Query 048349
Match_columns 94
No_of_seqs 121 out of 582
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:43:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048349.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048349hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.8 7.3E-18 1.6E-22 106.2 8.3 67 2-70 4-71 (73)
2 PF00403 HMA: Heavy-metal-asso 99.3 2.5E-11 5.5E-16 72.7 7.1 55 6-61 1-58 (62)
3 COG2608 CopZ Copper chaperone 98.7 1.3E-07 2.8E-12 59.2 7.5 60 3-64 2-64 (71)
4 KOG4656 Copper chaperone for s 98.4 2.4E-06 5.3E-11 64.8 8.0 67 4-72 8-74 (247)
5 PLN02957 copper, zinc superoxi 98.1 3.1E-05 6.7E-10 58.2 9.1 71 3-75 6-76 (238)
6 PRK10671 copA copper exporting 97.9 6.2E-05 1.3E-09 64.7 7.9 66 1-70 1-67 (834)
7 TIGR00003 copper ion binding p 95.9 0.11 2.4E-06 27.5 7.5 58 3-61 2-62 (68)
8 COG2217 ZntA Cation transport 94.2 0.19 4.1E-06 43.7 7.0 64 3-68 2-69 (713)
9 PRK10671 copA copper exporting 93.2 0.4 8.6E-06 41.6 7.2 62 5-69 101-164 (834)
10 KOG0207 Cation transport ATPas 91.0 0.38 8.2E-06 43.2 4.6 67 3-70 146-215 (951)
11 COG1888 Uncharacterized protei 89.0 1 2.2E-05 30.3 4.4 46 19-64 23-74 (97)
12 PF02680 DUF211: Uncharacteriz 87.7 1.1 2.4E-05 30.1 4.0 61 4-64 6-72 (95)
13 PRK11033 zntA zinc/cadmium/mer 84.4 4.8 0.0001 34.9 7.3 56 4-61 54-111 (741)
14 KOG0207 Cation transport ATPas 83.6 2.8 6.1E-05 37.9 5.6 63 10-73 2-65 (951)
15 PF03927 NapD: NapD protein; 73.9 12 0.00026 23.6 4.9 33 4-36 40-72 (79)
16 PF01883 DUF59: Domain of unkn 73.8 8.6 0.00019 23.1 4.1 32 4-35 35-72 (72)
17 PF13732 DUF4162: Domain of un 71.5 17 0.00038 22.0 5.2 40 24-64 26-65 (84)
18 cd04888 ACT_PheB-BS C-terminal 67.7 21 0.00046 20.8 4.9 31 5-35 43-74 (76)
19 PF03927 NapD: NapD protein; 65.4 31 0.00068 21.7 5.7 45 15-61 15-59 (79)
20 PF13291 ACT_4: ACT domain; PD 65.4 22 0.00048 21.4 4.7 31 4-34 49-79 (80)
21 PRK10553 assembly protein for 63.2 31 0.00067 22.4 5.3 46 15-61 17-62 (87)
22 PRK10553 assembly protein for 58.0 29 0.00064 22.5 4.5 34 4-37 43-76 (87)
23 PHA00514 dsDNA binding protein 55.5 22 0.00048 23.8 3.6 35 41-76 32-68 (98)
24 PF09358 UBA_e1_C: Ubiquitin-a 54.2 25 0.00055 24.0 3.9 32 41-73 35-67 (125)
25 cd06167 LabA_like LabA_like pr 52.8 27 0.00058 23.2 3.8 30 42-72 103-132 (149)
26 cd04910 ACT_AK-Ectoine_1 ACT d 50.8 43 0.00093 21.0 4.2 54 13-68 14-69 (71)
27 PF08712 Nfu_N: Scaffold prote 49.8 48 0.001 21.2 4.5 43 18-63 37-80 (87)
28 COG1432 Uncharacterized conser 49.4 30 0.00065 24.9 3.8 31 42-73 114-144 (181)
29 PF07683 CobW_C: Cobalamin syn 45.7 21 0.00045 22.0 2.2 24 38-61 69-92 (94)
30 cd04877 ACT_TyrR N-terminal AC 45.5 59 0.0013 19.3 4.2 28 7-34 41-68 (74)
31 TIGR00288 conserved hypothetic 45.4 38 0.00083 24.4 3.8 31 42-73 109-139 (160)
32 PF05922 Inhibitor_I9: Peptida 43.0 28 0.00061 20.6 2.5 20 18-37 58-77 (82)
33 PF14492 EFG_II: Elongation Fa 42.8 54 0.0012 20.1 3.8 48 19-67 23-72 (75)
34 COG2177 FtsX Cell division pro 42.6 85 0.0018 24.6 5.7 37 14-64 71-107 (297)
35 TIGR00300 conserved hypothetic 41.1 1.5E+02 0.0033 24.7 7.0 85 2-90 3-97 (407)
36 PF01936 NYN: NYN domain; Int 39.5 42 0.00091 21.8 3.1 29 42-71 99-127 (146)
37 PF08478 POTRA_1: POTRA domain 39.4 41 0.00089 19.5 2.8 29 17-45 36-64 (69)
38 TIGR00489 aEF-1_beta translati 38.9 56 0.0012 21.3 3.5 30 8-37 54-84 (88)
39 PF05193 Peptidase_M16_C: Pept 38.7 30 0.00065 22.4 2.3 24 40-64 19-42 (184)
40 smart00833 CobW_C Cobalamin sy 37.0 49 0.0011 20.1 2.9 23 39-61 68-90 (92)
41 PRK00435 ef1B elongation facto 36.8 57 0.0012 21.3 3.3 31 7-37 53-84 (88)
42 PRK06418 transcription elongat 36.8 85 0.0018 22.8 4.5 74 5-79 8-106 (166)
43 PF12164 SporV_AA: Stage V spo 36.6 42 0.00091 21.9 2.7 48 19-74 34-81 (93)
44 cd04878 ACT_AHAS N-terminal AC 36.2 79 0.0017 17.5 4.0 28 5-33 44-71 (72)
45 COG3643 Glutamate formiminotra 34.5 59 0.0013 25.8 3.6 44 17-63 20-66 (302)
46 PF04972 BON: BON domain; Int 34.1 92 0.002 17.7 3.7 29 6-34 29-57 (64)
47 PRK11023 outer membrane lipopr 33.5 67 0.0014 23.2 3.6 47 12-60 46-95 (191)
48 cd06471 ACD_LpsHSP_like Group 33.4 20 0.00043 22.4 0.7 23 25-48 16-40 (93)
49 PF10105 DUF2344: Uncharacteri 33.4 1.4E+02 0.003 21.6 5.3 33 42-75 65-98 (187)
50 PF12971 NAGLU_N: Alpha-N-acet 33.2 97 0.0021 19.6 3.9 40 28-69 29-71 (86)
51 PRK09577 multidrug efflux prot 32.4 1.2E+02 0.0026 27.4 5.6 46 17-63 158-210 (1032)
52 PRK10555 aminoglycoside/multid 31.3 1.1E+02 0.0024 27.7 5.2 45 17-62 159-210 (1037)
53 PF07338 DUF1471: Protein of u 31.0 59 0.0013 19.2 2.5 23 41-63 6-28 (56)
54 COG3062 NapD Uncharacterized p 30.8 1.7E+02 0.0036 19.6 4.8 44 15-60 18-61 (94)
55 cd03309 CmuC_like CmuC_like. P 30.6 66 0.0014 25.2 3.3 44 9-55 215-269 (321)
56 PRK13748 putative mercuric red 30.3 2.4E+02 0.0051 23.0 6.6 60 10-71 8-69 (561)
57 PF10369 ALS_ss_C: Small subun 29.7 1.4E+02 0.0031 18.4 4.4 65 4-72 4-68 (75)
58 COG2151 PaaD Predicted metal-s 29.6 86 0.0019 21.3 3.4 33 5-37 51-89 (111)
59 cd02643 R3H_NF-X1 R3H domain o 29.1 1E+02 0.0022 19.1 3.4 29 17-45 44-72 (74)
60 PF01424 R3H: R3H domain; Int 29.0 88 0.0019 18.1 3.0 34 13-46 28-61 (63)
61 smart00838 EFG_C Elongation fa 28.5 1.4E+02 0.0031 18.2 5.7 62 7-71 6-72 (85)
62 cd04098 eEF2_C_snRNP eEF2_C_sn 28.4 1.5E+02 0.0032 18.2 6.1 62 7-70 4-71 (80)
63 PRK15127 multidrug efflux syst 28.2 1.2E+02 0.0027 27.5 5.0 45 17-62 159-210 (1049)
64 TIGR03406 FeS_long_SufT probab 28.0 86 0.0019 22.8 3.4 34 4-37 114-153 (174)
65 TIGR02945 SUF_assoc FeS assemb 27.8 84 0.0018 19.8 3.0 21 17-37 57-77 (99)
66 PF15643 Tox-PL-2: Papain fold 27.2 52 0.0011 22.3 1.9 20 10-29 18-39 (100)
67 COG4004 Uncharacterized protei 27.2 99 0.0022 20.8 3.2 25 22-47 34-58 (96)
68 COG2092 EFB1 Translation elong 27.2 1.1E+02 0.0023 20.3 3.3 32 5-36 51-83 (88)
69 PRK10743 heat shock protein Ib 26.9 24 0.00051 24.5 0.2 24 24-48 50-75 (137)
70 KOG3411 40S ribosomal protein 26.9 47 0.001 23.8 1.7 44 14-61 97-140 (143)
71 smart00653 eIF2B_5 domain pres 26.6 1E+02 0.0022 20.8 3.3 29 33-64 50-78 (110)
72 PRK11198 LysM domain/BON super 26.6 1.4E+02 0.0031 20.6 4.2 55 14-70 25-80 (147)
73 PF14006 YqzL: YqzL-like prote 26.3 40 0.00086 19.9 1.1 40 44-88 8-47 (47)
74 cd06464 ACD_sHsps-like Alpha-c 26.1 30 0.00066 20.5 0.6 23 25-48 13-37 (88)
75 PRK11597 heat shock chaperone 25.7 25 0.00055 24.7 0.2 24 24-48 48-73 (142)
76 PRK10503 multidrug efflux syst 25.4 1.6E+02 0.0034 26.8 5.1 46 17-62 168-220 (1040)
77 TIGR00915 2A0602 The (Largely 25.0 1.6E+02 0.0034 26.8 5.0 44 17-61 159-209 (1044)
78 PRK04435 hypothetical protein; 24.9 2E+02 0.0042 20.0 4.6 20 16-35 124-143 (147)
79 cd06472 ACD_ScHsp26_like Alpha 24.9 49 0.0011 20.7 1.5 24 25-48 15-40 (92)
80 cd04879 ACT_3PGDH-like ACT_3PG 24.8 89 0.0019 17.1 2.4 18 17-34 52-69 (71)
81 PLN02625 uroporphyrin-III C-me 24.5 76 0.0017 23.7 2.6 33 39-71 13-46 (263)
82 COG4687 Uncharacterized protei 24.2 1.7E+02 0.0037 20.5 4.1 36 32-71 70-105 (122)
83 PRK10614 multidrug efflux syst 24.1 1.7E+02 0.0036 26.5 5.0 47 17-63 159-212 (1025)
84 PHA01634 hypothetical protein 24.1 27 0.00058 25.3 0.1 12 10-21 97-108 (156)
85 PF00736 EF1_GNE: EF-1 guanine 24.0 2.1E+02 0.0045 18.4 4.8 33 5-37 51-85 (89)
