.031 Sum_probs=38.4
Q ss_pred EEEEE-eccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc-CCCHHHHHHHHHhccCCcEEE
Q 032393 31 IVLKV-DMHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQKKSGRKVEL 94 (142)
Q Consensus 31 i~lkV-~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-~vd~~~I~~~I~kk~G~~ael 94 (142)
.++.+ ++.|+.-.-+..++|..++.- +.+.|..+ ..+...|...++ ..||.+..
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G---------~~L~V~~d~~~a~~di~~~~~-~~G~~v~~ 64 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKKG---------EILEVVSDCPQSINNIPLDAR-NHGYTVLD 64 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCCC---------CEEEEEeCCccHHHHHHHHHH-HcCCEEEE
Confidence 45666 599999999999999988532 22333322 256678888888 89998754
No 52
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=26.70 E-value=37 Score=26.48 Aligned_cols=46 Identities=15% Similarity=0.102 Sum_probs=33.5
Q ss_pred hhHHHHHHHHhhCCCCccEEEEecCCCE-------------------EEEecc--CCCHHHHHHHHH
Q 032393 40 EACARKVARALKGFEGVDDITADSKASK-------------------VVVKGK--TADPIKVCERLQ 85 (142)
Q Consensus 40 ~~Ca~kIekaL~~i~GV~~V~vd~~~~k-------------------VtV~g~--~vd~~~I~~~I~ 85 (142)
.||=+-+++.+.+++||.++.+-.++|. |.|+.+ .++..+|+..+.
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG~~~nptY~~Vcsg~TgHaE~V~V~yDp~~isy~~LL~~ff 79 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVTYDPKVISYEELLEVFF 79 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCCCCCCCChhhccCCCCCceEEEEEEeCCccccHHHHHHHHh
Confidence 4666677888999999999999887764 333333 467777877775
No 53
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=26.56 E-value=87 Score=23.43 Aligned_cols=33 Identities=18% Similarity=0.471 Sum_probs=22.4
Q ss_pred eEEEEEeccchhHHH------HHHHHhhCCCCccEEEEec
Q 032393 30 EIVLKVDMHCEACAR------KVARALKGFEGVDDITADS 63 (142)
Q Consensus 30 ~i~lkV~M~C~~Ca~------kIekaL~~i~GV~~V~vd~ 63 (142)
.+.+.|.++..+|.. .|+.+|..+ |+.+|.|++
T Consensus 26 ~V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~-Gv~~V~V~i 64 (146)
T TIGR02159 26 GVVVKFTPTYSGCPALEVIRQDIRDAVRAL-GVEVVEVST 64 (146)
T ss_pred EEEEEEEeCCCCCchHHHHHHHHHHHHHhc-CCCeEEEeE
Confidence 455666566555543 488888887 988887754
No 54
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=26.16 E-value=54 Score=24.66 Aligned_cols=42 Identities=21% Similarity=0.351 Sum_probs=28.0
Q ss_pred hhHHHHHHHHhhCCCCccEEEEecCCCEEE-EeccCCCHHHHHHHHH
Q 032393 40 EACARKVARALKGFEGVDDITADSKASKVV-VKGKTADPIKVCERLQ 85 (142)
Q Consensus 40 ~~Ca~kIekaL~~i~GV~~V~vd~~~~kVt-V~g~~vd~~~I~~~I~ 85 (142)
.+|..++.++|. .+.-|+.+...|+.. -.|. -|.+.|...|.
