Query 033335
Match_columns 121
No_of_seqs 156 out of 712
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 12:39:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033335.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033335hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.7 1.4E-16 3.1E-21 104.4 7.4 64 1-66 7-71 (73)
2 PF00403 HMA: Heavy-metal-asso 99.2 6.4E-11 1.4E-15 74.0 6.9 57 2-60 1-60 (62)
3 COG2608 CopZ Copper chaperone 98.3 2.3E-06 4.9E-11 55.7 6.0 57 3-61 6-65 (71)
4 KOG4656 Copper chaperone for s 98.2 5.9E-06 1.3E-10 64.9 7.3 65 2-68 10-74 (247)
5 PLN02957 copper, zinc superoxi 97.7 0.00019 4.1E-09 56.4 8.2 67 2-71 9-76 (238)
6 PRK10671 copA copper exporting 96.4 0.0057 1.2E-07 55.4 5.6 59 3-66 7-67 (834)
7 TIGR00003 copper ion binding p 92.8 0.73 1.6E-05 25.4 5.9 50 6-56 10-61 (68)
8 PRK10671 copA copper exporting 89.7 0.85 1.8E-05 41.6 5.9 56 6-64 107-163 (834)
9 COG2217 ZntA Cation transport 89.0 0.92 2E-05 41.3 5.6 56 6-64 10-69 (713)
10 PF02680 DUF211: Uncharacteriz 87.3 0.78 1.7E-05 31.9 3.2 46 15-60 21-72 (95)
11 COG1888 Uncharacterized protei 87.2 1.5 3.2E-05 30.5 4.5 46 15-60 23-74 (97)
12 KOG0207 Cation transport ATPas 81.2 3.8 8.1E-05 38.5 5.7 61 6-68 2-64 (951)
13 KOG0207 Cation transport ATPas 78.4 3 6.4E-05 39.2 4.1 61 5-66 153-215 (951)
14 PRK11033 zntA zinc/cadmium/mer 71.9 10 0.00022 34.4 5.8 52 6-60 61-113 (741)
15 PF13732 DUF4162: Domain of un 71.5 14 0.00031 23.4 5.0 38 20-58 26-63 (84)
16 cd04888 ACT_PheB-BS C-terminal 61.9 17 0.00036 22.3 3.8 20 12-31 55-74 (76)
17 PF01883 DUF59: Domain of unkn 60.6 12 0.00025 23.4 2.9 20 12-31 53-72 (72)
18 PF09358 UBA_e1_C: Ubiquitin-a 59.9 17 0.00037 25.9 3.9 32 37-69 35-67 (125)
19 PF13291 ACT_4: ACT domain; PD 58.1 20 0.00042 22.6 3.7 28 3-30 52-79 (80)
20 PF14492 EFG_II: Elongation Fa 57.7 27 0.00058 22.4 4.3 47 16-63 24-72 (75)
21 PF03927 NapD: NapD protein; 56.3 23 0.00051 23.2 3.9 30 2-31 42-71 (79)
22 COG1432 Uncharacterized conser 55.6 18 0.0004 27.1 3.7 31 38-69 114-144 (181)
23 cd06167 LabA_like LabA_like pr 50.0 28 0.00061 24.2 3.7 30 38-68 103-132 (149)
24 PF03927 NapD: NapD protein; 48.8 74 0.0016 20.8 5.7 45 11-57 15-59 (79)
25 TIGR00288 conserved hypothetic 48.1 30 0.00065 26.0 3.8 29 38-67 109-137 (160)
26 PRK10553 assembly protein for 46.4 78 0.0017 21.3 5.3 53 13-66 19-76 (87)
27 cd04910 ACT_AK-Ectoine_1 ACT d 45.7 57 0.0012 21.2 4.4 54 9-64 14-69 (71)
28 KOG3411 40S ribosomal protein 44.2 18 0.0004 26.7 2.0 44 10-57 97-140 (143)
29 PF14437 MafB19-deam: MafB19-l 43.4 44 0.00096 24.9 4.0 38 2-40 103-141 (146)
30 PF01936 NYN: NYN domain; Int 43.2 32 0.0007 23.4 3.1 29 38-67 99-127 (146)
31 cd04877 ACT_TyrR N-terminal AC 42.9 48 0.0011 20.6 3.7 16 14-29 52-67 (74)
32 PF08712 Nfu_N: Scaffold prote 41.2 71 0.0015 21.2 4.4 42 15-59 38-80 (87)
33 PF05193 Peptidase_M16_C: Pept 41.1 28 0.0006 23.8 2.5 23 37-60 20-42 (184)
34 PHA00514 dsDNA binding protein 40.5 47 0.001 22.9 3.5 34 37-71 32-67 (98)
35 PRK10553 assembly protein for 38.4 60 0.0013 21.9 3.7 31 2-32 45-75 (87)
36 PF07683 CobW_C: Cobalamin syn 37.4 35 0.00075 21.9 2.4 23 35-57 70-92 (94)
37 COG2177 FtsX Cell division pro 36.2 85 0.0018 25.7 5.0 38 10-61 71-108 (297)
38 PRK04021 hypothetical protein; 35.4 86 0.0019 21.3 4.2 46 8-56 43-91 (92)
39 cd04878 ACT_AHAS N-terminal AC 34.9 54 0.0012 19.0 2.8 9 48-56 55-63 (72)
40 TIGR00915 2A0602 The (Largely 33.8 79 0.0017 29.9 5.0 44 13-57 159-209 (1044)
41 PRK10555 aminoglycoside/multid 33.7 80 0.0017 29.9 5.0 45 13-58 159-210 (1037)
42 PRK15127 multidrug efflux syst 33.2 82 0.0018 29.9 5.0 44 13-57 159-209 (1049)
43 PF07338 DUF1471: Protein of u 32.0 58 0.0013 20.0 2.6 23 37-59 6-28 (56)
44 PRK10614 multidrug efflux syst 31.9 92 0.002 29.4 5.1 46 13-58 159-211 (1025)
45 PRK09577 multidrug efflux prot 31.9 83 0.0018 29.8 4.8 45 13-58 158-209 (1032)
46 PRK10503 multidrug efflux syst 31.7 94 0.002 29.5 5.1 44 14-57 169-219 (1040)
47 PF08478 POTRA_1: POTRA domain 31.2 58 0.0012 19.7 2.6 29 14-42 37-65 (69)
48 PF12164 SporV_AA: Stage V spo 31.1 56 0.0012 22.1 2.7 54 7-71 29-82 (93)
49 PF00873 ACR_tran: AcrB/AcrD/A 29.5 60 0.0013 30.3 3.4 47 12-58 157-210 (1021)
50 TIGR00489 aEF-1_beta translati 29.5 77 0.0017 21.5 3.1 23 11-33 62-84 (88)
51 PF05922 Inhibitor_I9: Peptida 28.6 57 0.0012 20.2 2.3 18 15-32 59-76 (82)
52 smart00833 CobW_C Cobalamin sy 28.5 86 0.0019 19.8 3.2 22 36-57 69-90 (92)
53 PF01253 SUI1: Translation ini 27.6 56 0.0012 21.3 2.2 30 38-67 19-53 (83)
54 cd03309 CmuC_like CmuC_like. P 27.4 87 0.0019 25.6 3.7 45 5-51 215-269 (321)
55 PRK09579 multidrug efflux prot 27.4 1.5E+02 0.0033 28.0 5.7 46 13-58 158-210 (1017)
56 PF04972 BON: BON domain; Int 27.2 1E+02 0.0022 18.3 3.2 23 8-30 35-57 (64)
57 PRK11198 LysM domain/BON super 26.7 1.4E+02 0.0031 21.5 4.3 51 10-65 25-79 (147)
58 COG0612 PqqL Predicted Zn-depe 26.3 65 0.0014 26.6 2.8 24 37-61 199-222 (438)
59 PF10369 ALS_ss_C: Small subun 26.3 1.7E+02 0.0038 18.7 4.3 60 2-65 6-65 (75)
60 PF00679 EFG_C: Elongation fac 25.8 1.9E+02 0.0041 18.6 5.4 61 3-65 7-72 (89)
61 PLN02625 uroporphyrin-III C-me 25.5 75 0.0016 24.9 2.9 32 36-67 14-46 (263)
62 PRK00435 ef1B elongation facto 25.4 89 0.0019 21.1 2.8 24 10-33 61-84 (88)
63 cd04879 ACT_3PGDH-like ACT_3PG 25.3 74 0.0016 18.3 2.3 19 13-31 52-70 (71)
64 smart00653 eIF2B_5 domain pres 25.3 1.1E+02 0.0025 21.3 3.5 29 29-60 50-78 (110)
65 PRK00378 nucleoid-associated p 24.7 89 0.0019 25.4 3.3 29 27-59 303-331 (334)
66 COG3062 NapD Uncharacterized p 24.2 2.3E+02 0.0049 19.7 4.7 44 11-56 18-61 (94)
67 cd04876 ACT_RelA-SpoT ACT dom 24.1 1.4E+02 0.003 16.4 3.6 12 46-57 51-62 (71)
68 COG0841 AcrB Cation/multidrug 24.1 1.4E+02 0.0031 28.5 4.8 46 12-57 156-208 (1009)
69 cd02643 R3H_NF-X1 R3H domain o 24.1 1.3E+02 0.0029 19.3 3.4 30 13-42 44-73 (74)
70 PF05137 PilN: Fimbrial assemb 23.8 1.7E+02 0.0036 17.9 3.8 41 26-69 16-61 (78)
71 PF13241 NAD_binding_7: Putati 23.0 1.4E+02 0.0031 19.8 3.5 39 30-69 2-40 (103)
72 cd04887 ACT_MalLac-Enz ACT_Mal 23.0 1.8E+02 0.0039 17.4 3.8 19 11-29 52-70 (74)
73 PF01424 R3H: R3H domain; Int 22.6 1.3E+02 0.0028 18.1 3.0 33 10-42 29-61 (63)
74 PF04468 PSP1: PSP1 C-terminal 22.3 2.4E+02 0.0052 18.6 6.0 53 11-65 30-86 (88)
75 cd04903 ACT_LSD C-terminal ACT 22.0 94 0.002 17.9 2.3 19 13-31 52-70 (71)
76 PRK11023 outer membrane lipopr 22.0 1.8E+02 0.004 21.8 4.4 48 8-57 46-96 (191)
77 COG2092 EFB1 Translation elong 21.9 1.1E+02 0.0023 21.0 2.7 29 4-32 54-83 (88)
78 TIGR00914 2A0601 heavy metal e 21.7 1.6E+02 0.0035 27.9 4.7 44 15-58 170-220 (1051)
79 cd06472 ACD_ScHsp26_like Alpha 21.6 72 0.0016 20.8 1.8 24 21-44 15-40 (92)
80 PRK13748 putative mercuric red 21.6 3.5E+02 0.0076 23.1 6.5 60 6-67 8-69 (561)
81 PRK06136 uroporphyrin-III C-me 20.9 1E+02 0.0022 23.5 2.8 31 37-67 3-34 (249)
82 TIGR02945 SUF_assoc FeS assemb 20.8 93 0.002 20.5 2.3 21 13-33 57-77 (99)
83 PF02107 FlgH: Flagellar L-rin 20.7 62 0.0013 24.4 1.5 44 22-67 110-156 (179)
84 TIGR03406 FeS_long_SufT probab 20.3 1.1E+02 0.0023 23.2 2.7 31 3-33 117-153 (174)
85 PF00070 Pyr_redox: Pyridine n 20.2 2E+02 0.0043 17.8 3.6 31 38-68 1-31 (80)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.68 E-value=1.4e-16 Score=104.37 Aligned_cols=64 Identities=34% Similarity=0.455 Sum_probs=57.9
Q ss_pred CEEEEeccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHhhcC-ceEEEe
Q 033335 1 MVIKVSMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRKKVG-YAEVVS 66 (121)
Q Consensus 1 vVlKV~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~-~aeivs 66 (121)
.+++|+|||+||++++++.+.++.||+++.+|++ +++|||.|. +||..|+++|+|+++ .+++|.