86 PF02107 FlgH: Flagellar L-rin 23.9 47 0.001 24.0 1.4 29 26-56 110-138 (179)
87 PF03990 DUF348: Domain of unk 23.9 1.2E+02 0.0027 16.6 2.9 39 32-73 3-41 (43)
88 cd04887 ACT_MalLac-Enz ACT_Mal 23.8 1.6E+02 0.0034 16.9 4.7 29 7-35 44-72 (74)
89 COG0612 PqqL Predicted Zn-depe 23.7 84 0.0018 24.8 2.8 25 39-64 197-221 (438)
90 PF03958 Secretin_N: Bacterial 22.1 1.2E+02 0.0025 18.1 2.7 23 32-55 47-69 (82)
91 PF00070 Pyr_redox: Pyridine n 21.5 1.9E+02 0.0041 17.1 3.7 35 42-76 1-35 (80)
92 PF00873 ACR_tran: AcrB/AcrD/A 21.4 1.1E+02 0.0023 27.4 3.3 48 16-63 157-211 (1021)
93 PF01253 SUI1: Translation ini 21.3 85 0.0018 19.6 2.0 32 40-71 17-53 (83)
94 PRK04021 hypothetical protein; 20.9 2.5E+02 0.0055 18.3 4.7 48 10-60 41-91 (92)
95 PF13241 NAD_binding_7: Putati 20.8 1.6E+02 0.0034 18.7 3.3 39 34-73 2-40 (103)
96 PRK00378 nucleoid-associated p 20.6 1.2E+02 0.0026 23.5 3.1 29 31-63 303-331 (334)
97 PRK09579 multidrug efflux prot 20.4 2.9E+02 0.0062 25.1 5.8 46 17-62 158-210 (1017)
98 cd04901 ACT_3PGDH C-terminal A 20.3 1.2E+02 0.0027 17.0 2.5 19 17-35 50-68 (69)
99 cd04903 ACT_LSD C-terminal ACT 20.2 1.2E+02 0.0025 16.7 2.3 20 16-35 51-70 (71)
100 PF01981 PTH2: Peptidyl-tRNA h 20.1 2.7E+02 0.0058 18.3 5.2 58 3-63 51-113 (116)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.75 E-value=7.3e-18 Score=106.23 Aligned_cols=67 Identities=21% Similarity=0.333 Sum_probs=62.2
Q ss_pred ceeEEEEEeCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcC-ceEEEe
Q 048349 2 KRMVGIEQPLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLR-YATFIA 70 (94)
Q Consensus 2 ~q~vVlKV~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~-~aeivs 70 (94)
.+..+++|+|||+||++++.+.+..++||+++.+|. ++++|||.|+ +||..|+++|+|.++ .+++|.
T Consensus 4 ~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~-~~~kvtV~g~-~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 4 IKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDI-KKQKVTVKGN-VDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred ccEEEEEECcccccHHHHHHHHhhccCCeEEEEecC-CCCEEEEEEe-cCHHHHHHHHHhcCCCceEEec
Confidence 578999999999999999999999999999999998 9999999999 999999999999774 666664
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=99.27 E-value=2.5e-11 Score=72.68 Aligned_cols=55 Identities=20% Similarity=0.254 Sum_probs=49.7
Q ss_pred EEEE-eCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccc--cCHHHHHHHHHh
Q 048349 6 GIEQ-PLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDG--MDAIVLFMSLRK 61 (94)
Q Consensus 6 VlKV-~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~--vDp~~l~~~LrK 61 (94)
.|+| +|+|++|++++.+++.+++||.++.+|. .+++++|.++. +++.++.++|++
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~-~~~~v~v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDL-ETKTVTVTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEET-TTTEEEEEESTTTSCHHHHHHHHHH
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEEC-CCCEEEEEEecCCCCHHHHHHHHHH
Confidence 4678 7999999999999999999999999998 99999999982 345999999998
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.69 E-value=1.3e-07 Score=59.19 Aligned_cols=60 Identities=10% Similarity=0.150 Sum_probs=50.2
Q ss_pred eeEEEEE-eCcchhhHHHHHHHhcCCCCeeEEEecCCCCC--cEEEEccccCHHHHHHHHHhhcC
Q 048349 3 RMVGIEQ-PLENDKSRSKALKIVGGMPGVESVAFKGDDRS--QIEVTGDGMDAIVLFMSLRKKLR 64 (94)
Q Consensus 3 q~vVlKV-~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~--kvtV~G~~vDp~~l~~~LrKk~~ 64 (94)
++..|++ .|+|+.|...+.++|.+++||.++++|. +.+ .+++.+..++..++...+.+ .|
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l-~~~~~~V~~d~~~~~~~~i~~ai~~-aG 64 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDL-EKGTATVTFDSNKVDIEAIIEAIED-AG 64 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEc-ccCeEEEEEcCCcCCHHHHHHHHHH-cC
Confidence 4567777 6999999999999999999999999998 884 45555533899999999988 44
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.35 E-value=2.4e-06 Score=64.79 Aligned_cols=67 Identities=13% Similarity=0.177 Sum_probs=60.3
Q ss_pred eEEEEEeCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcCceEEEecc
Q 048349 4 MVGIEQPLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLRYATFIASK 72 (94)
Q Consensus 4 ~vVlKV~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~ 72 (94)
++.+-|+|+|+.|...+++.+..++||++|++|. +++.|.|-+. +-|..+...|+...+.|-|.-.+
T Consensus 8 ~~efaV~M~cescvnavk~~L~~V~Gi~~vevdl-e~q~v~v~ts-~p~s~i~~~le~tGr~Avl~G~G 74 (247)
T KOG4656|consen 8 EAEFAVQMTCESCVNAVKACLKGVPGINSVEVDL-EQQIVSVETS-VPPSEIQNTLENTGRDAVLRGAG 74 (247)
T ss_pred eEEEEEechhHHHHHHHHHHhccCCCcceEEEEh-hhcEEEEEcc-CChHHHHHHHHhhChheEEecCC
Confidence 6788999999999999999999999999999999 9999999999 99999999999944577766544
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.09 E-value=3.1e-05 Score=58.19 Aligned_cols=71 Identities=13% Similarity=0.127 Sum_probs=62.2
Q ss_pred eeEEEEEeCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcCceEEEeccCCc
Q 048349 3 RMVGIEQPLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLRYATFIASKLRR 75 (94)
Q Consensus 3 q~vVlKV~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~p~k 75 (94)
+++.+.+.|.|+.|..++.+.+.+++||.++.++. ..++++|.+. .++..+...+++....+++++.+++.
T Consensus 6 ~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~-~~~~v~V~~~-~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 6 LLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDL-SNQVVRVLGS-SPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred EEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEc-CCCEEEEEec-CCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 56788999999999999999999999999999998 8899999987 89999999998844468888876654
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.86 E-value=6.2e-05 Score=64.73 Aligned_cols=66 Identities=17% Similarity=0.179 Sum_probs=57.4
Q ss_pred CceeEEEEE-eCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcCceEEEe
Q 048349 1 MKRMVGIEQ-PLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLRYATFIA 70 (94)
Q Consensus 1 M~q~vVlKV-~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivs 70 (94)
|++++.++| .|+|..|.+++.+++.+++||.++.++. + +.+|.+. .++..+...++.-+-.+++.+
T Consensus 1 ~~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~-~--~~~v~~~-~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 1 MSQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSI-T--EAHVTGT-ASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred CCeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEee-e--EEEEEec-CCHHHHHHHHHhcCCcccccc
Confidence 899999999 5999999999999999999999999997 4 5677787 899999999997433677764
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=95.85 E-value=0.11 Score=27.49 Aligned_cols=58 Identities=19% Similarity=0.279 Sum_probs=44.3
Q ss_pred eeEEEEE-eCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEcc--ccCHHHHHHHHHh
Q 048349 3 RMVGIEQ-PLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGD--GMDAIVLFMSLRK 61 (94)
Q Consensus 3 q~vVlKV-~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~--~vDp~~l~~~LrK 61 (94)
++..+.+ .+.|+.|...+.+.+..++|+.+..++. ..+.+.+..+ ..+...+...+..