T Consensus 97 ~~i~rkvlQ~Le---~~~~ve~hp~gGR~lt~~Gq-rdldrIa~~i~ 139 (143)
T KOG3411|consen 97 GGIARKVLQALE---KMGIVEKHPKGGRRLTEQGQ-RDLDRIAGQIR 139 (143)
T ss_pred cHHHHHHHHHHH---hCCceeeCCCCcceeCcccc-hhHHHHHHHHH
Confidence 455555555554 555677888776554 4587 78888887776
No 55
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=24.87 E-value=1.7e+02 Score=17.88 Aligned_cols=50 Identities=14% Similarity=0.145 Sum_probs=34.9
Q ss_pred eccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEecc-CCCHHHHHHHHHhccCCcEEEc
Q 032393 36 DMHCEACARKVARALKGFEGVDDITADSKASKVVVKGK-TADPIKVCERLQKKSGRKVELI 95 (142)
Q Consensus 36 ~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-~vd~~~I~~~I~kk~G~~aeli 95 (142)
++.|+.=...+.++|..++.- +.+.|..+ ......|...++ ..||.+..+
T Consensus 6 g~~CP~Pl~~~~~~l~~l~~g---------~~l~v~~d~~~~~~~i~~~~~-~~g~~~~~~ 56 (69)
T cd00291 6 GLPCPLPVLKTKKALEKLKSG---------EVLEVLLDDPGAVEDIPAWAK-ETGHEVLEV 56 (69)
T ss_pred CCcCCHHHHHHHHHHhcCCCC---------CEEEEEecCCcHHHHHHHHHH-HcCCEEEEE
Confidence 488998888888998886532 33444332 256788889998 899986543
No 56
>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=24.49 E-value=2.2e+02 Score=21.98 Aligned_cols=65 Identities=23% Similarity=0.325 Sum_probs=38.1
Q ss_pred CceEEEEEe-ccchh----HHHHHHHHhhCC--CCccEEEEecCCCEEEEeccCCC--HHHHHHHHHhccCCcEEEcC
Q 032393 28 TPEIVLKVD-MHCEA----CARKVARALKGF--EGVDDITADSKASKVVVKGKTAD--PIKVCERLQKKSGRKVELIS 96 (142)
Q Consensus 28 ~~~i~lkV~-M~C~~----Ca~kIekaL~~i--~GV~~V~vd~~~~kVtV~g~~vd--~~~I~~~I~kk~G~~aelis 96 (142)
..++++-++ --|.. |+.+|-..|.+. ++| ++.|-.+ ++--.....+ ..+=+..|. .+|-++.+++
T Consensus 73 ~y~ITwy~SwSPC~~~~~~Ca~~i~~FL~~~~~~~v-~L~I~~a--rLY~~~~~~~~~~~eGLr~L~-~aGv~v~iM~ 146 (188)
T PF08210_consen 73 IYRITWYLSWSPCPESDHCCAEKIAEFLKKHLKPNV-SLSIFAA--RLYYHWEPEPLWNQEGLRRLA-SAGVQVEIMS 146 (188)
T ss_dssp EEEEEEEESSS--CC----HHHHHHHHHCCC--TTE-EEEEEES--S--STTSTT---HHHHHHHHH-HCTEEEEE-S
T ss_pred eEEEEEEEecCCCcchhhHHHHHHHHHHHHhCCCCC-eEEEEEE--eeeeecCCcchhHHHHHHHHH-HcCCEEEEcC
Confidence 445677777 55999 999999999999 887 3444332 2211222121 334455555 5788888775
No 57
>PRK09577 multidrug efflux protein; Reviewed
Probab=24.44 E-value=2e+02 Score=28.02 Aligned_cols=46 Identities=13% Similarity=0.160 Sum_probs=35.5
Q ss_pred HHHHHHHhhCCCCccEEEEecCCCEEEEecc-------CCCHHHHHHHHHhccC
Q 032393 43 ARKVARALKGFEGVDDITADSKASKVVVKGK-------TADPIKVCERLQKKSG 89 (142)
Q Consensus 43 a~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-------~vd~~~I~~~I~kk~G 89 (142)
.+.|...|.+++||.+|.++-....+.|.-+ ++++.+|.++|+ ..+
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~-~~n 210 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVR-AHN 210 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHH-HhC
Confidence 4679999999999999999876555665311 478999999998 443
No 58
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=24.21 E-value=72 Score=22.13 Aligned_cols=24 Identities=29% Similarity=0.436 Sum_probs=15.2
Q ss_pred CCceEEEEEeccchhHHHHHHHHhh
Q 032393 27 ETPEIVLKVDMHCEACARKVARALK 51 (142)
Q Consensus 27 ~~~~i~lkV~M~C~~Ca~kIekaL~ 51 (142)
+..++++-.+..|++|..- ...|.