T Consensus 7 ~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~-~~kvtV~g~-~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 7 VVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIK-KQKVTVKGN-VDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred EEEEECcccccHHHHHHHHhhccCCeEEEEecCC-CCEEEEEEe-cCHHHHHHHHHhcCCCceEEec
Confidence 3789999999999999999999999999999997 689999999 999999999998764 566553
No 2
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.21 E-value=6.4e-11 Score=73.98 Aligned_cols=57 Identities=25% Similarity=0.294 Sum_probs=50.1
Q ss_pred EEEE-eccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccc--cCHHHHHHHHHhhcC
Q 033335 2 VIKV-SMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDG--VDAVALTTSLRKKVG 60 (121)
Q Consensus 2 VlKV-~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~--vDp~~l~~~LrKk~~ 60 (121)
+|+| +|+|++|.+++.++|.+++||.++.+|.. .++++|.++. +++.+|.++|++ .|
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~-~~~v~v~~~~~~~~~~~i~~~i~~-~G 60 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLE-TKTVTVTYDPDKTSIEKIIEAIEK-AG 60 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETT-TTEEEEEESTTTSCHHHHHHHHHH-TT
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECC-CCEEEEEEecCCCCHHHHHHHHHH-hC
Confidence 4777 89999999999999999999999999986 6899999982 345999999996 44
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.30 E-value=2.3e-06 Score=55.68 Aligned_cols=57 Identities=23% Similarity=0.325 Sum_probs=46.9
Q ss_pred EEE-eccchhhHHHHHHHhcCCCcccEEEecCCCCC--eEEEEccccCHHHHHHHHHhhcCc
Q 033335 3 IKV-SMNKHKSRSKALKVAVGFSGVESVALKGDDMS--QIEVTGDGVDAVALTTSLRKKVGY 61 (121)
Q Consensus 3 lKV-~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~--kvtV~G~~vDp~~l~~~LrKk~~~ 61 (121)
|++ +|+|+.|...+.++|.+++||.++.+|.+ .+ .|++.+..++...|...+.. .|+
T Consensus 6 l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~-~~~~~V~~d~~~~~~~~i~~ai~~-aGy 65 (71)
T COG2608 6 LKVEGMTCGHCVKTVEKALEEVDGVASVDVDLE-KGTATVTFDSNKVDIEAIIEAIED-AGY 65 (71)
T ss_pred EEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcc-cCeEEEEEcCCcCCHHHHHHHHHH-cCC
Confidence 444 79999999999999999999999999987 53 45555533899999999986 563
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.20 E-value=5.9e-06 Score=64.88 Aligned_cols=65 Identities=17% Similarity=0.195 Sum_probs=57.1
Q ss_pred EEEEeccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHhhcCceEEEecc
Q 033335 2 VIKVSMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRKKVGYAEVVSVG 68 (121)
Q Consensus 2 VlKV~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~ 68 (121)
.+-|+|||+.|...+++.|..++||++|++|.+ .+.|.|-+. +-+..+...|+.....|-|.-.+
T Consensus 10 efaV~M~cescvnavk~~L~~V~Gi~~vevdle-~q~v~v~ts-~p~s~i~~~le~tGr~Avl~G~G 74 (247)
T KOG4656|consen 10 EFAVQMTCESCVNAVKACLKGVPGINSVEVDLE-QQIVSVETS-VPPSEIQNTLENTGRDAVLRGAG 74 (247)
T ss_pred EEEEechhHHHHHHHHHHhccCCCcceEEEEhh-hcEEEEEcc-CChHHHHHHHHhhChheEEecCC
Confidence 466999999999999999999999999999997 578899998 99999999999743478877554
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=97.73 E-value=0.00019 Score=56.37 Aligned_cols=67 Identities=19% Similarity=0.247 Sum_probs=58.2
Q ss_pred EEEEeccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHhhcC-ceEEEeccCCC
Q 033335 2 VIKVSMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRKKVG-YAEVVSVGAAG 71 (121)
Q Consensus 2 VlKV~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv~~~k 71 (121)
.+.+.|+|+.|..++.+.+.+++||.++.++.. .++++|.+. .++..++..|++ .+ .+++++.+++.
T Consensus 9 ~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~-~~~v~V~~~-~~~~~I~~aIe~-~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 9 EFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLS-NQVVRVLGS-SPVKAMTAALEQ-TGRKARLIGQGDPE 76 (238)
T ss_pred EEEECccCHHHHHHHHHHHhcCCCeEEEEEEcC-CCEEEEEec-CCHHHHHHHHHH-cCCcEEEecCCCcc
Confidence 467899999999999999999999999999986 579999987 899999999986 56 68888776654
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.45 E-value=0.0057 Score=55.43 Aligned_cols=59 Identities=19% Similarity=0.226 Sum_probs=50.4
Q ss_pred EEE-eccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHhhcC-ceEEEe
Q 033335 3 IKV-SMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRKKVG-YAEVVS 66 (121)
Q Consensus 3 lKV-~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~-~aeivs 66 (121)
++| .|+|..|..++.+++.+++||.++.+|.+ +.+|.+. .++..+...++. .| .+++.+
T Consensus 7 l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~---~~~v~~~-~~~~~i~~~i~~-~Gy~~~~~~ 67 (834)
T PRK10671 7 LTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT---EAHVTGT-ASAEALIETIKQ-AGYDASVSH 67 (834)
T ss_pred EEECCcccHHHHHHHHHHHhcCCCcceEEEeee---EEEEEec-CCHHHHHHHHHh-cCCcccccc
Confidence 444 79999999999999999999999999973 5677888 899999999985 66 677764
No 7
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=92.77 E-value=0.73 Score=25.37 Aligned_cols=50 Identities=20% Similarity=0.250 Sum_probs=38.8
Q ss_pred eccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEcc--ccCHHHHHHHHH
Q 033335 6 SMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGD--GVDAVALTTSLR 56 (121)
Q Consensus 6 ~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~--~vDp~~l~~~Lr 56 (121)
.++|..|...+.+.+..+.|+.+..++.. ...+++..+ ..+...+...+.
T Consensus 10 ~~~~~~c~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 61 (68)
T TIGR00003 10 SMTCQHCVDKIEKFVGELEGVSKVQVKLE-KASVKVEFDAPQATEICIAEAIL 61 (68)
T ss_pred CeEcHHHHHHHHHHHhcCCCEEEEEEEcC-CCEEEEEeCCCCCCHHHHHHHHH
Confidence 46799999999999999999999999875 457777642 257777766654
No 8
>PRK10671 copA copper exporting ATPase; Provisional
Probab=89.66 E-value=0.85 Score=41.58 Aligned_cols=56 Identities=20% Similarity=0.197 Sum_probs=46.8
Q ss_pred eccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHhhcC-ceEE
Q 033335 6 SMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRKKVG-YAEV 64 (121)
Q Consensus 6 ~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~-~aei 64 (121)
.|+|..|...+.+.+.+++||.++.++.. .+++.+.+. .++..+.+.++. .| .+.+
T Consensus 107 Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~-t~~~~V~~~-~s~~~I~~~I~~-~Gy~a~~ 163 (834)
T PRK10671 107 GMSCASCVSRVQNALQSVPGVTQARVNLA-ERTALVMGS-ASPQDLVQAVEK-AGYGAEA 163 (834)
T ss_pred CcCcHHHHHHHHHHHhcCCCceeeeeecC-CCeEEEEcc-CCHHHHHHHHHh-cCCCccc
Confidence 68999999999999999999999999975 567888776 889998888875 56 4443
No 9
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=89.05 E-value=0.92 Score=41.29 Aligned_cols=56 Identities=21% Similarity=0.248 Sum_probs=46.7
Q ss_pred eccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccc--cC-HHHHHHHHHhhcC-ceEE
Q 033335 6 SMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDG--VD-AVALTTSLRKKVG-YAEV 64 (121)
Q Consensus 6 ~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~--vD-p~~l~~~LrKk~~-~aei 64 (121)
.|||..|..++. .+.+++||.+..++.. ..+++|..+. .+ +..+...+++ .| .+..
T Consensus 10 Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~-t~~~~v~~~~~~~~~~~~~~~~v~~-~gy~~~~ 69 (713)
T COG2217 10 GMTCAACASRIE-ALNKLPGVEEARVNLA-TERATVVYDPEEVDLPADIVAAVEK-AGYSARL 69 (713)
T ss_pred CcCcHHHHHHHH-HHhcCCCeeEEEeecc-cceEEEEecccccccHHHHHHHHHh-cCccccc
Confidence 699999999999 9999999999999985 6799988652 56 7889999886 45 4554
No 10
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=87.30 E-value=0.78 Score=31.90 Aligned_cols=46 Identities=20% Similarity=0.371 Sum_probs=32.7
Q ss_pred HHHHHhcCCCcccEEEe-----cCCCCC-eEEEEccccCHHHHHHHHHhhcC
Q 033335 15 KALKVAVGFSGVESVAL-----KGDDMS-QIEVTGDGVDAVALTTSLRKKVG 60 (121)
Q Consensus 15 K~~k~~~~~~GV~sv~~-----d~~~~~-kvtV~G~~vDp~~l~~~LrKk~~ 60 (121)
..-+.|++++||+.|.+ |.+-.+ ++||.|+.+|-..+.+.|.+.++
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg 72 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGG 72 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCC
Confidence 45567889999988754 432112 88999999999999999997433
No 11
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=87.24 E-value=1.5 Score=30.47 Aligned_cols=46 Identities=17% Similarity=0.266 Sum_probs=33.7
Q ss_pred HHHHHhcCCCcccEEEe-----cCCCCC-eEEEEccccCHHHHHHHHHhhcC
Q 033335 15 KALKVAVGFSGVESVAL-----KGDDMS-QIEVTGDGVDAVALTTSLRKKVG 60 (121)
Q Consensus 15 K~~k~~~~~~GV~sv~~-----d~~~~~-kvtV~G~~vDp~~l~~~LrKk~~ 60 (121)
..-+.|++++||+.|.+ |.+-.+ ++||-|..+|-..|.+.|-.-+|
T Consensus 23 e~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg 74 (97)
T COG1888 23 ELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGG 74 (97)
T ss_pred HHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCC
Confidence 34567888888877644 433222 89999988999999999997444
No 12
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=81.18 E-value=3.8 Score=38.54 Aligned_cols=61 Identities=13% Similarity=0.174 Sum_probs=49.2
Q ss_pred eccchhhHHHHHHHhcCCCcccEEEecCCCCC-eEEEEccccCHHHHHHHHHhhcC-ceEEEecc
Q 033335 6 SMNKHKSRSKALKVAVGFSGVESVALKGDDMS-QIEVTGDGVDAVALTTSLRKKVG-YAEVVSVG 68 (121)
Q Consensus 6 ~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~-kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv~ 68 (121)
.|.|..|.+.+.+.+++.+||.+++++...++ ++.-. ..++++.|.+.+.- .| .+++++-.