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKL-EKASVKVEFDAPQATEICIAEAILD 62 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEc-CCCEEEEEeCCCCCCHHHHHHHHHH
Confidence 3445777 5789999999999999999999999997 8788877642 2466666665543
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=94.18 E-value=0.19 Score=43.70 Aligned_cols=64 Identities=17% Similarity=0.186 Sum_probs=52.2
Q ss_pred eeEEEEE-eCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEcc--ccC-HHHHHHHHHhhcCceEE
Q 048349 3 RMVGIEQ-PLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGD--GMD-AIVLFMSLRKKLRYATF 68 (94)
Q Consensus 3 q~vVlKV-~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~--~vD-p~~l~~~LrKk~~~aei 68 (94)
++..|.+ .|+|..|.+++. .+.+++||.+..++. ..++++|..+ ..+ +..+...+++..-.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~-~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNL-ATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeec-ccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 3456777 599999999999 999999999999998 9999999865 256 78889998884434544
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=93.16 E-value=0.4 Score=41.65 Aligned_cols=62 Identities=16% Similarity=0.122 Sum_probs=51.1
Q ss_pred EEEEE-eCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcC-ceEEE
Q 048349 5 VGIEQ-PLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLR-YATFI 69 (94)
Q Consensus 5 vVlKV-~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~-~aeiv 69 (94)
+.+.+ .|+|..|...+.+.+..++||.+..++. ..++..+.+. .++..+...++. .+ .+.++
T Consensus 101 ~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl-~t~~~~V~~~-~s~~~I~~~I~~-~Gy~a~~~ 164 (834)
T PRK10671 101 QQLLLSGMSCASCVSRVQNALQSVPGVTQARVNL-AERTALVMGS-ASPQDLVQAVEK-AGYGAEAI 164 (834)
T ss_pred EEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeec-CCCeEEEEcc-CCHHHHHHHHHh-cCCCcccc
Confidence 45666 6999999999999999999999999997 8888888876 789888888876 55 44443
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=90.95 E-value=0.38 Score=43.15 Aligned_cols=67 Identities=13% Similarity=0.046 Sum_probs=52.8
Q ss_pred eeEEEEE-eCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEcc--ccCHHHHHHHHHhhcCceEEEe
Q 048349 3 RMVGIEQ-PLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGD--GMDAIVLFMSLRKKLRYATFIA 70 (94)
Q Consensus 3 q~vVlKV-~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~--~vDp~~l~~~LrKk~~~aeivs 70 (94)
++++|.| .|.|+.|..++.+.+.+++||.++.++. ..+++.|.=+ ..-|.++.+.|....-.+.+..
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~-~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~ 215 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSL-ATDTAIVVYDPEITGPRDIIKAIEETGFEASVRP 215 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEec-cCCceEEEecccccChHHHHHHHHhhcccceeee
Confidence 5778888 5999999999999999999999999998 8899888654 2467777777766332454444
No 11
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=88.98 E-value=1 Score=30.30 Aligned_cols=46 Identities=15% Similarity=0.177 Sum_probs=34.0
Q ss_pred HHHHHhcCCCCeeEEEe-----cCC-CCCcEEEEccccCHHHHHHHHHhhcC
Q 048349 19 KALKIVGGMPGVESVAF-----KGD-DRSQIEVTGDGMDAIVLFMSLRKKLR 64 (94)
Q Consensus 19 K~~k~i~~~~GV~sV~i-----d~~-~~~kvtV~G~~vDp~~l~~~LrKk~~ 64 (94)
..-+.+++++||+.|-+ |.+ .+=++|+-|+.+|-.++.+.|.+.++
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 34456778888876643 332 33488999999999999999999555
No 12
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=87.67 E-value=1.1 Score=30.12 Aligned_cols=61 Identities=15% Similarity=0.181 Sum_probs=38.6
Q ss_pred eEEEEEeCcchhhHHHHHHHhcCCCCeeEEEe-----cCCC-CCcEEEEccccCHHHHHHHHHhhcC
Q 048349 4 MVGIEQPLENDKSRSKALKIVGGMPGVESVAF-----KGDD-RSQIEVTGDGMDAIVLFMSLRKKLR 64 (94)
Q Consensus 4 ~vVlKV~m~c~~C~~K~~k~i~~~~GV~sV~i-----d~~~-~~kvtV~G~~vDp~~l~~~LrKk~~ 64 (94)
.+||-|.---+=-.-..-+.+++++||+.|.+ |.+- +=++|+.|+.+|...+.+.|.+.++
T Consensus 6 RlVLDVlKP~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg 72 (95)
T PF02680_consen 6 RLVLDVLKPHEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGG 72 (95)
T ss_dssp EEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-
T ss_pred EEEEEeecCCCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCC
Confidence 34444432222233445567889999988754 4311 2278999999999999999999555
No 13
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=84.44 E-value=4.8 Score=34.86 Aligned_cols=56 Identities=14% Similarity=0.142 Sum_probs=42.2
Q ss_pred eEEEEE-eCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccc-cCHHHHHHHHHh
Q 048349 4 MVGIEQ-PLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDG-MDAIVLFMSLRK 61 (94)
Q Consensus 4 ~vVlKV-~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~-vDp~~l~~~LrK 61 (94)
++.+++ .|+|..|..++.+.+.+++||.++.++. ...++.+..+. .+ ..+...++.
T Consensus 54 r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~-at~k~~V~~d~~~~-~~I~~aI~~ 111 (741)
T PRK11033 54 RYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLF-ATEKLVVDADNDIR-AQVESAVQK 111 (741)
T ss_pred eEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEc-CCCeEEEEecccch-HHHHHHHHh
Confidence 455666 5999999999999999999999999996 77777775431 22 455555555
No 14
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=83.57 E-value=2.8 Score=37.86 Aligned_cols=63 Identities=10% Similarity=0.094 Sum_probs=51.8
Q ss_pred eCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEc-cccCHHHHHHHHHhhcCceEEEeccC
Q 048349 10 PLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTG-DGMDAIVLFMSLRKKLRYATFIASKL 73 (94)
Q Consensus 10 ~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G-~~vDp~~l~~~LrKk~~~aeivsv~p 73 (94)
.|.|..|.+.+.+.+++.+||.+++++. .+++.+|.= .-+++..+.+.+.--+..+++.+...
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl-~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~~ 65 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSL-AQKRANVSYDNIVSPESIKETIEDMGFEASLLSDSE 65 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEe-ccccceEEEeeccCHHHHHHHhhcccceeeecccCc
Confidence 5899999999999999999999999998 777665533 34799999999988555788876543
No 15
>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=73.93 E-value=12 Score=23.64 Aligned_cols=33 Identities=15% Similarity=0.312 Sum_probs=27.4
Q ss_pred eEEEEEeCcchhhHHHHHHHhcCCCCeeEEEec
Q 048349 4 MVGIEQPLENDKSRSKALKIVGGMPGVESVAFK 36 (94)
Q Consensus 4 ~vVlKV~m~c~~C~~K~~k~i~~~~GV~sV~id 36 (94)
++|+-+.-...+-..+.++.+..++||-|+.+=
T Consensus 40 KiVVtiE~~~~~~~~~~~~~i~~l~GVlsa~lv 72 (79)
T PF03927_consen 40 KIVVTIEAESSEEEVDLIDAINALPGVLSASLV 72 (79)
T ss_dssp EEEEEEEESSHHHHHHHHHHHCCSTTEEEEEES
T ss_pred eEEEEEEeCChHHHHHHHHHHHcCCCceEEEEE
Confidence 567777777888888999999999999998764
No 16
>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=73.76 E-value=8.6 Score=23.07 Aligned_cols=32 Identities=25% Similarity=0.399 Sum_probs=21.8
Q ss_pred eEEEEEeCcchhh------HHHHHHHhcCCCCeeEEEe
Q 048349 4 MVGIEQPLENDKS------RSKALKIVGGMPGVESVAF 35 (94)
Q Consensus 4 ~vVlKV~m~c~~C------~~K~~k~i~~~~GV~sV~i 35 (94)
++-+.+.+...+| +..+..++..++||.+|.+
T Consensus 35 ~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 35 KVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 3555666665555 5788899999999999875
No 17
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=71.55 E-value=17 Score=22.02 Aligned_cols=40 Identities=33% Similarity=0.426 Sum_probs=31.2
Q ss_pred hcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcC
Q 048349 24 VGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLR 64 (94)
Q Consensus 24 i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~ 64 (94)
+..++||.++..+.+..-.+.+... .++..|+..|..+.-
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~-~~~~~ll~~l~~~g~ 65 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDE-ETANELLQELIEKGI 65 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCc-ccHHHHHHHHHhCCC
Confidence 6777999999987522257788876 899999999988543
No 18
>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=67.73 E-value=21 Score=20.84 Aligned_cols=31 Identities=23% Similarity=0.250 Sum_probs=22.3
Q ss_pred EEEEEeCcchh-hHHHHHHHhcCCCCeeEEEe
Q 048349 5 VGIEQPLENDK-SRSKALKIVGGMPGVESVAF 35 (94)
Q Consensus 5 vVlKV~m~c~~-C~~K~~k~i~~~~GV~sV~i 35 (94)
+.+-+...... --..+++.+.+++||.+|.+
T Consensus 43 i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 43 VTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 34445555554 66888888999999998875
No 19
>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=65.44 E-value=31 Score=21.68 Aligned_cols=45 Identities=20% Similarity=0.208 Sum_probs=34.1
Q ss_pred hhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHh
Q 048349 15 KSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRK 61 (94)
Q Consensus 15 ~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrK 61 (94)
+-...+...++.++|++=-..+. + +|+.|+=+.-+...+.+.+..