T Consensus 5 a~~~i~~f~D~~Cp~C~~~-~~~l~ 28 (154)
T cd03023 5 GDVTIVEFFDYNCGYCKKL-APELE 28 (154)
T ss_pred CCEEEEEEECCCChhHHHh-hHHHH
Confidence 4455555558999999854 44443
No 59
>PRK11670 antiporter inner membrane protein; Provisional
Probab=24.18 E-value=2.3e+02 Score=24.12 Aligned_cols=69 Identities=14% Similarity=0.192 Sum_probs=40.9
Q ss_pred eEEEEEeccchhH------HHHHHHHhhCCCCccEEEEecCC------------------CEEEEe---cc---CCCHHH
Q 032393 30 EIVLKVDMHCEAC------ARKVARALKGFEGVDDITADSKA------------------SKVVVK---GK---TADPIK 79 (142)
Q Consensus 30 ~i~lkV~M~C~~C------a~kIekaL~~i~GV~~V~vd~~~------------------~kVtV~---g~---~vd~~~ 79 (142)
.+.|.+.+.-.+| ...++.+|..++||.++.+.+.. ..+.|. |. .....-
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avN 127 (369)
T PRK11670 48 TLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVN 127 (369)
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHH
Confidence 3445555443444 34688999999999887765532 222342 21 122334
Q ss_pred HHHHHHhccCCcEEEcCCCC
Q 032393 80 VCERLQKKSGRKVELISPLP 99 (142)
Q Consensus 80 I~~~I~kk~G~~aelis~~p 99 (142)
|...+. +.|+++-++..-+
T Consensus 128 LA~aLA-~~G~rVlLID~D~ 146 (369)
T PRK11670 128 LALALA-AEGAKVGILDADI 146 (369)
T ss_pred HHHHHH-HCCCcEEEEeCCC
Confidence 556777 7899988877443
No 60
>PF03434 DUF276: DUF276 ; InterPro: IPR005096 This family is specific to Borrelia burgdorferi (Lyme disease spirochete). The protein is encoded on extrachromosomal DNA and is of unknown function.
Probab=23.93 E-value=1.2e+02 Score=25.27 Aligned_cols=30 Identities=23% Similarity=0.335 Sum_probs=26.6
Q ss_pred hHHHHHHHHhhCCCCccEEEEecCCCEEEE
Q 032393 41 ACARKVARALKGFEGVDDITADSKASKVVV 70 (142)
Q Consensus 41 ~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV 70 (142)
.-...|+++|..++||..+.+-...|++.+
T Consensus 87 tTy~Avk~aLL~~~gv~haNI~SsaGtini 116 (291)
T PF03434_consen 87 TTYEAVKSALLNLNGVEHANIKSSAGTINI 116 (291)
T ss_pred chHHHHHHHhcCCCCceeeeeecCCCeeEE
Confidence 345679999999999999999999999986
No 61
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=23.73 E-value=2e+02 Score=18.17 Aligned_cols=54 Identities=9% Similarity=0.189 Sum_probs=37.7
Q ss_pred EEE-eccchhHHHHHHHHhhCCCCccEEEEecCCCEEEEec-cCCCHHHHHHHHHhccCCcEEEcC
Q 032393 33 LKV-DMHCEACARKVARALKGFEGVDDITADSKASKVVVKG-KTADPIKVCERLQKKSGRKVELIS 96 (142)
Q Consensus 33 lkV-~M~C~~Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g-~~vd~~~I~~~I~kk~G~~aelis 96 (142)
+.+ ++.|+.=.-.+.++|..+..- +.+.|.. +..+...|....+ ..||.+..+.