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~-~~~~~~~i~~~ied-~gf~~~~~~~~ 64 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYD-NIVSPESIKETIED-MGFEASLLSDS 64 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEe-eccCHHHHHHHhhc-ccceeeecccC
Confidence 58999999999999999999999999886422 45556 44899999999885 45 78887543
No 13
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=78.44 E-value=3 Score=39.21 Aligned_cols=61 Identities=16% Similarity=0.064 Sum_probs=46.7
Q ss_pred EeccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEcc--ccCHHHHHHHHHhhcCceEEEe
Q 033335 5 VSMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGD--GVDAVALTTSLRKKVGYAEVVS 66 (121)
Q Consensus 5 V~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~--~vDp~~l~~~LrKk~~~aeivs 66 (121)
..|.|+.|..++.+.+.+++||.+++++.. .+++.|.=+ ..-|.++.+.|-...-.+.+..
T Consensus 153 ~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~-t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~ 215 (951)
T KOG0207|consen 153 LGMTCASCVSKIESILERLRGVKSFSVSLA-TDTAIVVYDPEITGPRDIIKAIEETGFEASVRP 215 (951)
T ss_pred ecccccchhhhhHHHHhhccCeeEEEEecc-CCceEEEecccccChHHHHHHHHhhcccceeee
Confidence 478999999999999999999999999975 678888654 2566777777764322455544
No 14
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=71.94 E-value=10 Score=34.39 Aligned_cols=52 Identities=17% Similarity=0.282 Sum_probs=38.5
Q ss_pred eccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccc-cCHHHHHHHHHhhcC
Q 033335 6 SMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDG-VDAVALTTSLRKKVG 60 (121)
Q Consensus 6 ~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~-vDp~~l~~~LrKk~~ 60 (121)
.|+|..|..++.+.+.+++||.++.++.. ..++.+..+. .+ ..+.+.++. .|
T Consensus 61 Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~a-t~k~~V~~d~~~~-~~I~~aI~~-~G 113 (741)
T PRK11033 61 GMDCPSCARKVENAVRQLAGVNQVQVLFA-TEKLVVDADNDIR-AQVESAVQK-AG 113 (741)
T ss_pred CCCcHHHHHHHHHHHhcCCCeeeEEEEcC-CCeEEEEecccch-HHHHHHHHh-cc
Confidence 58999999999999999999999999865 4566665331 23 555555554 44
No 15
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=71.50 E-value=14 Score=23.41 Aligned_cols=38 Identities=32% Similarity=0.378 Sum_probs=30.0
Q ss_pred hcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHhh
Q 033335 20 AVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRKK 58 (121)
Q Consensus 20 ~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk 58 (121)
+..++||.++..+....-.+.+... .++..|++.|..+
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~-~~~~~ll~~l~~~ 63 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDE-ETANELLQELIEK 63 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCc-ccHHHHHHHHHhC
Confidence 7778999999986543247777776 8999999999864
No 16
>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=61.94 E-value=17 Score=22.28 Aligned_cols=20 Identities=30% Similarity=0.343 Sum_probs=13.7
Q ss_pred hHHHHHHHhcCCCcccEEEe
Q 033335 12 SRSKALKVAVGFSGVESVAL 31 (121)
Q Consensus 12 C~~K~~k~~~~~~GV~sv~~ 31 (121)
--..+++.|.+++||.+|.+
T Consensus 55 ~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 55 DIDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHHhcCCCeEEEEE
Confidence 45667777777777777664
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=60.58 E-value=12 Score=23.43 Aligned_cols=20 Identities=25% Similarity=0.343 Sum_probs=15.7
Q ss_pred hHHHHHHHhcCCCcccEEEe
Q 033335 12 SRSKALKVAVGFSGVESVAL 31 (121)
Q Consensus 12 C~~K~~k~~~~~~GV~sv~~ 31 (121)
=+..+.++|..++||.+|++
T Consensus 53 l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 53 LREEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHHhCCCCceEeC
Confidence 45778889999999999875
No 18
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=59.94 E-value=17 Score=25.92 Aligned_cols=32 Identities=31% Similarity=0.500 Sum_probs=26.7
Q ss_pred CeEEEEccccCHHHHHHHHHhhcC-ceEEEeccC
Q 033335 37 SQIEVTGDGVDAVALTTSLRKKVG-YAEVVSVGA 69 (121)
Q Consensus 37 ~kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv~~ 69 (121)
+++.|.|+ +....|++.|+++.| .+.++|.|.
T Consensus 35 Dr~~v~~~-~Tl~~li~~~~~~~~lev~ml~~g~ 67 (125)
T PF09358_consen 35 DRIEVNGD-MTLQELIDYFKEKYGLEVTMLSQGV 67 (125)
T ss_dssp -EEEEES---BHHHHHHHHHHTTS-EEEEEEETT
T ss_pred eEEEEcCC-CCHHHHHHHHHHHhCceEEEEEeCC
Confidence 68999997 999999999999988 899999874
No 19
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=58.07 E-value=20 Score=22.58 Aligned_cols=28 Identities=18% Similarity=0.261 Sum_probs=20.7
Q ss_pred EEEeccchhhHHHHHHHhcCCCcccEEE
Q 033335 3 IKVSMNKHKSRSKALKVAVGFSGVESVA 30 (121)
Q Consensus 3 lKV~m~C~~C~~K~~k~~~~~~GV~sv~ 30 (121)
|.+....-.--..+++.|.+++||.+|.
T Consensus 52 l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 52 LTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 4555666666778888888888888774
No 20
>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=57.70 E-value=27 Score=22.38 Aligned_cols=47 Identities=19% Similarity=0.245 Sum_probs=31.2
Q ss_pred HHHHhcCCCcccEEEecCCCCCeEEEEccc-cCHHHHHHHHHhhcC-ceE
Q 033335 16 ALKVAVGFSGVESVALKGDDMSQIEVTGDG-VDAVALTTSLRKKVG-YAE 63 (121)
Q Consensus 16 ~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~-vDp~~l~~~LrKk~~-~ae 63 (121)
+++.|..-+=--.+..|-+ .+++.|.|-| +--.-++++|+.+++ .++
T Consensus 24 aL~~l~~eDP~l~~~~d~e-t~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 24 ALQKLSEEDPSLRVERDEE-TGELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp HHHHHHHH-TTSEEEEETT-TSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred HHHHHHhcCCeEEEEEcch-hceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 3333333333447788754 6788887765 888899999998887 444
No 21
>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=56.25 E-value=23 Score=23.17 Aligned_cols=30 Identities=17% Similarity=0.313 Sum_probs=21.1
Q ss_pred EEEEeccchhhHHHHHHHhcCCCcccEEEe
Q 033335 2 VIKVSMNKHKSRSKALKVAVGFSGVESVAL 31 (121)
Q Consensus 2 VlKV~m~C~~C~~K~~k~~~~~~GV~sv~~ 31 (121)
|+-+.-...+-..+.++.|..++||-|+.+
T Consensus 42 VVtiE~~~~~~~~~~~~~i~~l~GVlsa~l 71 (79)
T PF03927_consen 42 VVTIEAESSEEEVDLIDAINALPGVLSASL 71 (79)
T ss_dssp EEEEEESSHHHHHHHHHHHCCSTTEEEEEE
T ss_pred EEEEEeCChHHHHHHHHHHHcCCCceEEEE
Confidence 344445556677777888888888888776
No 22
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=55.64 E-value=18 Score=27.09 Aligned_cols=31 Identities=26% Similarity=0.324 Sum_probs=27.2
Q ss_pred eEEEEccccCHHHHHHHHHhhcCceEEEeccC
Q 033335 38 QIEVTGDGVDAVALTTSLRKKVGYAEVVSVGA 69 (121)
Q Consensus 38 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~~ 69 (121)
-+.++|+ -|-.-+++.+|.+++.++++++++
T Consensus 114 ivl~SgD-~DF~p~v~~~~~~G~rv~v~~~~~ 144 (181)
T COG1432 114 IVLFSGD-GDFIPLVEAARDKGKRVEVAGIEP 144 (181)
T ss_pred EEEEcCC-ccHHHHHHHHHHcCCEEEEEecCC
Confidence 5667899 899999999998888999999986
No 23
>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=49.95 E-value=28 Score=24.22 Aligned_cols=30 Identities=33% Similarity=0.323 Sum_probs=25.0
Q ss_pred eEEEEccccCHHHHHHHHHhhcCceEEEecc
Q 033335 38 QIEVTGDGVDAVALTTSLRKKVGYAEVVSVG 68 (121)
Q Consensus 38 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~ 68 (121)
=+.|+|+ -|-.-++++||.+...+.+++..
T Consensus 103 ivLvSgD-~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 103 IVLVSGD-SDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEEECC-ccHHHHHHHHHHcCCEEEEEccC
Confidence 5677999 89999999999875588888764
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=48.78 E-value=74 Score=20.76 Aligned_cols=45 Identities=16% Similarity=0.123 Sum_probs=32.7
Q ss_pred hhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHh
Q 033335 11 KSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRK 57 (121)
Q Consensus 11 ~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrK 57 (121)
.=...+.+.|..++|++=-..+. .+|++|+=++-+...+.+.|..
T Consensus 15 ~~~~~v~~~l~~~~gvEVh~~~~--~GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 15 ERLEEVAEALAAIPGVEVHAVDE--DGKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp CCHHHHHHHHCCSTTEEEEEEET--TTEEEEEEEESSHHHHHHHHHH
T ss_pred hhHHHHHHHHHcCCCcEEEeeCC--CCeEEEEEEeCChHHHHHHHHH
Confidence 34567889999999996666663 3788887765666777777664
No 25
>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=48.13 E-value=30 Score=26.00 Aligned_cols=29 Identities=17% Similarity=0.142 Sum_probs=24.3
Q ss_pred eEEEEccccCHHHHHHHHHhhcCceEEEec
Q 033335 38 QIEVTGDGVDAVALTTSLRKKVGYAEVVSV 67 (121)
Q Consensus 38 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv 67 (121)
=+.|+|+ -|-.-|+.+||.++..+..+++
T Consensus 109 ~vLvSgD-~DF~~Lv~~lre~G~~V~v~g~ 137 (160)
T TIGR00288 109 VALVTRD-ADFLPVINKAKENGKETIVIGA 137 (160)
T ss_pred EEEEecc-HhHHHHHHHHHHCCCEEEEEeC
Confidence 5778999 8999999999987447888875
No 26
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=46.37 E-value=78 Score=21.32 Aligned_cols=53 Identities=19% Similarity=0.181 Sum_probs=35.1
Q ss_pred HHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHH---hhcC--ceEEEe
Q 033335 13 RSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLR---KKVG--YAEVVS 66 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~Lr---Kk~~--~aeivs 66 (121)
...+.+.|..++|++=-..|.+ .+|++|+=++-+...++++|. .-=| .|.++-
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~-~GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVY 76 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAP-SGQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVY 76 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCC-CCeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEE
Confidence 5678889999999988877754 568877665455665555554 3223 455654
No 27
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=45.69 E-value=57 Score=21.16 Aligned_cols=54 Identities=20% Similarity=0.198 Sum_probs=39.1
Q ss_pred chhhHHHHHHHhcCCCcccEEEecCCCCCeEEE--EccccCHHHHHHHHHhhcCceEE
Q 033335 9 KHKSRSKALKVAVGFSGVESVALKGDDMSQIEV--TGDGVDAVALTTSLRKKVGYAEV 64 (121)
Q Consensus 9 C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV--~G~~vDp~~l~~~LrKk~~~aei 64 (121)
..+-..+++.+|.+. +|.=|.-+.. .|.+|. .|..-+...++..|.+.++.|+|
T Consensus 14 ~~g~d~~i~~~l~~~-~v~ii~K~~n-ANtit~yl~~~~k~~~r~~~~Le~~~p~a~i 69 (71)
T cd04910 14 EVGYDLEILELLQRF-KVSIIAKDTN-ANTITHYLAGSLKTIKRLTEDLENRFPNAEI 69 (71)
T ss_pred ChhHHHHHHHHHHHc-CCeEEEEecC-CCeEEEEEEcCHHHHHHHHHHHHHhCccCcc
Confidence 345677889999885 6766666764 577765 56534678899999888887776
No 28
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=44.23 E-value=18 Score=26.73 Aligned_cols=44 Identities=14% Similarity=0.114 Sum_probs=31.1
Q ss_pred hhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHh
Q 033335 10 HKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRK 57 (121)
Q Consensus 10 ~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrK 57 (121)
.+|.++++.+|.++ .-|+.+.++-.+||=.|. =|...|..+|+.