T Consensus 15 ~~~~~v~~~l~~~~gvEVh~~~~-~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 15 ERLEEVAEALAAIPGVEVHAVDE-D-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp CCHHHHHHHHCCSTTEEEEEEET-T-TEEEEEEEESSHHHHHHHHHH
T ss_pred hhHHHHHHHHHcCCCcEEEeeCC-C-CeEEEEEEeCChHHHHHHHHH
Confidence 34677899999999997767773 4 888887665577777777765
No 20
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=65.42 E-value=22 Score=21.38 Aligned_cols=31 Identities=16% Similarity=0.311 Sum_probs=25.8
Q ss_pred eEEEEEeCcchhhHHHHHHHhcCCCCeeEEE
Q 048349 4 MVGIEQPLENDKSRSKALKIVGGMPGVESVA 34 (94)
Q Consensus 4 ~vVlKV~m~c~~C~~K~~k~i~~~~GV~sV~ 34 (94)
.+.|.+....-.--..+++.+.+++||.+|.
T Consensus 49 ~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 49 RITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 4566777778888889999999999999885
No 21
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=63.18 E-value=31 Score=22.43 Aligned_cols=46 Identities=17% Similarity=0.238 Sum_probs=33.8
Q ss_pred hhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHh
Q 048349 15 KSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRK 61 (94)
Q Consensus 15 ~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrK 61 (94)
.-...+.+.+..++|++=-..|. +.+|+.|+=++-+...+++.|..
T Consensus 17 e~~~~V~~~l~~ipg~Evh~~d~-~~GKiVVtiE~~~~~~~~~~i~~ 62 (87)
T PRK10553 17 ERISDISTQLNAFPGCEVAVSDA-PSGQLIVVVEAEDSETLLQTIES 62 (87)
T ss_pred HHHHHHHHHHHcCCCcEEEeecC-CCCeEEEEEEeCChHHHHHHHHH
Confidence 33677889999999999988886 77888776554466656555543
No 22
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=58.02 E-value=29 Score=22.54 Aligned_cols=34 Identities=15% Similarity=0.162 Sum_probs=29.2
Q ss_pred eEEEEEeCcchhhHHHHHHHhcCCCCeeEEEecC
Q 048349 4 MVGIEQPLENDKSRSKALKIVGGMPGVESVAFKG 37 (94)
Q Consensus 4 ~vVlKV~m~c~~C~~K~~k~i~~~~GV~sV~id~ 37 (94)
|+|+-+.-.+.+-.-..+..+..++||-|+.+=.
T Consensus 43 KiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVY 76 (87)
T PRK10553 43 QLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVY 76 (87)
T ss_pred eEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEE
Confidence 6777788888888889999999999999998754
No 23
>PHA00514 dsDNA binding protein
Probab=55.46 E-value=22 Score=23.80 Aligned_cols=35 Identities=11% Similarity=0.123 Sum_probs=29.2
Q ss_pred CcEEEEccccCHHHHHHHHHhhc--CceEEEeccCCcc
Q 048349 41 SQIEVTGDGMDAIVLFMSLRKKL--RYATFIASKLRRK 76 (94)
Q Consensus 41 ~kvtV~G~~vDp~~l~~~LrKk~--~~aeivsv~p~k~ 76 (94)
+..|..|+ +....--.+|.|+. +.+.++|++|+-+
T Consensus 32 ~~~Tl~GN-LtiEqAQ~e~~k~~k~~pvqVvsVEpnt~ 68 (98)
T PHA00514 32 NEQTLLGN-LTIEQAQKELSKQYKHGPVQVVSVEPNTK 68 (98)
T ss_pred Ccceeecc-eeHHHHHHHHhhcccCCCeeEEEecCCCE
Confidence 45688999 89999999999885 4799999998643
No 24
>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=54.25 E-value=25 Score=24.01 Aligned_cols=32 Identities=28% Similarity=0.403 Sum_probs=26.3
Q ss_pred CcEEEEccccCHHHHHHHHHhhcC-ceEEEeccC
Q 048349 41 SQIEVTGDGMDAIVLFMSLRKKLR-YATFIASKL 73 (94)
Q Consensus 41 ~kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv~p 73 (94)
+++.|.|+ +....+++.++++++ .+..++.+.
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 999999999999998 899988764
No 25
>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=52.80 E-value=27 Score=23.21 Aligned_cols=30 Identities=23% Similarity=0.276 Sum_probs=26.1
Q ss_pred cEEEEccccCHHHHHHHHHhhcCceEEEecc
Q 048349 42 QIEVTGDGMDAIVLFMSLRKKLRYATFIASK 72 (94)
Q Consensus 42 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~ 72 (94)
=+.|+|+ -|-.-++++||..+..+.++++.
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 4677999 79999999999987789999886
No 26
>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=50.77 E-value=43 Score=20.96 Aligned_cols=54 Identities=15% Similarity=0.076 Sum_probs=40.1
Q ss_pred chhhHHHHHHHhcCCCCeeEEEecCCCCCcEEE--EccccCHHHHHHHHHhhcCceEE
Q 048349 13 NDKSRSKALKIVGGMPGVESVAFKGDDRSQIEV--TGDGMDAIVLFMSLRKKLRYATF 68 (94)
Q Consensus 13 c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV--~G~~vDp~~l~~~LrKk~~~aei 68 (94)
..|=..+++.++++ .+|.=|.-+. +.|.+|. .|..-+...++..|++.++.|++
T Consensus 14 ~~g~d~~i~~~l~~-~~v~ii~K~~-nANtit~yl~~~~k~~~r~~~~Le~~~p~a~i 69 (71)
T cd04910 14 EVGYDLEILELLQR-FKVSIIAKDT-NANTITHYLAGSLKTIKRLTEDLENRFPNAEI 69 (71)
T ss_pred ChhHHHHHHHHHHH-cCCeEEEEec-CCCeEEEEEEcCHHHHHHHHHHHHHhCccCcc
Confidence 34556788888876 5777777787 8888875 55523668899999888887776
No 27
>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=49.77 E-value=48 Score=21.20 Aligned_cols=43 Identities=28% Similarity=0.262 Sum_probs=30.7
Q ss_pred HHHHHHhcCCCCeeEEEecCCCCCcEEEEcc-ccCHHHHHHHHHhhc
Q 048349 18 SKALKIVGGMPGVESVAFKGDDRSQIEVTGD-GMDAIVLFMSLRKKL 63 (94)
Q Consensus 18 ~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~-~vDp~~l~~~LrKk~ 63 (94)
+-.-+.|-.++||.||-+.. |=|||+-+ .+|-..|...++...
T Consensus 37 spLA~~Lf~i~gV~~Vf~~~---dfItVtK~~~~~W~~l~~~I~~~I 80 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIGD---DFITVTKNPDADWEDLKPEIREVI 80 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEET---TEEEEEE-TTS-HHHHHHHHHHHT
T ss_pred CHHHHHhcCCCCEeEEEEEC---CEEEEeeCCCCCHHHHHHHHHHHH
Confidence 33445556999999999987 67888654 389999988887644
No 28
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=49.43 E-value=30 Score=24.85 Aligned_cols=31 Identities=23% Similarity=0.176 Sum_probs=27.5
Q ss_pred cEEEEccccCHHHHHHHHHhhcCceEEEeccC
Q 048349 42 QIEVTGDGMDAIVLFMSLRKKLRYATFIASKL 73 (94)
Q Consensus 42 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~p 73 (94)
-+.++|+ -|-.-+++.++.+++.+++++.+|
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 4567899 799999999999899999999987
No 29
>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=45.71 E-value=21 Score=22.02 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=16.7
Q ss_pred CCCCcEEEEccccCHHHHHHHHHh
Q 048349 38 DDRSQIEVTGDGMDAIVLFMSLRK 61 (94)
Q Consensus 38 ~~~~kvtV~G~~vDp~~l~~~LrK 61 (94)
+..++++++|.++|...|-+.|..
T Consensus 69 ~~~~~lV~IG~~ld~~~l~~~l~~ 92 (94)
T PF07683_consen 69 DRDSRLVFIGKNLDKEALREALDA 92 (94)
T ss_dssp ---EEEEEEEES--HHHHHHHHHT
T ss_pred CCCeEEEEEECCCCHHHHHHHHHc
Confidence 366899999999999998888764
No 30
>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=45.46 E-value=59 Score=19.32 Aligned_cols=28 Identities=18% Similarity=0.226 Sum_probs=17.0
Q ss_pred EEEeCcchhhHHHHHHHhcCCCCeeEEE
Q 048349 7 IEQPLENDKSRSKALKIVGGMPGVESVA 34 (94)
Q Consensus 7 lKV~m~c~~C~~K~~k~i~~~~GV~sV~ 34 (94)
+.+....-.--..+++.+.+++||.+|.