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~G---------~~l~V~~d~~~a~~di~~~~~-~~G~~~~~~~ 57 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQDG---------EQLEVKASDPGFARDAQAWCK-STGNTLISLE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCC---------CEEEEEECCccHHHHHHHHHH-HcCCEEEEEE
Confidence 344 488999999999999887532 2334432 2357778888888 8999876443
No 62
>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=23.39 E-value=85 Score=21.62 Aligned_cols=24 Identities=25% Similarity=0.507 Sum_probs=20.6
Q ss_pred hhHHHHHHHHhhCCCCccEEEEec
Q 032393 40 EACARKVARALKGFEGVDDITADS 63 (142)
Q Consensus 40 ~~Ca~kIekaL~~i~GV~~V~vd~ 63 (142)
.+-...|+.+|++++||+++.+-.
T Consensus 61 ~g~td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 61 EGGTEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred CcChHHHHHHHhcCCCccEEEEEE
Confidence 366789999999999999998754
No 63
>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=22.95 E-value=1.2e+02 Score=23.23 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=24.7
Q ss_pred EEEeccCCCHHHHHHHHHhccCCcEEEcCCCC
Q 032393 68 VVVKGKTADPIKVCERLQKKSGRKVELISPLP 99 (142)
Q Consensus 68 VtV~g~~vd~~~I~~~I~kk~G~~aelis~~p 99 (142)
+.|+|+ -|...|+.+|+ ..|..+..++.++
T Consensus 110 vLvSgD-~DF~~Lv~~lr-e~G~~V~v~g~~~ 139 (160)
T TIGR00288 110 ALVTRD-ADFLPVINKAK-ENGKETIVIGAEP 139 (160)
T ss_pred EEEecc-HhHHHHHHHHH-HCCCEEEEEeCCC
Confidence 445787 89999999999 7899999999644
No 64
>PF15235 GRIN_C: G protein-regulated inducer of neurite outgrowth C-terminus
Probab=22.90 E-value=1.2e+02 Score=22.75 Aligned_cols=42 Identities=26% Similarity=0.313 Sum_probs=34.2
Q ss_pred CCCCccEEEEecCCCEEEEeccCCCHHHHHHHHHhccCCcEE
Q 032393 52 GFEGVDDITADSKASKVVVKGKTADPIKVCERLQKKSGRKVE 93 (142)
Q Consensus 52 ~i~GV~~V~vd~~~~kVtV~g~~vd~~~I~~~I~kk~G~~ae 93 (142)
.-.-|.+|.+|-.+-+=.|.|..+|++.|--+|+|.+-.+++
T Consensus 40 ~~spVrdV~WDe~GMTWEVYGAs~DpEvLG~AIQkHLE~qi~ 81 (137)
T PF15235_consen 40 AKSPVRDVSWDEQGMTWEVYGASVDPEVLGMAIQKHLERQIE 81 (137)
T ss_pred cCCccccceecCCCceEEEeccccCHHHHHHHHHHHHHHHHH
Confidence 334588999999998889999879999999999876665554
No 65
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=22.70 E-value=3.4e+02 Score=20.40 Aligned_cols=38 Identities=16% Similarity=0.174 Sum_probs=29.5
Q ss_pred EEEEecCCCEEEEec-cCCCHHHHHHHHHhccCCcEEEcC
Q 032393 58 DITADSKASKVVVKG-KTADPIKVCERLQKKSGRKVELIS 96 (142)
Q Consensus 58 ~V~vd~~~~kVtV~g-~~vd~~~I~~~I~kk~G~~aelis 96 (142)