T Consensus 97 ~~i~rkvlQ~Le~~---~~ve~hp~gGR~lt~~Gq-rdldrIa~~i~~ 140 (143)
T KOG3411|consen 97 GGIARKVLQALEKM---GIVEKHPKGGRRLTEQGQ-RDLDRIAGQIRE 140 (143)
T ss_pred cHHHHHHHHHHHhC---CceeeCCCCcceeCcccc-hhHHHHHHHHHh
Confidence 35666666666655 345555443459999999 899999999874
No 29
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=43.45 E-value=44 Score=24.87 Aligned_cols=38 Identities=13% Similarity=0.141 Sum_probs=25.6
Q ss_pred EEEEec-cchhhHHHHHHHhcCCCcccEEEecCCCCCeEE
Q 033335 2 VIKVSM-NKHKSRSKALKVAVGFSGVESVALKGDDMSQIE 40 (121)
Q Consensus 2 VlKV~m-~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvt 40 (121)
.|.|+- -|.-|+..+.+.+.++ |++++++-..+.+++.
T Consensus 103 tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 103 TMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred EEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 455553 3999997777666664 9999998754334443
No 30
>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=43.16 E-value=32 Score=23.44 Aligned_cols=29 Identities=31% Similarity=0.362 Sum_probs=20.0
Q ss_pred eEEEEccccCHHHHHHHHHhhcCceEEEec
Q 033335 38 QIEVTGDGVDAVALTTSLRKKVGYAEVVSV 67 (121)
Q Consensus 38 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv 67 (121)
=+.|+|+ -|-..++++||.++..+.++..
T Consensus 99 ivLvSgD-~Df~~~v~~l~~~g~~V~v~~~ 127 (146)
T PF01936_consen 99 IVLVSGD-SDFAPLVRKLRERGKRVIVVGA 127 (146)
T ss_dssp EEEE----GGGHHHHHHHHHH--EEEEEE-
T ss_pred EEEEECc-HHHHHHHHHHHHcCCEEEEEEe
Confidence 5778999 9999999999976557888874
No 31
>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=42.95 E-value=48 Score=20.58 Aligned_cols=16 Identities=25% Similarity=0.306 Sum_probs=7.7
Q ss_pred HHHHHHhcCCCcccEE
Q 033335 14 SKALKVAVGFSGVESV 29 (121)
Q Consensus 14 ~K~~k~~~~~~GV~sv 29 (121)
..+++.|.+++||.+|
T Consensus 52 ~~li~~L~~i~gV~~V 67 (74)
T cd04877 52 QTLMPEIRRIDGVEDV 67 (74)
T ss_pred HHHHHHHhCCCCceEE
Confidence 4444444455554444
No 32
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=41.17 E-value=71 Score=21.23 Aligned_cols=42 Identities=24% Similarity=0.304 Sum_probs=30.2
Q ss_pred HHHHHhcCCCcccEEEecCCCCCeEEEEcc-ccCHHHHHHHHHhhc
Q 033335 15 KALKVAVGFSGVESVALKGDDMSQIEVTGD-GVDAVALTTSLRKKV 59 (121)
Q Consensus 15 K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~-~vDp~~l~~~LrKk~ 59 (121)
-.-+.|-.++||.+|-+.. |=|||+-. .+|-..|...++.-+
T Consensus 38 pLA~~Lf~i~gV~~Vf~~~---dfItVtK~~~~~W~~l~~~I~~~I 80 (87)
T PF08712_consen 38 PLAQALFAIPGVKSVFIGD---DFITVTKNPDADWEDLKPEIREVI 80 (87)
T ss_dssp HHHHHHHTSTTEEEEEEET---TEEEEEE-TTS-HHHHHHHHHHHT
T ss_pred HHHHHhcCCCCEeEEEEEC---CEEEEeeCCCCCHHHHHHHHHHHH
Confidence 3445566999999999974 57888654 389999998887543
No 33
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=41.15 E-value=28 Score=23.78 Aligned_cols=23 Identities=26% Similarity=0.465 Sum_probs=19.9
Q ss_pred CeEEEEccccCHHHHHHHHHhhcC
Q 033335 37 SQIEVTGDGVDAVALTTSLRKKVG 60 (121)
Q Consensus 37 ~kvtV~G~~vDp~~l~~~LrKk~~ 60 (121)
-.|.++|+ +|+..+.+.+++.++
T Consensus 20 ~~l~i~Gd-~~~~~~~~~i~~~~~ 42 (184)
T PF05193_consen 20 MTLVIVGD-IDPDELEKLIEKYFG 42 (184)
T ss_dssp EEEEEEES-SGHHHHHHHHHHHHT
T ss_pred eEEEEEcC-ccHHHHHHHHHhhhh
Confidence 37889999 999999999997765
No 34
>PHA00514 dsDNA binding protein
Probab=40.50 E-value=47 Score=22.94 Aligned_cols=34 Identities=24% Similarity=0.306 Sum_probs=27.8
Q ss_pred CeEEEEccccCHHHHHHHHHhhc--CceEEEeccCCC
Q 033335 37 SQIEVTGDGVDAVALTTSLRKKV--GYAEVVSVGAAG 71 (121)
Q Consensus 37 ~kvtV~G~~vDp~~l~~~LrKk~--~~aeivsv~~~k 71 (121)
+..|..|+ ...+.--..|.|+. +.+.++||+|.-
T Consensus 32 ~~~Tl~GN-LtiEqAQ~e~~k~~k~~pvqVvsVEpnt 67 (98)
T PHA00514 32 NEQTLLGN-LTIEQAQKELSKQYKHGPVQVVSVEPNT 67 (98)
T ss_pred Ccceeecc-eeHHHHHHHHhhcccCCCeeEEEecCCC
Confidence 46788999 99999999998874 479999998744
No 35
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=38.44 E-value=60 Score=21.88 Aligned_cols=31 Identities=16% Similarity=0.281 Sum_probs=23.6
Q ss_pred EEEEeccchhhHHHHHHHhcCCCcccEEEec
Q 033335 2 VIKVSMNKHKSRSKALKVAVGFSGVESVALK 32 (121)
Q Consensus 2 VlKV~m~C~~C~~K~~k~~~~~~GV~sv~~d 32 (121)
|+-+.-.+.+-..+.++.|..++||-|+.+=
T Consensus 45 VVtiE~~~~~~~~~~i~~I~~l~GVlsa~lV 75 (87)
T PRK10553 45 IVVVEAEDSETLLQTIESVRNVEGVLAVSLV 75 (87)
T ss_pred EEEEEeCChHHHHHHHHHHHcCCCceEEEEE
Confidence 4445555666667888999999999999874
No 36
>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.
Probab=37.45 E-value=35 Score=21.93 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=16.7
Q ss_pred CCCeEEEEccccCHHHHHHHHHh
Q 033335 35 DMSQIEVTGDGVDAVALTTSLRK 57 (121)
Q Consensus 35 ~~~kvtV~G~~vDp~~l~~~LrK 57 (121)
..++++++|.++|...|.+.|..
T Consensus 70 ~~~~lV~IG~~ld~~~l~~~l~~ 92 (94)
T PF07683_consen 70 RDSRLVFIGKNLDKEALREALDA 92 (94)
T ss_dssp --EEEEEEEES--HHHHHHHHHT
T ss_pred CCeEEEEEECCCCHHHHHHHHHc
Confidence 35699999999999999988864
No 37
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=36.24 E-value=85 Score=25.68 Aligned_cols=38 Identities=18% Similarity=0.311 Sum_probs=31.7
Q ss_pred hhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHhhcCc
Q 033335 10 HKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRKKVGY 61 (121)
Q Consensus 10 ~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~~ 61 (121)
+.|+..+...+.+++||.|+.+ +|.++-.+.|++..|.