T Consensus 41 l~i~v~~~~~L~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 41 LNFPTIEFEKLQTLMPEIRRIDGVEDVK 68 (74)
T ss_pred EEeEecCHHHHHHHHHHHhCCCCceEEE
Confidence 3344444444566777777777777765
No 31
>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=45.43 E-value=38 Score=24.45 Aligned_cols=31 Identities=16% Similarity=0.127 Sum_probs=26.0
Q ss_pred cEEEEccccCHHHHHHHHHhhcCceEEEeccC
Q 048349 42 QIEVTGDGMDAIVLFMSLRKKLRYATFIASKL 73 (94)
Q Consensus 42 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~p 73 (94)
=+-|+|+ -|-.-|+.+||..+..+..+++++
T Consensus 109 ~vLvSgD-~DF~~Lv~~lre~G~~V~v~g~~~ 139 (160)
T TIGR00288 109 VALVTRD-ADFLPVINKAKENGKETIVIGAEP 139 (160)
T ss_pred EEEEecc-HhHHHHHHHHHHCCCEEEEEeCCC
Confidence 4678999 799999999999766899888643
No 32
>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=43.03 E-value=28 Score=20.65 Aligned_cols=20 Identities=25% Similarity=0.336 Sum_probs=16.5
Q ss_pred HHHHHHhcCCCCeeEEEecC
Q 048349 18 SKALKIVGGMPGVESVAFKG 37 (94)
Q Consensus 18 ~K~~k~i~~~~GV~sV~id~ 37 (94)
....+.+.+.|||.+|+.|.
T Consensus 58 ~~~i~~L~~~p~V~~Ve~D~ 77 (82)
T PF05922_consen 58 EEEIEKLRKDPGVKSVEPDQ 77 (82)
T ss_dssp HHHHHHHHTSTTEEEEEEEC
T ss_pred HHHHHHHHcCCCeEEEEeCc
Confidence 34567888999999999985
No 33
>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=42.79 E-value=54 Score=20.09 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=31.7
Q ss_pred HHHHHhcCCCCeeEEEecCCCCCcEEEEccc-cCHHHHHHHHHhhcC-ceE
Q 048349 19 KALKIVGGMPGVESVAFKGDDRSQIEVTGDG-MDAIVLFMSLRKKLR-YAT 67 (94)
Q Consensus 19 K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~-vDp~~l~~~LrKk~~-~ae 67 (94)
.+++.+..-+=--.+..|. +.+.+.+.|-| +-..-++++|++.++ .++
T Consensus 23 ~aL~~l~~eDP~l~~~~d~-et~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 23 EALQKLSEEDPSLRVERDE-ETGELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp HHHHHHHHH-TTSEEEEET-TTSEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred HHHHHHHhcCCeEEEEEcc-hhceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 3344444333334677775 77888887654 778889999999887 454
No 34
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=42.59 E-value=85 Score=24.63 Aligned_cols=37 Identities=24% Similarity=0.332 Sum_probs=30.5
Q ss_pred hhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcC
Q 048349 14 DKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLR 64 (94)
Q Consensus 14 ~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~ 64 (94)
+.|...+...+.+++||.|+..- |.++-++.|++..|
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~~--------------sre~~l~~L~~~lg 107 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRFI--------------SREEALKELQPWLG 107 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEEe--------------CHHHHHHHHHHHcC
Confidence 78899999999999999999874 56666777777666
No 35
>TIGR00300 conserved hypothetical protein TIGR00300. All members of the family come from genome projects. A partial length search brings in two plant lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzymes hitting the N-terminal region of the family.
Probab=41.07 E-value=1.5e+02 Score=24.69 Aligned_cols=85 Identities=20% Similarity=0.193 Sum_probs=59.3
Q ss_pred ceeEEEEEeCcchhhHHHHHHHhcCCCC---eeEEEecCC----CCCcEEEEccccCHH---HHHHHHHhhcCceEEEec
Q 048349 2 KRMVGIEQPLENDKSRSKALKIVGGMPG---VESVAFKGD----DRSQIEVTGDGMDAI---VLFMSLRKKLRYATFIAS 71 (94)
Q Consensus 2 ~q~vVlKV~m~c~~C~~K~~k~i~~~~G---V~sV~id~~----~~~kvtV~G~~vDp~---~l~~~LrKk~~~aeivsv 71 (94)
+++|+|+=++-+.+--.+++-.+..+-| |..+++... +.-+++|.|. |+. .++.+|.. .| |.++.+
T Consensus 3 ~r~iel~GHiiDs~il~~~lD~i~d~gG~f~v~~f~vG~~k~d~S~a~~~V~a~--~~~~l~~Il~~l~~-~G-a~~~~~ 78 (407)
T TIGR00300 3 SREIELEGHLIDSLILPKALDIILDMGGDFRVLEFNIGKRKNDPSYARILVSAR--DHQHLEEILTELID-LG-AVIPEI 78 (407)
T ss_pred ceEEEEeeeeechhhHHHHHHHHHhcCCceEEEEEecCCccCCCccEEEEEecC--CHHHHHHHHHHHHH-cC-CCcCCC
Confidence 3578888888899999999999998877 566666432 2237999998 655 45555555 33 556677
Q ss_pred cCCcccCccCCccccceee
Q 048349 72 KLRRKVFLSDRSLVSHHVY 90 (94)
Q Consensus 72 ~p~k~~~~~~~~~~~~~~~ 90 (94)
++.+-++.+..-..|-++|
T Consensus 79 ~~a~l~~a~~DgV~P~~Fy 97 (407)
T TIGR00300 79 EEVELETAPQDGVLPDDFY 97 (407)
T ss_pred ccceEeEccccCcCCCCce
Confidence 7777666666666666665
No 36
>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=39.54 E-value=42 Score=21.80 Aligned_cols=29 Identities=24% Similarity=0.334 Sum_probs=20.4
Q ss_pred cEEEEccccCHHHHHHHHHhhcCceEEEec
Q 048349 42 QIEVTGDGMDAIVLFMSLRKKLRYATFIAS 71 (94)
Q Consensus 42 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv 71 (94)
=+.|+|+ -|-.-++++||.++..+.++..
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 5678999 7999999999987778999984
No 37
>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=39.37 E-value=41 Score=19.49 Aligned_cols=29 Identities=21% Similarity=0.210 Sum_probs=22.7
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCcEEE
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQIEV 45 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~kvtV 45 (94)
..++.+.+.++|.|.++.+...--+++.|
T Consensus 36 ~~~~~~~l~~~p~V~~v~V~r~~P~~l~I 64 (69)
T PF08478_consen 36 LKKIEQRLEKLPWVKSVSVSRRFPNTLEI 64 (69)
T ss_dssp HHHHHHCCCCTTTEEEEEEEEETTTEEEE
T ss_pred HHHHHHHHHcCCCEEEEEEEEeCCCEEEE
Confidence 35677788889999999998756666665
No 38
>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=38.92 E-value=56 Score=21.33 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=22.9
Q ss_pred EEeCcch-hhHHHHHHHhcCCCCeeEEEecC
Q 048349 8 EQPLEND-KSRSKALKIVGGMPGVESVAFKG 37 (94)
Q Consensus 8 KV~m~c~-~C~~K~~k~i~~~~GV~sV~id~ 37 (94)
-+-|.++ +--..+..++++++||+|+++..
T Consensus 54 ~~vv~D~~g~td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 54 MVVMGDAEGGTEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred EEEEecCCcChHHHHHHHhcCCCccEEEEEE
Confidence 3344333 66788999999999999999863
No 39
>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=38.71 E-value=30 Score=22.44 Aligned_cols=24 Identities=21% Similarity=0.250 Sum_probs=20.3
Q ss_pred CCcEEEEccccCHHHHHHHHHhhcC
Q 048349 40 RSQIEVTGDGMDAIVLFMSLRKKLR 64 (94)
Q Consensus 40 ~~kvtV~G~~vDp~~l~~~LrKk~~ 64 (94)
+-.+.+.|+ +|+..+.+.+++.++
T Consensus 19 n~~l~i~Gd-~~~~~~~~~i~~~~~ 42 (184)
T PF05193_consen 19 NMTLVIVGD-IDPDELEKLIEKYFG 42 (184)
T ss_dssp GEEEEEEES-SGHHHHHHHHHHHHT
T ss_pred ceEEEEEcC-ccHHHHHHHHHhhhh
Confidence 347888999 999999999998775
No 40
>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=36.96 E-value=49 Score=20.09 Aligned_cols=23 Identities=17% Similarity=0.326 Sum_probs=18.8
Q ss_pred CCCcEEEEccccCHHHHHHHHHh
Q 048349 39 DRSQIEVTGDGMDAIVLFMSLRK 61 (94)
Q Consensus 39 ~~~kvtV~G~~vDp~~l~~~LrK 61 (94)
..++++++|.++|...|-+.|..
T Consensus 68 ~~~~lV~IG~~l~~~~l~~~l~~ 90 (92)
T smart00833 68 RRTRLVFIGRDLDEEAIRAALDA 90 (92)
T ss_pred cceEEEEEeCCCCHHHHHHHHHH
Confidence 35789999998999988887764
No 41
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=36.82 E-value=57 Score=21.29 Aligned_cols=31 Identities=16% Similarity=0.232 Sum_probs=23.4
Q ss_pred EEEeCcc-hhhHHHHHHHhcCCCCeeEEEecC
Q 048349 7 IEQPLEN-DKSRSKALKIVGGMPGVESVAFKG 37 (94)
Q Consensus 7 lKV~m~c-~~C~~K~~k~i~~~~GV~sV~id~ 37 (94)
+.+-+.+ ++--..+...++.++||+|+++..