-+-+|+..+-+.+.. ...+..+|+..|. .+|+.+-+.+
T Consensus 45 iAildL~G~~l~l~S~R~~~~~evi~~I~-~~G~PviVAt 83 (138)
T PF04312_consen 45 IAILDLDGELLDLKSSRNMSRSEVIEWIS-EYGKPVIVAT 83 (138)
T ss_pred EEEEecCCcEEEEEeecCCCHHHHHHHHH-HcCCEEEEEe
Confidence 356777777777754 3589999999999 8998876665
No 66
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=22.36 E-value=2.2e+02 Score=27.73 Aligned_cols=44 Identities=18% Similarity=0.225 Sum_probs=34.3
Q ss_pred HHHHHHHHhhCCCCccEEEEecCCCEEEEecc-------CCCHHHHHHHHH
Q 032393 42 CARKVARALKGFEGVDDITADSKASKVVVKGK-------TADPIKVCERLQ 85 (142)
Q Consensus 42 Ca~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-------~vd~~~I~~~I~ 85 (142)
-++.++..|++++||.+|.++-....+.|.-+ ++++.+|..+|+
T Consensus 158 ~~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~ 208 (1037)
T PRK10555 158 VASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIE 208 (1037)
T ss_pred HHHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 34678999999999999999865554666421 579999999998
No 67
>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=21.82 E-value=1.1e+02 Score=20.42 Aligned_cols=22 Identities=14% Similarity=0.280 Sum_probs=16.7
Q ss_pred cCCCEEEEeccCCCHHHHHHHHH
Q 032393 63 SKASKVVVKGKTADPIKVCERLQ 85 (142)
Q Consensus 63 ~~~~kVtV~g~~vd~~~I~~~I~ 85 (142)
+.+|+++++|. -+.+++..+++
T Consensus 55 F~sGki~itGa-ks~~~~~~a~~ 76 (86)
T PF00352_consen 55 FSSGKIVITGA-KSEEEAKKAIE 76 (86)
T ss_dssp ETTSEEEEEEE-SSHHHHHHHHH
T ss_pred EcCCEEEEEec-CCHHHHHHHHH
Confidence 58899999997 67777666655
No 68
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=21.61 E-value=63 Score=22.57 Aligned_cols=30 Identities=23% Similarity=0.506 Sum_probs=19.9
Q ss_pred CEEEEeccCCCHHHHHHHHHhccCCcEEEcCC
Q 032393 66 SKVVVKGKTADPIKVCERLQKKSGRKVELISP 97 (142)
Q Consensus 66 ~kVtV~g~~vd~~~I~~~I~kk~G~~aelis~ 97 (142)
.-+.|+|+ .|...++..++ ..|+++.++..
T Consensus 98 ~ivLvSgD-~Df~~~v~~l~-~~g~~V~v~~~ 127 (146)
T PF01936_consen 98 TIVLVSGD-SDFAPLVRKLR-ERGKRVIVVGA 127 (146)
T ss_dssp EEEEE----GGGHHHHHHHH-HH--EEEEEE-
T ss_pred EEEEEECc-HHHHHHHHHHH-HcCCEEEEEEe
Confidence 34556788 88999999999 89999998884
No 69
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=21.60 E-value=1.5e+02 Score=20.34 Aligned_cols=24 Identities=25% Similarity=0.468 Sum_probs=21.0
Q ss_pred hhHHHHHHHHhhCCCCccEEEEec
Q 032393 40 EACARKVARALKGFEGVDDITADS 63 (142)
Q Consensus 40 ~~Ca~kIekaL~~i~GV~~V~vd~ 63 (142)
.+-...++.+|++++||+++.+-.