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~--------------~sre~~l~~L~~~lg~ 108 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRF--------------ISREEALKELQPWLGF 108 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEE--------------eCHHHHHHHHHHHcCc
Confidence 7888889999999999999988 4566777888877774
No 38
>PRK04021 hypothetical protein; Reviewed
Probab=35.44 E-value=86 Score=21.34 Aligned_cols=46 Identities=17% Similarity=0.270 Sum_probs=31.9
Q ss_pred cchhhHHHHHHHhcCCCcccEEEecCCC--CCe-EEEEccccCHHHHHHHHH
Q 033335 8 NKHKSRSKALKVAVGFSGVESVALKGDD--MSQ-IEVTGDGVDAVALTTSLR 56 (121)
Q Consensus 8 ~C~~C~~K~~k~~~~~~GV~sv~~d~~~--~~k-vtV~G~~vDp~~l~~~Lr 56 (121)
...++...+.+.|++.-|+ +|++-... ++| |.+.| +|++.|..+|+
T Consensus 43 ~~GkAN~ali~~LAk~l~~-~I~I~~G~~sr~K~v~i~g--~~~e~l~~~L~ 91 (92)
T PRK04021 43 VKGKANKELVKFFSKLLGA-EVEIIRGETSREKDLLVKG--ISLEEVKKKLK 91 (92)
T ss_pred CCChHHHHHHHHHHHHhCC-CEEEEecCCcCceEEEEec--CCHHHHHHHhc
Confidence 3557788888899988898 68774322 233 33434 79999998875
No 39
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=34.91 E-value=54 Score=19.04 Aligned_cols=9 Identities=11% Similarity=0.169 Sum_probs=4.1
Q ss_pred HHHHHHHHH
Q 033335 48 AVALTTSLR 56 (121)
Q Consensus 48 p~~l~~~Lr 56 (121)
...|+++|+
T Consensus 55 ~~~l~~~l~ 63 (72)
T cd04878 55 IEQIVKQLN 63 (72)
T ss_pred HHHHHHHHh
Confidence 444444444
No 40
>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=33.80 E-value=79 Score=29.95 Aligned_cols=44 Identities=14% Similarity=0.213 Sum_probs=34.9
Q ss_pred HHHHHHHhcCCCcccEEEecCCCCCeEEEE-------ccccCHHHHHHHHHh
Q 033335 13 RSKALKVAVGFSGVESVALKGDDMSQIEVT-------GDGVDAVALTTSLRK 57 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~-------G~~vDp~~l~~~LrK 57 (121)
...++..+.+++||.+|++.+. ..++.|. .-|+++.++.+.|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~-~~ei~V~vD~~kl~~~gls~~dV~~~i~~ 209 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGS-QYAMRIWLDPAKLNSYQLTPADVISAIQA 209 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCC-ceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 4568889999999999999987 6667764 235677888888886
No 41
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=33.65 E-value=80 Score=29.88 Aligned_cols=45 Identities=11% Similarity=0.135 Sum_probs=34.4
Q ss_pred HHHHHHHhcCCCcccEEEecCCCCCeEEEE-------ccccCHHHHHHHHHhh
Q 033335 13 RSKALKVAVGFSGVESVALKGDDMSQIEVT-------GDGVDAVALTTSLRKK 58 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~-------G~~vDp~~l~~~LrKk 58 (121)
++.++..|.+++||.+|++.+. ..++.|. .-|+++.++.+.|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~-~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGS-QYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCC-ceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 4668889999999999999985 4556553 2257778888889853
No 42
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=33.17 E-value=82 Score=29.89 Aligned_cols=44 Identities=16% Similarity=0.161 Sum_probs=32.8
Q ss_pred HHHHHHHhcCCCcccEEEecCCCCCeEEEE-------ccccCHHHHHHHHHh
Q 033335 13 RSKALKVAVGFSGVESVALKGDDMSQIEVT-------GDGVDAVALTTSLRK 57 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~-------G~~vDp~~l~~~LrK 57 (121)
+..++..|.+++||.+|++.+. ..++.|. .-|+++.+|.+.|+.
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~-~~ei~V~vDp~kl~~~gls~~~V~~~l~~ 209 (1049)
T PRK15127 159 AANMKDPISRTSGVGDVQLFGS-QYAMRIWMNPNELNKFQLTPVDVINAIKA 209 (1049)
T ss_pred HHHHHHHHhcCCCceEEEEcCC-ceEEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 3568889999999999999986 4556663 224667777788884
No 43
>PF07338 DUF1471: Protein of unknown function (DUF1471); InterPro: IPR010854 This entry consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some of the proteins are annotated as ydgH precursors and contain two copies of this region, one at the N terminus and the other at the C terminus. The function of this family is unknown.; PDB: 2NOC_A 2JNA_B 4EVU_B.
Probab=32.00 E-value=58 Score=19.99 Aligned_cols=23 Identities=26% Similarity=0.248 Sum_probs=18.6
Q ss_pred CeEEEEccccCHHHHHHHHHhhc
Q 033335 37 SQIEVTGDGVDAVALTTSLRKKV 59 (121)
Q Consensus 37 ~kvtV~G~~vDp~~l~~~LrKk~ 59 (121)
+.|+|.|..-.+.++...|.+|.
T Consensus 6 G~Isvs~~~~s~~d~~~~la~kA 28 (56)
T PF07338_consen 6 GTISVSGNFGSPDDAEEALAKKA 28 (56)
T ss_dssp EEEEEEEECSSHHHHHHHHHHHH
T ss_pred EEEEEccccCCHHHHHHHHHHHH
Confidence 57899997668999999998763
No 44
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=31.94 E-value=92 Score=29.42 Aligned_cols=46 Identities=15% Similarity=0.283 Sum_probs=33.0
Q ss_pred HHHHHHHhcCCCcccEEEecCCCCCeEEEEc-------cccCHHHHHHHHHhh
Q 033335 13 RSKALKVAVGFSGVESVALKGDDMSQIEVTG-------DGVDAVALTTSLRKK 58 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G-------~~vDp~~l~~~LrKk 58 (121)
+..++..+.+++||.+|++.+....++.|.= -|+.+.++.+.|+..
T Consensus 159 ~~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 211 (1025)
T PRK10614 159 STQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQAISNA 211 (1025)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 4578899999999999999975444565541 135666677777754
No 45
>PRK09577 multidrug efflux protein; Reviewed
Probab=31.89 E-value=83 Score=29.78 Aligned_cols=45 Identities=18% Similarity=0.282 Sum_probs=34.7
Q ss_pred HHHHHHHhcCCCcccEEEecCCCCCeEEEE-------ccccCHHHHHHHHHhh
Q 033335 13 RSKALKVAVGFSGVESVALKGDDMSQIEVT-------GDGVDAVALTTSLRKK 58 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~-------G~~vDp~~l~~~LrKk 58 (121)
+.+++..|.+++||.+|++++. ..++.|. .-|+++.+|.+.|+..
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~-e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~ 209 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGA-EYAMRIWPDPVKLAALGLTASDIASAVRAH 209 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCC-ceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 4678899999999999999985 4566663 2356777888899864
No 46
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=31.75 E-value=94 Score=29.48 Aligned_cols=44 Identities=20% Similarity=0.320 Sum_probs=32.6
Q ss_pred HHHHHHhcCCCcccEEEecCCCCCeEEEE-------ccccCHHHHHHHHHh
Q 033335 14 SKALKVAVGFSGVESVALKGDDMSQIEVT-------GDGVDAVALTTSLRK 57 (121)
Q Consensus 14 ~K~~k~~~~~~GV~sv~~d~~~~~kvtV~-------G~~vDp~~l~~~LrK 57 (121)
..++..+.+++||.+|++.+....++.|. .-|+++.++.+.|+.
T Consensus 169 ~~l~~~L~~i~gV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~~v~~ai~~ 219 (1040)
T PRK10503 169 TRVAQKISQVSGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETVRTAITG 219 (1040)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 56888999999999999998644456653 224667777788874
No 47
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=31.18 E-value=58 Score=19.67 Aligned_cols=29 Identities=17% Similarity=0.104 Sum_probs=22.0
Q ss_pred HHHHHHhcCCCcccEEEecCCCCCeEEEE
Q 033335 14 SKALKVAVGFSGVESVALKGDDMSQIEVT 42 (121)
Q Consensus 14 ~K~~k~~~~~~GV~sv~~d~~~~~kvtV~ 42 (121)
.++.+.|.+++.|.++.+...--++|.|.
T Consensus 37 ~~~~~~l~~~p~V~~v~V~r~~P~~l~I~ 65 (69)
T PF08478_consen 37 KKIEQRLEKLPWVKSVSVSRRFPNTLEIK 65 (69)
T ss_dssp HHHHHCCCCTTTEEEEEEEEETTTEEEEE
T ss_pred HHHHHHHHcCCCEEEEEEEEeCCCEEEEE
Confidence 56777888899999999975545666653
No 48
>PF12164 SporV_AA: Stage V sporulation protein AA; InterPro: IPR021997 This domain family is found in bacteria - primarily Firmicutes, and is approximately 90 amino acids in length. There is a single completely conserved residue G that may be functionally important. Most annotation associated with this domain suggests that it is involved in the fifth stage of sporulation, however there is little publication to back this up. ; PDB: 3G74_B.
Probab=31.14 E-value=56 Score=22.14 Aligned_cols=54 Identities=6% Similarity=0.152 Sum_probs=31.2
Q ss_pred ccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHhhcCceEEEeccCCC
Q 033335 7 MNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRKKVGYAEVVSVGAAG 71 (121)
Q Consensus 7 m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~~~k 71 (121)
+.|+. .+...|..+ .=..++..++++++ +|..++++++++.++++++-.+|++.
T Consensus 29 i~~~~---~~~~klk~l---~i~~~~~~d~~r~V-----isvm~II~~I~~~~p~l~I~~iGe~~ 82 (93)
T PF12164_consen 29 IYCDD---EIENKLKAL---PIYKIKKKDKNRYV-----ISVMKIIEKIQEEYPNLDIQNIGETD 82 (93)
T ss_dssp EEESS---HHHHHHHTS---EEEE-BTTT--EEE-----EEHHHHHHHHHHH-SSEEEEE-S-SE
T ss_pred EEeCH---HHHHHhhcc---EeeeecCCCCCEEE-----EEHHHHHHHHHHHCCCcEEEEcCCCc
Confidence 44554 444455444 12234544444443 57899999999999999999998754
No 49
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=29.52 E-value=60 Score=30.33 Aligned_cols=47 Identities=15% Similarity=0.275 Sum_probs=32.9
Q ss_pred hHHHHHHHhcCCCcccEEEecCCCCCeEEEE-------ccccCHHHHHHHHHhh
Q 033335 12 SRSKALKVAVGFSGVESVALKGDDMSQIEVT-------GDGVDAVALTTSLRKK 58 (121)
Q Consensus 12 C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~-------G~~vDp~~l~~~LrKk 58 (121)
.+..++..|.+++||.+|++.|....++.|. ..|+++.+|.+.|+..
T Consensus 157 ~~~~l~~~L~~i~gV~~v~~~G~~~~ei~i~~d~~kl~~~gls~~~v~~~l~~~ 210 (1021)
T PF00873_consen 157 AEEQLKPRLERIPGVARVDISGGREREIQIELDPEKLAAYGLSLSDVAQALQAN 210 (1021)
T ss_dssp HHHCTHHHHHTSTTEEEEEESSS--EEEEEEE-HHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHhccceeEEEEEEeccchhhhhhheechhhhhhhCCCHHHHHHHHHHh
Confidence 3456888999999999999998655566664 2346777788888864
No 50
>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=29.50 E-value=77 Score=21.45 Aligned_cols=23 Identities=30% Similarity=0.371 Sum_probs=19.5
Q ss_pred hhHHHHHHHhcCCCcccEEEecC
Q 033335 11 KSRSKALKVAVGFSGVESVALKG 33 (121)
Q Consensus 11 ~C~~K~~k~~~~~~GV~sv~~d~ 33 (121)
+--..+-.+++.++||+|+++..
T Consensus 62 g~td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 62 GGTEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred cChHHHHHHHhcCCCccEEEEEE
Confidence 56678888999999999999863
No 51
>PF05922 Inhibitor_I9: Peptidase inhibitor I9; InterPro: IPR010259 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes []. The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route []. The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus. Proteinase propeptide inhibitors (sometimes refered to as activation peptides) are responsible for the modulation of folding and activity of the pro-enzyme or zymogen. The pro-segment docks into the enzyme moiety shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology [], despite often low sequence identities []. The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology. This group of sequences contain the propeptide domain at the N terminus of peptidases belonging to MEROPS family S8A, subtilisins. A number of the members of this group of sequences belong to MEROPS inhibitor family I9, clan I-. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.; GO: 0004252 serine-type endopeptidase activity, 0042802 identical protein binding, 0043086 negative regulation of catalytic activity; PDB: 3CNQ_P 1SPB_P 3CO0_P 1ITP_A 1V5I_B 1SCJ_B 3P5B_P 2XTJ_P 2W2M_P 2P4E_P ....