T Consensus 53 i~~vv~D~~~~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 53 LYVIMPDEEGGTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred EEEEEEcCCcCcHHHHHHHhccCCCcEEEEEE
Confidence 3333444 477788899999999999999863
No 42
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=36.77 E-value=85 Score=22.82 Aligned_cols=74 Identities=15% Similarity=0.086 Sum_probs=45.7
Q ss_pred EEEEEeCcchhhHHH------------HHHHhcCC------CCeeEEEecCCCCCcEE-EE--cccc---CHHHHHHHHH
Q 048349 5 VGIEQPLENDKSRSK------------ALKIVGGM------PGVESVAFKGDDRSQIE-VT--GDGM---DAIVLFMSLR 60 (94)
Q Consensus 5 vVlKV~m~c~~C~~K------------~~k~i~~~------~GV~sV~id~~~~~kvt-V~--G~~v---Dp~~l~~~Lr 60 (94)
+=+|=.+-|.+|.++ +++.+.++ .+++....=. ..|++. |+ |+++ --...+++|+
T Consensus 8 ~c~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~-~ddrvIfvV~~gdg~aIGk~G~~ik~l~ 86 (166)
T PRK06418 8 VCVKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYE-VDDLVILLVTSGPRIPIGKGGKIAKALS 86 (166)
T ss_pred EEeccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEE-eCCEEEEEEeCCCcccccccchHHHHHH
Confidence 335557889999886 46677665 4555443332 224554 33 3321 1236788998
Q ss_pred hhcC-ceEEEeccCCcccCc
Q 048349 61 KKLR-YATFIASKLRRKVFL 79 (94)
Q Consensus 61 Kk~~-~aeivsv~p~k~~~~ 79 (94)
++.| ++++|.-.+..+.+.
T Consensus 87 ~~lgk~VevVE~s~d~~~fl 106 (166)
T PRK06418 87 RKLGKKVRVVEKTNDIKKLA 106 (166)
T ss_pred HHhCCcEEEEEcCCCHHHHH
Confidence 8887 899998776655443
No 43
>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=36.58 E-value=42 Score=21.90 Aligned_cols=48 Identities=4% Similarity=0.066 Sum_probs=28.5
Q ss_pred HHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcCceEEEeccCC
Q 048349 19 KALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLRYATFIASKLR 74 (94)
Q Consensus 19 K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~p~ 74 (94)
.+...+..+ .=..++..+++++. +|..++++.+++.++.+++-..||.
T Consensus 34 ~~~~klk~l---~i~~~~~~d~~r~V-----isvm~II~~I~~~~p~l~I~~iGe~ 81 (93)
T PF12164_consen 34 EIENKLKAL---PIYKIKKKDKNRYV-----ISVMKIIEKIQEEYPNLDIQNIGET 81 (93)
T ss_dssp HHHHHHHTS---EEEE-BTTT--EEE-----EEHHHHHHHHHHH-SSEEEEE-S-S
T ss_pred HHHHHhhcc---EeeeecCCCCCEEE-----EEHHHHHHHHHHHCCCcEEEEcCCC
Confidence 445555444 23334542344443 5889999999999999999999875
No 44
>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=36.23 E-value=79 Score=17.46 Aligned_cols=28 Identities=14% Similarity=0.121 Sum_probs=17.1
Q ss_pred EEEEEeCcchhhHHHHHHHhcCCCCeeEE
Q 048349 5 VGIEQPLENDKSRSKALKIVGGMPGVESV 33 (94)
Q Consensus 5 vVlKV~m~c~~C~~K~~k~i~~~~GV~sV 33 (94)
+.+.+.... .--..+++.+.+++||.+|
T Consensus 44 ~~~~~~~~~-~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 44 ITIVVEGDD-DVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred EEEEEECCH-HHHHHHHHHHhCCccEEEe
Confidence 445555432 4456667777777777766
No 45
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=34.47 E-value=59 Score=25.77 Aligned_cols=44 Identities=16% Similarity=0.206 Sum_probs=30.2
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCc---EEEEccccCHHHHHHHHHhhc
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQ---IEVTGDGMDAIVLFMSLRKKL 63 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~k---vtV~G~~vDp~~l~~~LrKk~ 63 (94)
-.++...+...++|.-+++++|.+.. +|+.| ||.++++..-+-.
T Consensus 20 ie~i~a~~~~~~~v~ildve~danhNRsViT~vg---dp~~~~~A~f~~i 66 (302)
T COG3643 20 IEKIVAAAKSIPTVKILDVEMDANHNRSVITLVG---DPSKVVNAAFALI 66 (302)
T ss_pred HHHHHHHHhcCCceEEEEeccCCCCCceEEEEec---ChHHHHHHHHHHH
Confidence 35677778899999988887754433 45555 6888877765433
No 46
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=34.10 E-value=92 Score=17.74 Aligned_cols=29 Identities=17% Similarity=0.350 Sum_probs=21.8
Q ss_pred EEEEeCcchhhHHHHHHHhcCCCCeeEEE
Q 048349 6 GIEQPLENDKSRSKALKIVGGMPGVESVA 34 (94)
Q Consensus 6 VlKV~m~c~~C~~K~~k~i~~~~GV~sV~ 34 (94)
.|.=....+..+.++..++..++||.+|.
T Consensus 29 ~L~G~v~s~~~~~~a~~~a~~v~gv~~V~ 57 (64)
T PF04972_consen 29 TLSGEVPSQEQRDAAERLARSVAGVREVV 57 (64)
T ss_dssp EEEEEESSCHHHHHHHHHHHCC-STSEEE
T ss_pred EEEeeCcHHHHHHhHHhhhccCCCcCEEE
Confidence 33334556778999999999999999886
No 47
>PRK11023 outer membrane lipoprotein; Provisional
Probab=33.47 E-value=67 Score=23.23 Aligned_cols=47 Identities=6% Similarity=0.097 Sum_probs=33.1
Q ss_pred cchhhHHHHHHHhcCCCCee---EEEecCCCCCcEEEEccccCHHHHHHHHH
Q 048349 12 ENDKSRSKALKIVGGMPGVE---SVAFKGDDRSQIEVTGDGMDAIVLFMSLR 60 (94)
Q Consensus 12 ~c~~C~~K~~k~i~~~~GV~---sV~id~~~~~kvtV~G~~vDp~~l~~~Lr 60 (94)
.+..-..++...+..-+++. .|.+.. .++.|+.+|. ++-.....+..
T Consensus 46 dD~~i~~~V~~aL~~~~~l~~~~~I~V~v-~~G~V~L~G~-V~~~~~k~~A~ 95 (191)
T PRK11023 46 DDGTLELRVNNALSKDEQIKKEARINVTA-YQGKVLLTGQ-SPNAELSERAK 95 (191)
T ss_pred hhHHHHHHHHHHHhhCcccCcCceEEEEE-ECCEEEEEEE-eCCHHHHHHHH
Confidence 34455778888887767664 588887 7889999998 76655544443
No 48
>cd06471 ACD_LpsHSP_like Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Transcription of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is regulated by a variety of stresses including heat, cold and ethanol. Early growing L. plantarum cells contain elevated levels of these mRNAs which rapidly fall of as the cells enter stationary phase. Also belonging to this group is Bifidobacterium breve (Bb) HSP20 and Oenococcus oenis (syn. Leuconostoc oenos) (Oo) HSP18. Transcription of the gene encoding BbHSP20 is strongly induced following heat or osmotic shock, and that of the gene encoding OoHSP18 following heat, ethanol or acid shock. OoHSP18 is peripherally associated with the cytoplasmic me
Probab=33.45 E-value=20 Score=22.38 Aligned_cols=23 Identities=13% Similarity=0.439 Sum_probs=18.2
Q ss_pred cCCCCe--eEEEecCCCCCcEEEEcc
Q 048349 25 GGMPGV--ESVAFKGDDRSQIEVTGD 48 (94)
Q Consensus 25 ~~~~GV--~sV~id~~~~~kvtV~G~ 48 (94)
..+||| +.++++. ..+.|+|.|+
T Consensus 16 ~~lPGv~~edi~v~~-~~~~L~I~g~ 40 (93)
T cd06471 16 ADLPGFKKEDIKLDY-KDGYLTISAK 40 (93)
T ss_pred EECCCCCHHHeEEEE-ECCEEEEEEE
Confidence 467888 5677776 6789999998
No 49
>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=33.43 E-value=1.4e+02 Score=21.64 Aligned_cols=33 Identities=18% Similarity=0.189 Sum_probs=26.3
Q ss_pred cEEEEccccCHHHHHHHHHhhcC-ceEEEeccCCc
Q 048349 42 QIEVTGDGMDAIVLFMSLRKKLR-YATFIASKLRR 75 (94)
Q Consensus 42 kvtV~G~~vDp~~l~~~LrKk~~-~aeivsv~p~k 75 (94)
-+....+ +|+.++..+|.+..+ .-+++.+.+.+
T Consensus 65 di~l~~~-~~~~~~~~rLn~~lP~Gl~i~~~~~i~ 98 (187)
T PF10105_consen 65 DIELEED-IDPEEVLERLNAVLPEGLRILEAEEIP 98 (187)
T ss_pred EEEEecC-CCHHHHHHHHHHhCCCCCEEEEEEEcc
Confidence 4566777 999999999999887 68888777543
No 50
>PF12971 NAGLU_N: Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; InterPro: IPR024240 Alpha-N-acetylglucosaminidase, is a lysosomal enzyme required for the stepwise degradation of heparan sulphate []. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations []. The structure shows that the enzyme is composed of three domains. This entry represents the N-terminal domain of Alpha-N-acetylglucosaminidase which has an alpha-beta fold [].; PDB: 4A4A_A 2VC9_A 2VCC_A 2VCB_A 2VCA_A.
Probab=33.19 E-value=97 Score=19.61 Aligned_cols=40 Identities=18% Similarity=0.282 Sum_probs=26.2
Q ss_pred CCeeEEEecCCCCCcEEEEccccCHHHHHHHHH---hhcCceEEE
Q 048349 28 PGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLR---KKLRYATFI 69 (94)
Q Consensus 28 ~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~Lr---Kk~~~aeiv 69 (94)
.|-+.+++.....++++|.|+ +++.++.-|. |.++++.+.