T Consensus 61 ~~~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 61 EGGTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred CcCcHHHHHHHhccCCCcEEEEEE
Confidence 477899999999999999998854
No 70
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=20.89 E-value=3.9e+02 Score=20.51 Aligned_cols=71 Identities=21% Similarity=0.356 Sum_probs=44.9
Q ss_pred ceEEEEEeccchhHHHHHH------------HHhhCC------CCccEEEEecCCCEEEE-e--ccC--CCH-HHHHHHH
Q 032393 29 PEIVLKVDMHCEACARKVA------------RALKGF------EGVDDITADSKASKVVV-K--GKT--ADP-IKVCERL 84 (142)
Q Consensus 29 ~~i~lkV~M~C~~Ca~kIe------------kaL~~i------~GV~~V~vd~~~~kVtV-~--g~~--vd~-~~I~~~I 84 (142)
..+-++-++-|++|.+++. ++|..+ .++.....-...+++.+ . |++ +.. -..+.++
T Consensus 6 ~~~c~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~l 85 (166)
T PRK06418 6 CEVCVKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKAL 85 (166)
T ss_pred eeEEeccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHHH
Confidence 3444555689999998764 556554 45555555445677764 2 331 111 2467778
Q ss_pred HhccCCcEEEcCCCC
Q 032393 85 QKKSGRKVELISPLP 99 (142)
Q Consensus 85 ~kk~G~~aelis~~p 99 (142)
++.+|++++++....
T Consensus 86 ~~~lgk~VevVE~s~ 100 (166)
T PRK06418 86 SRKLGKKVRVVEKTN 100 (166)
T ss_pred HHHhCCcEEEEEcCC
Confidence 778999999998655
No 71
>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=20.53 E-value=96 Score=19.40 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=24.0
Q ss_pred HHHHhhCCCCccEEEEec----CCC-EEEEeccCCCHHHHHHHHHh
Q 032393 46 VARALKGFEGVDDITADS----KAS-KVVVKGKTADPIKVCERLQK 86 (142)
Q Consensus 46 IekaL~~i~GV~~V~vd~----~~~-kVtV~g~~vd~~~I~~~I~k 86 (142)
|+.+|.+++||.++.+=. ..| .+...-. .+...|.+.++.
T Consensus 2 IE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv-~~~~~i~~~~~~ 46 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAVVGVPDEDWGERLVAFVV-LDEEEIRDHLRD 46 (73)
T ss_dssp HHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEE-EHHHHHHHHHHH
T ss_pred HHHHHhcCCCccEEEEEEEEcccccccceeEEE-eeecccccchhh
Confidence 788999999998876643 222 2221111 134677777764
No 72
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=20.24 E-value=2.6e+02 Score=27.27 Aligned_cols=43 Identities=14% Similarity=0.214 Sum_probs=33.7
Q ss_pred HHHHHHHhhCCCCccEEEEecCCCEEEEecc-------CCCHHHHHHHHH
Q 032393 43 ARKVARALKGFEGVDDITADSKASKVVVKGK-------TADPIKVCERLQ 85 (142)
Q Consensus 43 a~kIekaL~~i~GV~~V~vd~~~~kVtV~g~-------~vd~~~I~~~I~ 85 (142)
.+.|...|++++||.+|.+.-....+.|.-+ ++++.+|.++|+
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~ 208 (1049)
T PRK15127 159 AANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIK 208 (1049)
T ss_pred HHHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHH
Confidence 3568999999999999998766544666421 478999999998
No 73
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=20.16 E-value=2e+02 Score=21.14 Aligned_cols=29 Identities=24% Similarity=0.469 Sum_probs=23.3
Q ss_pred ceEEEEEe-ccchhHHHHHHHHhhCCCCcc
Q 032393 29 PEIVLKVD-MHCEACARKVARALKGFEGVD 57 (142)
Q Consensus 29 ~~i~lkV~-M~C~~Ca~kIekaL~~i~GV~ 57 (142)
.++.|-.. -.|.+|..-|.+-....++|.
T Consensus 97 G~i~l~te~~pC~SC~~vi~qF~~~~pni~ 126 (133)
T PF14424_consen 97 GTIDLFTELPPCESCSNVIEQFKKDFPNIK 126 (133)
T ss_pred ceEEEEecCCcChhHHHHHHHHHHHCCCcE
Confidence 34555555 779999999999999999985
Done!