Probab=28.65 E-value=57 Score=20.15 Aligned_cols=18 Identities=22% Similarity=0.189 Sum_probs=15.5
Q ss_pred HHHHHhcCCCcccEEEec
Q 033335 15 KALKVAVGFSGVESVALK 32 (121)
Q Consensus 15 K~~k~~~~~~GV~sv~~d 32 (121)
...+.|++.+||.+|+-|
T Consensus 59 ~~i~~L~~~p~V~~Ve~D 76 (82)
T PF05922_consen 59 EEIEKLRKDPGVKSVEPD 76 (82)
T ss_dssp HHHHHHHTSTTEEEEEEE
T ss_pred HHHHHHHcCCCeEEEEeC
Confidence 456788999999999998
No 52
>smart00833 CobW_C Cobalamin synthesis protein cobW C-terminal domain. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis PUBMED:12869542. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression PUBMED:7765511.
Probab=28.46 E-value=86 Score=19.81 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=18.1
Q ss_pred CCeEEEEccccCHHHHHHHHHh
Q 033335 36 MSQIEVTGDGVDAVALTTSLRK 57 (121)
Q Consensus 36 ~~kvtV~G~~vDp~~l~~~LrK 57 (121)
.++|+++|..+|...|-+.|..
T Consensus 69 ~~~lV~IG~~l~~~~l~~~l~~ 90 (92)
T smart00833 69 RTRLVFIGRDLDEEAIRAALDA 90 (92)
T ss_pred ceEEEEEeCCCCHHHHHHHHHH
Confidence 4689999988999988888763
No 53
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=27.59 E-value=56 Score=21.27 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=21.4
Q ss_pred eEEEEc----cccCHHHHHHHHHhhcC-ceEEEec
Q 033335 38 QIEVTG----DGVDAVALTTSLRKKVG-YAEVVSV 67 (121)
Q Consensus 38 kvtV~G----~~vDp~~l~~~LrKk~~-~aeivsv 67 (121)
.||++. .++|+.+|++.|+++++ .+.+..-
T Consensus 19 ~vT~V~gl~~~~~d~~~lak~lkk~~ac~~sv~~~ 53 (83)
T PF01253_consen 19 FVTIVSGLELFGIDLKELAKELKKKFACGGSVTKD 53 (83)
T ss_dssp EEEEEES--STTSHHHHHHHHHHHHHTS-EEEEE-
T ss_pred EEEEEECCcccccCHHHHHHHHHHhccCceEEeec
Confidence 566643 25899999999999988 6666643
No 54
>cd03309 CmuC_like CmuC_like. Proteins similar to the putative corrinoid methyltransferase CmuC. Its function has been inferred from sequence similarity to the methyltransferases CmuA and MtaA. Mutants of Methylobacterium sp. disrupted in cmuC and purU appear deficient in some step of chloromethane metabolism.
Probab=27.45 E-value=87 Score=25.63 Aligned_cols=45 Identities=18% Similarity=0.258 Sum_probs=30.7
Q ss_pred EeccchhhHHHHHHHhcCCCcccEEEecCCC----------CCeEEEEccccCHHHH
Q 033335 5 VSMNKHKSRSKALKVAVGFSGVESVALKGDD----------MSQIEVTGDGVDAVAL 51 (121)
Q Consensus 5 V~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~----------~~kvtV~G~~vDp~~l 51 (121)
+-+|..|....+...+..+ |++.+.+|... .+++++.|. +||.-|
T Consensus 215 iilH~cG~~~~~l~~~~e~-g~dvl~~d~~~~dl~eak~~~g~k~~l~GN-lDp~~L 269 (321)
T cd03309 215 IVHHSCGAAASLVPSMAEM-GVDSWNVVMTANNTAELRRLLGDKVVLAGA-IDDVAL 269 (321)
T ss_pred eEEEeCCCcHHHHHHHHHc-CCCEEEecCCCCCHHHHHHHhCCCeEEEcC-CChHHh
Confidence 5567777766677777766 88888887542 136778887 777543
No 55
>PRK09579 multidrug efflux protein; Reviewed
Probab=27.36 E-value=1.5e+02 Score=28.01 Aligned_cols=46 Identities=13% Similarity=0.172 Sum_probs=34.6
Q ss_pred HHHHHHHhcCCCcccEEEecCCCCCeEEEEc-------cccCHHHHHHHHHhh
Q 033335 13 RSKALKVAVGFSGVESVALKGDDMSQIEVTG-------DGVDAVALTTSLRKK 58 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G-------~~vDp~~l~~~LrKk 58 (121)
.+.++..|.+++||.+|++.+....++.|.= -|+.+.+|.+.|+..
T Consensus 158 ~~~i~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 210 (1017)
T PRK09579 158 SRVIQPKLATLPGMAEAEILGNQVFAMRLWLDPVKLAGFGLSAGDVTQAVRRY 210 (1017)
T ss_pred HHHHHHHhhcCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 4567889999999999999886444566632 256778888999864
No 56
>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=27.18 E-value=1e+02 Score=18.31 Aligned_cols=23 Identities=26% Similarity=0.390 Sum_probs=18.6
Q ss_pred cchhhHHHHHHHhcCCCcccEEE
Q 033335 8 NKHKSRSKALKVAVGFSGVESVA 30 (121)
Q Consensus 8 ~C~~C~~K~~k~~~~~~GV~sv~ 30 (121)
.-...+.+|.+++..+.||.+|.
T Consensus 35 ~s~~~~~~a~~~a~~v~gv~~V~ 57 (64)
T PF04972_consen 35 PSQEQRDAAERLARSVAGVREVV 57 (64)
T ss_dssp SSCHHHHHHHHHHHCC-STSEEE
T ss_pred cHHHHHHhHHhhhccCCCcCEEE
Confidence 45678899999999999999886
No 57
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=26.72 E-value=1.4e+02 Score=21.52 Aligned_cols=51 Identities=14% Similarity=0.199 Sum_probs=34.2
Q ss_pred hhhHHHHHHHhcCCCcc--c--EEEecCCCCCeEEEEccccCHHHHHHHHHhhcCceEEE
Q 033335 10 HKSRSKALKVAVGFSGV--E--SVALKGDDMSQIEVTGDGVDAVALTTSLRKKVGYAEVV 65 (121)
Q Consensus 10 ~~C~~K~~k~~~~~~GV--~--sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeiv 65 (121)
+.-++++++.|.+ .|. . +|+++ .+.||+.|. +.......++....+.+.-+
T Consensus 25 ~~~~~~i~~~i~~-~~~~~~~i~V~v~---~G~v~l~G~-v~s~~~~~~~~~aa~~v~GV 79 (147)
T PRK11198 25 EDAADALKEHISK-QGLGDADVNVQVE---DGKATVSGD-AASQEAKEKILLAVGNIQGI 79 (147)
T ss_pred HHHHHHHHHHHHh-cCCCcCCceEEEe---CCEEEEEEE-eCCHHHHHHHHHHhccCCCc
Confidence 4456777777765 343 2 45554 479999999 88888888877666654443
No 58
>COG0612 PqqL Predicted Zn-dependent peptidases [General function prediction only]
Probab=26.30 E-value=65 Score=26.64 Aligned_cols=24 Identities=33% Similarity=0.405 Sum_probs=21.3
Q ss_pred CeEEEEccccCHHHHHHHHHhhcCc
Q 033335 37 SQIEVTGDGVDAVALTTSLRKKVGY 61 (121)
Q Consensus 37 ~kvtV~G~~vDp~~l~~~LrKk~~~ 61 (121)
=.|.|+|+ +|+..+...+.+.++.
T Consensus 199 ~~l~vvGd-i~~~~v~~~~~~~f~~ 222 (438)
T COG0612 199 MVLVVVGD-VDAEEVVELIEKYFGD 222 (438)
T ss_pred eEEEEecC-CCHHHHHHHHHHHHcc
Confidence 37889999 9999999999998873
No 59
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=26.26 E-value=1.7e+02 Score=18.68 Aligned_cols=60 Identities=30% Similarity=0.355 Sum_probs=37.3
Q ss_pred EEEEeccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHHhhcCceEEE
Q 033335 2 VIKVSMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLRKKVGYAEVV 65 (121)
Q Consensus 2 VlKV~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeiv 65 (121)
.+||.. -..-+..+++++..+.| .=|+++.+ .=.+.++|+.-.-..+++.|++ ++-.+++
T Consensus 6 LiKV~~-~~~~r~ei~~l~~~f~a-~ivd~~~~-~~iie~tG~~~kid~fi~~l~~-~gi~Ei~ 65 (75)
T PF10369_consen 6 LIKVKA-TPENRSEILQLAEIFRA-RIVDVSPD-SIIIELTGTPEKIDAFIKLLKP-FGILEIA 65 (75)
T ss_dssp EEEEE--SCHHHHHHHHHHHHTT--EEEEEETT-EEEEEEEE-HHHHHHHHHHSTG-GGEEEEE
T ss_pred EEEEEC-CccCHHHHHHHHHHhCC-EEEEECCC-EEEEEEcCCHHHHHHHHHHhhh-cCCEEEE
Confidence 567777 55778888888888776 44555532 3477779984455556666665 6656655
No 60
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=25.76 E-value=1.9e+02 Score=18.63 Aligned_cols=61 Identities=11% Similarity=0.121 Sum_probs=40.6
Q ss_pred EEEeccc-hhhHHHHHHHhcCCCc-ccEEEecCCCCCeEEEEcc--ccCHHHHHHHHHhhcC-ceEEE
Q 033335 3 IKVSMNK-HKSRSKALKVAVGFSG-VESVALKGDDMSQIEVTGD--GVDAVALTTSLRKKVG-YAEVV 65 (121)
Q Consensus 3 lKV~m~C-~~C~~K~~k~~~~~~G-V~sv~~d~~~~~kvtV~G~--~vDp~~l~~~LrKk~~-~aeiv 65 (121)
.++.+.| +.+..+++..|++..| |.++..+ +.+..+|.|. ......+...||..+. .|.+-
T Consensus 7 ~~~~I~~p~~~~g~v~~~l~~r~g~i~~~~~~--~~~~~~i~~~iP~~~~~gf~~~Lr~~T~G~a~~~ 72 (89)
T PF00679_consen 7 MSVEISVPEEYLGKVISDLSKRRGEILSMDPI--GGDRVVIEAEIPVRELFGFRSELRSLTSGRASFS 72 (89)
T ss_dssp EEEEEEEEGGGHHHHHHHHHHTT-EEEEEEEE--STTEEEEEEEEEGGGHTTHHHHHHHHTTTS-EEE
T ss_pred EEEEEEECHHHHHHHHHHhcccccEEEechhh--hhhheeEEEEEChhhhhhHHHHhhccCCCEEEEE
Confidence 4455555 6889999999999888 4555555 2468888887 2355667788886654 66543
No 61
>PLN02625 uroporphyrin-III C-methyltransferase
Probab=25.55 E-value=75 Score=24.88 Aligned_cols=32 Identities=25% Similarity=0.232 Sum_probs=27.3
Q ss_pred CCeEEEEcccc-CHHHHHHHHHhhcCceEEEec
Q 033335 36 MSQIEVTGDGV-DAVALTTSLRKKVGYAEVVSV 67 (121)
Q Consensus 36 ~~kvtV~G~~v-Dp~~l~~~LrKk~~~aeivsv 67 (121)
.++|+++|.|. ||.-|+-+.++....|++|-.