T Consensus 29 ~~~d~F~l~~~~~gki~I~G~--s~vala~Gl~~YLk~~c~~~is 71 (86)
T PF12971_consen 29 NGKDVFELSSADNGKIVIRGN--SGVALASGLNWYLKYYCHVHIS 71 (86)
T ss_dssp TTBEEEEEEE-SSS-EEEEES--SHHHHHHHHHHHHHHHS--B--
T ss_pred CCCCEEEEEeCCCCeEEEEeC--CHHHHHHHHHHHHHHHhCceEe
Confidence 378888887447889999998 8888888775 334455543
No 51
>PRK09577 multidrug efflux protein; Reviewed
Probab=32.40 E-value=1.2e+02 Score=27.42 Aligned_cols=46 Identities=20% Similarity=0.277 Sum_probs=36.7
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCcEEEE-------ccccCHHHHHHHHHhhc
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQIEVT-------GDGMDAIVLFMSLRKKL 63 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~kvtV~-------G~~vDp~~l~~~LrKk~ 63 (94)
+.++...+.+++||.+|++.+ ...++.|. ..|+++.++.+.|+...
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G-~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n 210 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWG-AEYAMRIWPDPVKLAALGLTASDIASAVRAHN 210 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecC-CceEEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 467889999999999999998 66677762 34578888999998744
No 52
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=31.27 E-value=1.1e+02 Score=27.71 Aligned_cols=45 Identities=11% Similarity=0.110 Sum_probs=35.2
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCcEEEE-------ccccCHHHHHHHHHhh
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQIEVT-------GDGMDAIVLFMSLRKK 62 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~kvtV~-------G~~vDp~~l~~~LrKk 62 (94)
++.++..+.+++||.+|++.+ ...++.|. ..|+++.++.+.|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G-~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYG-SQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcC-CceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 466888999999999999998 45556552 3367888999999864
No 53
>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=30.95 E-value=59 Score=19.23 Aligned_cols=23 Identities=26% Similarity=0.094 Sum_probs=18.8
Q ss_pred CcEEEEccccCHHHHHHHHHhhc
Q 048349 41 SQIEVTGDGMDAIVLFMSLRKKL 63 (94)
Q Consensus 41 ~kvtV~G~~vDp~~l~~~LrKk~ 63 (94)
+.|+|+|..-+|.++...|.+|.
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 57889997569999999998765
No 54
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=30.84 E-value=1.7e+02 Score=19.64 Aligned_cols=44 Identities=16% Similarity=0.222 Sum_probs=33.6
Q ss_pred hhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHH
Q 048349 15 KSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLR 60 (94)
Q Consensus 15 ~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~Lr 60 (94)
.-...++..++.+||++=..-|. + +|+.|+=++=|...|++.+.
T Consensus 18 e~l~av~~~L~~ip~~EV~~~d~-~-GKlVVVie~~~~~~l~~tie 61 (94)
T COG3062 18 ERLSAVKTALLAIPGCEVYGEDA-E-GKLVVVIEAEDSETLLETIE 61 (94)
T ss_pred HHHHHHHHHHhcCCCcEeeccCC-C-ceEEEEEEcCchHHHHHHHH
Confidence 34567888999999999887774 5 88888766457777877765
No 55
>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=30.55 E-value=66 Score=25.20 Aligned_cols=44 Identities=16% Similarity=0.223 Sum_probs=32.3
Q ss_pred EeCcchhhHHHHHHHhcCCCCeeEEEecCCCC-----------CcEEEEccccCHHHH
Q 048349 9 QPLENDKSRSKALKIVGGMPGVESVAFKGDDR-----------SQIEVTGDGMDAIVL 55 (94)
Q Consensus 9 V~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~-----------~kvtV~G~~vDp~~l 55 (94)
+-+|..|........+..+ |++.+.+|. .. +++++.|+ +||.-|
T Consensus 215 iilH~cG~~~~~l~~~~e~-g~dvl~~d~-~~~dl~eak~~~g~k~~l~GN-lDp~~L 269 (321)
T cd03309 215 IVHHSCGAAASLVPSMAEM-GVDSWNVVM-TANNTAELRRLLGDKVVLAGA-IDDVAL 269 (321)
T ss_pred eEEEeCCCcHHHHHHHHHc-CCCEEEecC-CCCCHHHHHHHhCCCeEEEcC-CChHHh
Confidence 4567666666677777766 888888886 54 57999998 898544
No 56
>PRK13748 putative mercuric reductase; Provisional
Probab=30.29 E-value=2.4e+02 Score=23.02 Aligned_cols=60 Identities=17% Similarity=0.222 Sum_probs=42.0
Q ss_pred eCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEcc-ccCHHHHHHHHHhhcC-ceEEEec
Q 048349 10 PLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGD-GMDAIVLFMSLRKKLR-YATFIAS 71 (94)
Q Consensus 10 ~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~-~vDp~~l~~~LrKk~~-~aeivsv 71 (94)
.++|..|..++...+..++|+....++. ..+...+... ..++..+...+.. .+ .++....
T Consensus 8 g~~C~~c~~~ie~~l~~~~gv~~a~~~~-~~~~~~v~~~~~~~~~~i~~~i~~-~g~~~~~~~~ 69 (561)
T PRK13748 8 GMTCDSCAAHVKDALEKVPGVQSADVSY-PKGSAQLAIEVGTSPDALTAAVAG-LGYRATLADA 69 (561)
T ss_pred CeecHHHHHHHHHHHhcCCCeeEEEEEc-CCCEEEEEECCCCCHHHHHHHHHH-cCCeeeccCc
Confidence 5789999999999999999999888886 6666666521 2466666666654 33 3444433
No 57
>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=29.67 E-value=1.4e+02 Score=18.38 Aligned_cols=65 Identities=17% Similarity=0.158 Sum_probs=41.6
Q ss_pred eEEEEEeCcchhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcCceEEEecc
Q 048349 4 MVGIEQPLENDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLRYATFIASK 72 (94)
Q Consensus 4 ~vVlKV~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~ 72 (94)
-+.+||.. ...-+..+++.+..+.| .=++++. +.=.+.++|+.=.-..+++.|++ ++-.|++.-|
T Consensus 4 l~LiKV~~-~~~~r~ei~~l~~~f~a-~ivd~~~-~~~iie~tG~~~kid~fi~~l~~-~gi~Ei~RtG 68 (75)
T PF10369_consen 4 LALIKVKA-TPENRSEILQLAEIFRA-RIVDVSP-DSIIIELTGTPEKIDAFIKLLKP-FGILEIARTG 68 (75)
T ss_dssp EEEEEEE--SCHHHHHHHHHHHHTT--EEEEEET-TEEEEEEEE-HHHHHHHHHHSTG-GGEEEEEEEE
T ss_pred EEEEEEEC-CccCHHHHHHHHHHhCC-EEEEECC-CEEEEEEcCCHHHHHHHHHHhhh-cCCEEEEccc
Confidence 36788887 56778888888876665 6667764 55677778874445556666666 6667766543
No 58
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=29.63 E-value=86 Score=21.33 Aligned_cols=33 Identities=21% Similarity=0.315 Sum_probs=26.9
Q ss_pred EEEEEeCcchhh------HHHHHHHhcCCCCeeEEEecC
Q 048349 5 VGIEQPLENDKS------RSKALKIVGGMPGVESVAFKG 37 (94)
Q Consensus 5 vVlKV~m~c~~C------~~K~~k~i~~~~GV~sV~id~ 37 (94)
+.+++.+.-.+| ...+..++..++||+++.++.
T Consensus 51 v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 51 VKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 556666677777 788999999999999998875
No 59
>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=29.05 E-value=1e+02 Score=19.13 Aligned_cols=29 Identities=14% Similarity=0.364 Sum_probs=21.7
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCcEEE
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQIEV 45 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~kvtV 45 (94)
.+++...++...|+.|.+.|-+.+..|.|
T Consensus 44 eR~iIH~la~~~~l~S~S~G~ep~R~VvI 72 (74)
T cd02643 44 KRRIVHELAEHFGIESVSYDQEPKRNVVA 72 (74)
T ss_pred HHHHHHHHHhhCCCEEEecCCCCCceEEE
Confidence 56777778889999999999744444544
No 60
>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=29.01 E-value=88 Score=18.07 Aligned_cols=34 Identities=12% Similarity=0.109 Sum_probs=23.2
Q ss_pred chhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEE
Q 048349 13 NDKSRSKALKIVGGMPGVESVAFKGDDRSQIEVT 46 (94)
Q Consensus 13 c~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~ 46 (94)
...=.+++...++...|+.|-+.+.+.+..|+|.
T Consensus 28 m~~~~R~~iH~~a~~~gL~s~S~g~~~~R~vvv~ 61 (63)
T PF01424_consen 28 MNSFERKLIHELAEYYGLKSKSEGEGPNRRVVVS 61 (63)
T ss_dssp --SHHHHHHHHHHHHCTEEEEEESSSSSSEEEEE
T ss_pred CCHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEE
Confidence 3455677777777799999999986344455553
No 61
>smart00838 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
Probab=28.54 E-value=1.4e+02 Score=18.16 Aligned_cols=62 Identities=8% Similarity=0.060 Sum_probs=42.3
Q ss_pred EEEeCcch-hhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEcccc---CHHHHHHHHHhhcC-ceEEEec
Q 048349 7 IEQPLEND-KSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGM---DAIVLFMSLRKKLR-YATFIAS 71 (94)
Q Consensus 7 lKV~m~c~-~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~v---Dp~~l~~~LrKk~~-~aeivsv 71 (94)
+.+.+.|. .+..+++..+++.+|.- .+++. ..+.+.+.|. + ....+...||..+. .|.+...