T Consensus 14 ~g~l~vVG~GpGdp~~LTl~a~~~l~~ADvI~~ 46 (263)
T PLN02625 14 PGNVFLVGTGPGDPDLLTLKALRLLQTADVVLY 46 (263)
T ss_pred CCEEEEEEeCCCChHHhHHHHHHHHhcCCEEEE
Confidence 46899999987 999999988888888888765
No 62
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=25.36 E-value=89 Score=21.15 Aligned_cols=24 Identities=21% Similarity=0.246 Sum_probs=19.9
Q ss_pred hhhHHHHHHHhcCCCcccEEEecC
Q 033335 10 HKSRSKALKVAVGFSGVESVALKG 33 (121)
Q Consensus 10 ~~C~~K~~k~~~~~~GV~sv~~d~ 33 (121)
++--..+..+++.++||+|+++..
T Consensus 61 ~~~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 61 EGGTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred CcCcHHHHHHHhccCCCcEEEEEE
Confidence 367778888999999999998863
No 63
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=25.28 E-value=74 Score=18.28 Aligned_cols=19 Identities=21% Similarity=0.309 Sum_probs=15.7
Q ss_pred HHHHHHHhcCCCcccEEEe
Q 033335 13 RSKALKVAVGFSGVESVAL 31 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~ 31 (121)
-..+++.|..++||.+|..
T Consensus 52 ~~~l~~~l~~~~~V~~v~~ 70 (71)
T cd04879 52 PEEVLEELKALPGIIRVRL 70 (71)
T ss_pred CHHHHHHHHcCCCeEEEEE
Confidence 4578999999999998864
No 64
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=25.26 E-value=1.1e+02 Score=21.34 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=23.3
Q ss_pred EEecCCCCCeEEEEccccCHHHHHHHHHhhcC
Q 033335 29 VALKGDDMSQIEVTGDGVDAVALTTSLRKKVG 60 (121)
Q Consensus 29 v~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~ 60 (121)
..+|+ ++++++.|. +++..|-+.|++-+.
T Consensus 50 g~id~--~~rlii~G~-~~~~~i~~~l~~yI~ 78 (110)
T smart00653 50 GSIDG--KGRLIVNGR-FTPKKLQDLLRRYIK 78 (110)
T ss_pred eeECC--CCeEEEEEe-eCHHHHHHHHHHHHH
Confidence 45564 379999999 999999999987543
No 65
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=24.70 E-value=89 Score=25.36 Aligned_cols=29 Identities=14% Similarity=0.347 Sum_probs=24.0
Q ss_pred cEEEecCCCCCeEEEEccccCHHHHHHHHHhhc
Q 033335 27 ESVALKGDDMSQIEVTGDGVDAVALTTSLRKKV 59 (121)
Q Consensus 27 ~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~ 59 (121)
+.|.+|.. +++||+.|. |..|.+.|++..
T Consensus 303 ~~i~yd~~-~~~ltI~~~---p~~l~~ql~r~~ 331 (334)
T PRK00378 303 ERIFYDPA-TDTLTIKGT---PPNLRDQLQRRL 331 (334)
T ss_pred CceEEcCC-CCEEEEeCC---CHHHHHHHHHHh
Confidence 47888854 789999998 999999997644
No 66
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=24.18 E-value=2.3e+02 Score=19.67 Aligned_cols=44 Identities=14% Similarity=0.196 Sum_probs=33.1
Q ss_pred hhHHHHHHHhcCCCcccEEEecCCCCCeEEEEccccCHHHHHHHHH
Q 033335 11 KSRSKALKVAVGFSGVESVALKGDDMSQIEVTGDGVDAVALTTSLR 56 (121)
Q Consensus 11 ~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~~Lr 56 (121)
.=...++..|+.++|++=-.-|.+ +|++|+=++-|...|+..|.
T Consensus 18 e~l~av~~~L~~ip~~EV~~~d~~--GKlVVVie~~~~~~l~~tie 61 (94)
T COG3062 18 ERLSAVKTALLAIPGCEVYGEDAE--GKLVVVIEAEDSETLLETIE 61 (94)
T ss_pred HHHHHHHHHHhcCCCcEeeccCCC--ceEEEEEEcCchHHHHHHHH
Confidence 345678889999999987777743 68888766568888877764
No 67
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=24.13 E-value=1.4e+02 Score=16.36 Aligned_cols=12 Identities=17% Similarity=0.254 Sum_probs=7.0
Q ss_pred cCHHHHHHHHHh
Q 033335 46 VDAVALTTSLRK 57 (121)
Q Consensus 46 vDp~~l~~~LrK 57 (121)
.+...+++.|++
T Consensus 51 ~~~~~~~~~l~~ 62 (71)
T cd04876 51 EHLARIMRKLRQ 62 (71)
T ss_pred HHHHHHHHHHhC
Confidence 455666666664
No 68
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=24.10 E-value=1.4e+02 Score=28.52 Aligned_cols=46 Identities=20% Similarity=0.254 Sum_probs=34.0
Q ss_pred hHHHHHHHhcCCCcccEEEecCCCCCeEEEE-------ccccCHHHHHHHHHh
Q 033335 12 SRSKALKVAVGFSGVESVALKGDDMSQIEVT-------GDGVDAVALTTSLRK 57 (121)
Q Consensus 12 C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~-------G~~vDp~~l~~~LrK 57 (121)
-.+.++..|++++||-+|++-|.....+-|. +-|+++.+|.+.|+.
T Consensus 156 ~~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~~ 208 (1009)
T COG0841 156 AASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIRA 208 (1009)
T ss_pred HHHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 3566888999999999999998644455552 335677777888874
No 69
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=24.06 E-value=1.3e+02 Score=19.29 Aligned_cols=30 Identities=17% Similarity=0.274 Sum_probs=21.8
Q ss_pred HHHHHHHhcCCCcccEEEecCCCCCeEEEE
Q 033335 13 RSKALKVAVGFSGVESVALKGDDMSQIEVT 42 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~ 42 (121)
.+++...++...||.|.+.|-+....|+|+
T Consensus 44 eR~iIH~la~~~~l~S~S~G~ep~R~VvI~ 73 (74)
T cd02643 44 KRRIVHELAEHFGIESVSYDQEPKRNVVAT 73 (74)
T ss_pred HHHHHHHHHhhCCCEEEecCCCCCceEEEe
Confidence 456666678889999999997654455543
No 70
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating [].
Probab=23.82 E-value=1.7e+02 Score=17.87 Aligned_cols=41 Identities=12% Similarity=0.190 Sum_probs=25.1
Q ss_pred ccEEEecCCCCCeEEEEccccCHHHHHHHHHhh--cC---ceEEEeccC
Q 033335 26 VESVALKGDDMSQIEVTGDGVDAVALTTSLRKK--VG---YAEVVSVGA 69 (121)
Q Consensus 26 V~sv~~d~~~~~kvtV~G~~vDp~~l~~~LrKk--~~---~aeivsv~~ 69 (121)
+++++++ .++|++.|...+...|...+++- .+ .+.+.++..
T Consensus 16 l~~l~~~---~~~l~i~G~a~~~~~v~~f~~~L~~~~~f~~v~l~~~~~ 61 (78)
T PF05137_consen 16 LTSLSIN---GNTLSISGYADSYQSVAAFLRNLEQSPFFSDVSLSSISR 61 (78)
T ss_pred EEEEEEe---CCEEEEEEEECCHHHHHHHHHHHhhCCCccceEEEEEEe
Confidence 3566665 35999999965666665555431 22 466666644
No 71
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=23.04 E-value=1.4e+02 Score=19.80 Aligned_cols=39 Identities=21% Similarity=0.117 Sum_probs=22.7
Q ss_pred EecCCCCCeEEEEccccCHHHHHHHHHhhcCceEEEeccC
Q 033335 30 ALKGDDMSQIEVTGDGVDAVALTTSLRKKVGYAEVVSVGA 69 (121)
Q Consensus 30 ~~d~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~~ 69 (121)
-+|.++ .++.|+|-|--...-+..|.+...+..++|...
T Consensus 2 ~l~l~~-~~vlVvGgG~va~~k~~~Ll~~gA~v~vis~~~ 40 (103)
T PF13241_consen 2 FLDLKG-KRVLVVGGGPVAARKARLLLEAGAKVTVISPEI 40 (103)
T ss_dssp EE--TT--EEEEEEESHHHHHHHHHHCCCTBEEEEEESSE
T ss_pred EEEcCC-CEEEEECCCHHHHHHHHHHHhCCCEEEEECCch
Confidence 356654 489999987445555555554333777777653
No 72
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.98 E-value=1.8e+02 Score=17.44 Aligned_cols=19 Identities=5% Similarity=0.125 Sum_probs=9.4
Q ss_pred hhHHHHHHHhcCCCcccEE
Q 033335 11 KSRSKALKVAVGFSGVESV 29 (121)
Q Consensus 11 ~C~~K~~k~~~~~~GV~sv 29 (121)
.--..+++.|.+++||...
T Consensus 52 ~~l~~i~~~L~~i~gV~~~ 70 (74)
T cd04887 52 EHAETIVAAVRALPEVKVL 70 (74)
T ss_pred HHHHHHHHHHhcCCCeEEE
Confidence 3344455555555555443
No 73
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=22.58 E-value=1.3e+02 Score=18.09 Aligned_cols=33 Identities=12% Similarity=0.150 Sum_probs=22.5
Q ss_pred hhhHHHHHHHhcCCCcccEEEecCCCCCeEEEE
Q 033335 10 HKSRSKALKVAVGFSGVESVALKGDDMSQIEVT 42 (121)
Q Consensus 10 ~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~ 42 (121)
..=.+++...++...|+.|.+.+.+....|+|.
T Consensus 29 ~~~~R~~iH~~a~~~gL~s~S~g~~~~R~vvv~ 61 (63)
T PF01424_consen 29 NSFERKLIHELAEYYGLKSKSEGEGPNRRVVVS 61 (63)
T ss_dssp -SHHHHHHHHHHHHCTEEEEEESSSSSSEEEEE
T ss_pred CHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEE
Confidence 445566667677789999999986544456553
No 74
>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=22.31 E-value=2.4e+02 Score=18.58 Aligned_cols=53 Identities=19% Similarity=0.202 Sum_probs=33.0
Q ss_pred hhHHHHHHHhcCCCcccEEEecCCCCCeEEE--Eccc-cCHHHHHHHHHhhcC-ceEEE
Q 033335 11 KSRSKALKVAVGFSGVESVALKGDDMSQIEV--TGDG-VDAVALTTSLRKKVG-YAEVV 65 (121)
Q Consensus 11 ~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV--~G~~-vDp~~l~~~LrKk~~-~aeiv 65 (121)
-|++.+...-..|. +-+++...+ .+++|+ ++++ +|--.|++-|.+.++ .+++-
T Consensus 30 ~c~~~~~~~~L~m~-lvd~e~~~D-~~k~~fyy~a~~rvDFR~Lvr~L~~~f~~RIem~ 86 (88)
T PF04468_consen 30 FCRELVKELGLPMK-LVDVEYQFD-GSKLTFYYTAESRVDFRELVRDLAREFKTRIEMR 86 (88)
T ss_pred HHHHHHHHcCCCeE-EEEEEEEcC-CCEEEEEEEeCCcCcHHHHHHHHHHHhCceEEEE
Confidence 35555544433332 445555543 468888 4443 999999999998776 45543
No 75
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.01 E-value=94 Score=17.93 Aligned_cols=19 Identities=11% Similarity=0.209 Sum_probs=15.0
Q ss_pred HHHHHHHhcCCCcccEEEe
Q 033335 13 RSKALKVAVGFSGVESVAL 31 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~ 31 (121)
-.++++.|.+++||.+|..
T Consensus 52 ~~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 52 DEEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred CHHHHHHHHcCCCceEEEE
Confidence 4577888899999988864
No 76
>PRK11023 outer membrane lipoprotein; Provisional
Probab=22.01 E-value=1.8e+02 Score=21.82 Aligned_cols=48 Identities=6% Similarity=0.110 Sum_probs=32.9
Q ss_pred cchhhHHHHHHHhcCCCccc---EEEecCCCCCeEEEEccccCHHHHHHHHHh
Q 033335 8 NKHKSRSKALKVAVGFSGVE---SVALKGDDMSQIEVTGDGVDAVALTTSLRK 57 (121)
Q Consensus 8 ~C~~C~~K~~k~~~~~~GV~---sv~~d~~~~~kvtV~G~~vDp~~l~~~LrK 57 (121)
.+..-..+++.+|..-+++. .|.+... .+.|+++|. ++-.....+..+
T Consensus 46 dD~~i~~~V~~aL~~~~~l~~~~~I~V~v~-~G~V~L~G~-V~~~~~k~~A~~ 96 (191)
T PRK11023 46 DDGTLELRVNNALSKDEQIKKEARINVTAY-QGKVLLTGQ-SPNAELSERAKQ 96 (191)
T ss_pred hhHHHHHHHHHHHhhCcccCcCceEEEEEE-CCEEEEEEE-eCCHHHHHHHHH
Confidence 34455778888887766663 4777665 579999999 877665555443
No 77
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=21.86 E-value=1.1e+02 Score=21.04 Aligned_cols=29 Identities=21% Similarity=0.218 Sum_probs=21.8
Q ss_pred EEeccc-hhhHHHHHHHhcCCCcccEEEec
Q 033335 4 KVSMNK-HKSRSKALKVAVGFSGVESVALK 32 (121)
Q Consensus 4 KV~m~C-~~C~~K~~k~~~~~~GV~sv~~d 32 (121)
.+-|.. +|--..+...++.++||+|+++.
T Consensus 54 ~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 54 YVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred EEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 344433 45567888899999999999885
No 78
>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=21.70 E-value=1.6e+02 Score=27.88 Aligned_cols=44 Identities=18% Similarity=0.176 Sum_probs=31.4
Q ss_pred HHHHHhcCCCcccEEEecCCCCCeEEEEc-------cccCHHHHHHHHHhh
Q 033335 15 KALKVAVGFSGVESVALKGDDMSQIEVTG-------DGVDAVALTTSLRKK 58 (121)
Q Consensus 15 K~~k~~~~~~GV~sv~~d~~~~~kvtV~G-------~~vDp~~l~~~LrKk 58 (121)
.++..|.+++||.+|++.+....++.|.= -|+++.+|.+.|+..
T Consensus 170 ~l~~~L~~i~GV~~V~~~G~~~~ei~V~iD~~kl~~~glt~~dV~~~l~~~ 220 (1051)
T TIGR00914 170 IIRPQLRTVPGVAEVNSIGGYVKQFLVAPDPEKLAAYGLSLADVVNALERN 220 (1051)
T ss_pred HHHHHHhcCCCceEeeecCCceEEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 36678999999999999886544555532 245667777888753
No 79
>cd06472 ACD_ScHsp26_like Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large 24-mers storage forms which upon heat shock disassociate into dimers. These dimers initiate the interaction with non-native substrate proteins and re-assemble into large globular assemblies having one monomer of substrate bound per dimer. This group also contains Arabidopsis thaliana (Ath) Hsp15.7, a peroxisomal matrix protein which can complement the morphological phenotype of S. cerevisiae mutants deficient in Hsps26. AthHsp15.7 is minimally expressed under normal conditions and is strongly induced by heat and oxidative st
Probab=21.61 E-value=72 Score=20.76 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=15.9
Q ss_pred cCCCcc--cEEEecCCCCCeEEEEcc
Q 033335 21 VGFSGV--ESVALKGDDMSQIEVTGD 44 (121)
Q Consensus 21 ~~~~GV--~sv~~d~~~~~kvtV~G~ 44 (121)
..++|| +++.++..+.+.|+|.|.
T Consensus 15 ~~lPGv~~edi~i~v~~~~~L~I~g~ 40 (92)
T cd06472 15 ADVPGVKKEDVKVEVEDGRVLRISGE 40 (92)
T ss_pred EECCCCChHhEEEEEeCCCEEEEEEE
Confidence 457887 455555543358999998
No 80
>PRK13748 putative mercuric reductase; Provisional
Probab=21.60 E-value=3.5e+02 Score=23.10 Aligned_cols=60 Identities=17% Similarity=0.209 Sum_probs=40.9
Q ss_pred eccchhhHHHHHHHhcCCCcccEEEecCCCCCeEEEEcc-ccCHHHHHHHHHhhcC-ceEEEec
Q 033335 6 SMNKHKSRSKALKVAVGFSGVESVALKGDDMSQIEVTGD-GVDAVALTTSLRKKVG-YAEVVSV 67 (121)
Q Consensus 6 ~m~C~~C~~K~~k~~~~~~GV~sv~~d~~~~~kvtV~G~-~vDp~~l~~~LrKk~~-~aeivsv 67 (121)
.++|..|..++...+..++|+....++.. .....+... ..+...+...+.. .+ .++..+.
T Consensus 8 g~~C~~c~~~ie~~l~~~~gv~~a~~~~~-~~~~~v~~~~~~~~~~i~~~i~~-~g~~~~~~~~ 69 (561)
T PRK13748 8 GMTCDSCAAHVKDALEKVPGVQSADVSYP-KGSAQLAIEVGTSPDALTAAVAG-LGYRATLADA 69 (561)
T ss_pred CeecHHHHHHHHHHHhcCCCeeEEEEEcC-CCEEEEEECCCCCHHHHHHHHHH-cCCeeeccCc
Confidence 57899999999999999999988888765 345555521 2566766666653 44 3444433
No 81
>PRK06136 uroporphyrin-III C-methyltransferase; Reviewed
Probab=20.94 E-value=1e+02 Score=23.51 Aligned_cols=31 Identities=23% Similarity=0.243 Sum_probs=26.4
Q ss_pred CeEEEEcccc-CHHHHHHHHHhhcCceEEEec
Q 033335 37 SQIEVTGDGV-DAVALTTSLRKKVGYAEVVSV 67 (121)
Q Consensus 37 ~kvtV~G~~v-Dp~~l~~~LrKk~~~aeivsv 67 (121)
++|.++|.|. ||.-|+-+-++....|++|-.
T Consensus 3 g~l~iVGvGpGdp~~lT~~A~~~L~~advI~~ 34 (249)
T PRK06136 3 GKVYLVGAGPGDPDLITLKGVRLLEQADVVLY 34 (249)
T ss_pred cEEEEEEECCCChHHHHHHHHHHHhcCCEEEE
Confidence 5899999987 999999998888888887765
No 82
>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=20.79 E-value=93 Score=20.50 Aligned_cols=21 Identities=19% Similarity=0.192 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCCcccEEEecC
Q 033335 13 RSKALKVAVGFSGVESVALKG 33 (121)
Q Consensus 13 ~~K~~k~~~~~~GV~sv~~d~ 33 (121)
+..+..++..++|+++|.+..
T Consensus 57 ~~~i~~al~~l~gv~~v~v~i 77 (99)
T TIGR02945 57 PGEVENAVRAVPGVGSVTVEL 77 (99)
T ss_pred HHHHHHHHHhCCCCceEEEEE
Confidence 355778889999999998864
No 83
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=20.74 E-value=62 Score=24.35 Aligned_cols=44 Identities=18% Similarity=0.286 Sum_probs=30.8
Q ss_pred CCCcccEEEecCCCCCeEEEEccccCHHHHHH---HHHhhcCceEEEec
Q 033335 22 GFSGVESVALKGDDMSQIEVTGDGVDAVALTT---SLRKKVGYAEVVSV 67 (121)
Q Consensus 22 ~~~GV~sv~~d~~~~~kvtV~G~~vDp~~l~~---~LrKk~~~aeivsv 67 (121)
.++|-..|.++.+ .+.|++.|. |.|.+|.. -+-.++-.|+|.-.
T Consensus 110 ~I~G~k~i~vn~e-~~~i~lsGi-VRp~DI~~~NtV~S~~IAda~I~y~ 156 (179)
T PF02107_consen 110 VIEGEKQIRVNGE-EQYIRLSGI-VRPEDIDPDNTVLSSKIADARIEYS 156 (179)
T ss_pred EEEEEEEEEECCC-EEEEEEEEE-ECHHHCCCCCeEchheeEeEEEEEc
Confidence 3568889999976 689999999 99999862 11223445666544
No 84
>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=20.34 E-value=1.1e+02 Score=23.21 Aligned_cols=31 Identities=10% Similarity=0.179 Sum_probs=21.3
Q ss_pred EEEeccchhhH------HHHHHHhcCCCcccEEEecC
Q 033335 3 IKVSMNKHKSR------SKALKVAVGFSGVESVALKG 33 (121)
Q Consensus 3 lKV~m~C~~C~------~K~~k~~~~~~GV~sv~~d~ 33 (121)
|.+.+...+|. ..+..+|..++||.+|.++.
T Consensus 117 I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 117 IEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 44445444443 55788889999999988764
No 85
>PF00070 Pyr_redox: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR001327 FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase [, , ]. Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently []. Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases [] and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) []. Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase [], thioredoxin reductase [], mercuric reductase [], lipoamide dehydrogenase [], trypanothione reductase [] and NADH peroxidase [] have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication []. This entry describes a small NADH binding domain within a larger FAD binding domain described by IPR023753 from INTERPRO. It is found in both class I and class II oxidoreductases. ; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZKQ_A 3DGZ_A 1ZDL_A 2R9Z_B 2RAB_A 2A87_B 1M6I_A 2YVG_A 2GR1_A 2GQW_A ....
Probab=20.25 E-value=2e+02 Score=17.78 Aligned_cols=31 Identities=16% Similarity=0.251 Sum_probs=20.4
Q ss_pred eEEEEccccCHHHHHHHHHhhcCceEEEecc
Q 033335 38 QIEVTGDGVDAVALTTSLRKKVGYAEVVSVG 68 (121)
Q Consensus 38 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~ 68 (121)
+++|+|-|+-...+...|++....+.++.-.
T Consensus 1 ~vvViGgG~ig~E~A~~l~~~g~~vtli~~~ 31 (80)
T PF00070_consen 1 RVVVIGGGFIGIELAEALAELGKEVTLIERS 31 (80)
T ss_dssp EEEEESSSHHHHHHHHHHHHTTSEEEEEESS
T ss_pred CEEEECcCHHHHHHHHHHHHhCcEEEEEecc
Confidence 4677777777777777777533366666443
Done!