T Consensus 6 ~~~~I~~p~~~~g~v~~~l~~rrG~i-~~~~~-~~~~~~i~~~-iP~~~~~~~~~~Lrs~T~G~~~~~~~ 72 (85)
T smart00838 6 MKVEVTVPEEYMGDVIGDLNSRRGKI-EGMEQ-RGGAQVIKAK-VPLSEMFGYATDLRSATQGRATWSME 72 (85)
T ss_pred EEEEEEeCHHHHHHHHHHHHHcCCEE-ECeec-cCCcEEEEEE-CCHHHHhchHHHHHHhcCCeEEEEEE
Confidence 44555554 67889999999999955 24442 3467889998 5 44556778888774 7776553
No 62
>cd04098 eEF2_C_snRNP eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to the C-terminal domain of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=28.44 E-value=1.5e+02 Score=18.20 Aligned_cols=62 Identities=13% Similarity=0.021 Sum_probs=40.4
Q ss_pred EEEeCcch-hhHHHHHHHhcCCCCe-eEEEecCCCCCcEEEEcccc---CHHHHHHHHHhhcC-ceEEEe
Q 048349 7 IEQPLEND-KSRSKALKIVGGMPGV-ESVAFKGDDRSQIEVTGDGM---DAIVLFMSLRKKLR-YATFIA 70 (94)
Q Consensus 7 lKV~m~c~-~C~~K~~k~i~~~~GV-~sV~id~~~~~kvtV~G~~v---Dp~~l~~~LrKk~~-~aeivs 70 (94)
+++.++|. .+-.+++..|.+..|. .+.+... ......+.|. + +...+...||..+. .+.+..
T Consensus 4 ~~~ei~~p~~~~g~v~~~L~~rrg~i~~~~~~~-~~~~~~i~a~-vP~~e~~~~~~~Lrs~T~G~~~~~~ 71 (80)
T cd04098 4 YEVEITCPADAVSAVYEVLSRRRGHVIYDTPIP-GTPLYEVKAF-IPVIESFGFETDLRVHTQGQAFCQS 71 (80)
T ss_pred EEEEEEECHHHHhHHHHHHhhCCcEEeeeeccC-CCCcEEEEEE-CCHHHHhChHHHHHhhCCCceEEEE
Confidence 44555544 6777999999998884 3333221 3333889998 5 55566788998885 666543
No 63
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=28.24 E-value=1.2e+02 Score=27.45 Aligned_cols=45 Identities=9% Similarity=0.182 Sum_probs=34.3
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCcEEEE-------ccccCHHHHHHHHHhh
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQIEVT-------GDGMDAIVLFMSLRKK 62 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~kvtV~-------G~~vDp~~l~~~LrKk 62 (94)
++.++..+.+++||.+|++.+ ....+.|. ..|+++.++.+.|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G-~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 159 AANMKDPISRTSGVGDVQLFG-SQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHHhcCCCceEEEEcC-CceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 356888899999999999998 45556663 3357778888888853
No 64
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=28.04 E-value=86 Score=22.75 Aligned_cols=34 Identities=24% Similarity=0.213 Sum_probs=26.2
Q ss_pred eEEEEEeCcchhhH------HHHHHHhcCCCCeeEEEecC
Q 048349 4 MVGIEQPLENDKSR------SKALKIVGGMPGVESVAFKG 37 (94)
Q Consensus 4 ~vVlKV~m~c~~C~------~K~~k~i~~~~GV~sV~id~ 37 (94)
++-+.+.+...+|. ..+..++..++||.++.++.
T Consensus 114 ~V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 114 RVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 46677777766663 55888889999999998875
No 65
>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=27.80 E-value=84 Score=19.85 Aligned_cols=21 Identities=29% Similarity=0.357 Sum_probs=17.3
Q ss_pred HHHHHHHhcCCCCeeEEEecC
Q 048349 17 RSKALKIVGGMPGVESVAFKG 37 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~ 37 (94)
++.+..++..++|++++.++.
T Consensus 57 ~~~i~~al~~l~gv~~v~v~i 77 (99)
T TIGR02945 57 PGEVENAVRAVPGVGSVTVEL 77 (99)
T ss_pred HHHHHHHHHhCCCCceEEEEE
Confidence 456788888999999999875
No 66
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=27.17 E-value=52 Score=22.28 Aligned_cols=20 Identities=20% Similarity=0.370 Sum_probs=15.6
Q ss_pred eCcchhhHHHHHHHhc--CCCC
Q 048349 10 PLENDKSRSKALKIVG--GMPG 29 (94)
Q Consensus 10 ~m~c~~C~~K~~k~i~--~~~G 29 (94)
..+|..|++.+++.+. +++|
T Consensus 18 ~~qC~~cA~Al~~~L~~~gI~G 39 (100)
T PF15643_consen 18 IFQCVECASALKQFLKQAGIPG 39 (100)
T ss_pred ceehHHHHHHHHHHHHHCCCCc
Confidence 3679999999999984 4444
No 67
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.16 E-value=99 Score=20.79 Aligned_cols=25 Identities=24% Similarity=0.534 Sum_probs=22.4
Q ss_pred HHhcCCCCeeEEEecCCCCCcEEEEc
Q 048349 22 KIVGGMPGVESVAFKGDDRSQIEVTG 47 (94)
Q Consensus 22 k~i~~~~GV~sV~id~~~~~kvtV~G 47 (94)
.+++.++|+..|++.. ++.++-|.+
T Consensus 34 ~ivas~pgis~ieik~-E~kkL~v~t 58 (96)
T COG4004 34 RIVASSPGISRIEIKP-ENKKLLVNT 58 (96)
T ss_pred EEEEecCCceEEEEec-ccceEEEec
Confidence 4678899999999997 999999988
No 68
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=27.16 E-value=1.1e+02 Score=20.32 Aligned_cols=32 Identities=19% Similarity=0.250 Sum_probs=24.1
Q ss_pred EEEEEeCc-chhhHHHHHHHhcCCCCeeEEEec
Q 048349 5 VGIEQPLE-NDKSRSKALKIVGGMPGVESVAFK 36 (94)
Q Consensus 5 vVlKV~m~-c~~C~~K~~k~i~~~~GV~sV~id 36 (94)
+.|.+-|. -+|--..+...+..++||+|+++.
T Consensus 51 l~l~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 51 LKLYVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred EEEEEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 34445554 346678889999999999999986
No 69
>PRK10743 heat shock protein IbpA; Provisional
Probab=26.95 E-value=24 Score=24.55 Aligned_cols=24 Identities=13% Similarity=0.264 Sum_probs=17.1
Q ss_pred hcCCCCee--EEEecCCCCCcEEEEcc
Q 048349 24 VGGMPGVE--SVAFKGDDRSQIEVTGD 48 (94)
Q Consensus 24 i~~~~GV~--sV~id~~~~~kvtV~G~ 48 (94)
-+.+|||. .|+++. +.+.||+.|+
T Consensus 50 ~aelPGv~kedi~V~v-~~~~LtI~ge 75 (137)
T PRK10743 50 AIAVAGFAESELEITA-QDNLLVVKGA 75 (137)
T ss_pred EEECCCCCHHHeEEEE-ECCEEEEEEE
Confidence 35678884 466665 5679999997
No 70
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=26.87 E-value=47 Score=23.82 Aligned_cols=44 Identities=16% Similarity=0.125 Sum_probs=31.4
Q ss_pred hhhHHHHHHHhcCCCCeeEEEecCCCCCcEEEEccccCHHHHHHHHHh
Q 048349 14 DKSRSKALKIVGGMPGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRK 61 (94)
Q Consensus 14 ~~C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrK 61 (94)
.+|.++++.++.++ .-|+.+.+...++|=.|. =|...+..+++.
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 35777777777554 445555434459999999 799999988875
No 71
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=26.59 E-value=1e+02 Score=20.81 Aligned_cols=29 Identities=21% Similarity=0.321 Sum_probs=23.9
Q ss_pred EEecCCCCCcEEEEccccCHHHHHHHHHhhcC
Q 048349 33 VAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLR 64 (94)
Q Consensus 33 V~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~ 64 (94)
..+|+ + +++++.|. .++..+-+.|++...
T Consensus 50 g~id~-~-~rlii~G~-~~~~~i~~~l~~yI~ 78 (110)
T smart00653 50 GSIDG-K-GRLIVNGR-FTPKKLQDLLRRYIK 78 (110)
T ss_pred eeECC-C-CeEEEEEe-eCHHHHHHHHHHHHH
Confidence 35564 4 99999999 999999999998654
No 72
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=26.59 E-value=1.4e+02 Score=20.63 Aligned_cols=55 Identities=13% Similarity=0.073 Sum_probs=35.1
Q ss_pred hhhHHHHHHHhcCC-CCeeEEEecCCCCCcEEEEccccCHHHHHHHHHhhcCceEEEe
Q 048349 14 DKSRSKALKIVGGM-PGVESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLRYATFIA 70 (94)
Q Consensus 14 ~~C~~K~~k~i~~~-~GV~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivs 70 (94)
+.-++++++.+.+. -+...+.+.. +.+.||+.|. +....-..++....+.++-++
T Consensus 25 ~~~~~~i~~~i~~~~~~~~~i~V~v-~~G~v~l~G~-v~s~~~~~~~~~aa~~v~GV~ 80 (147)
T PRK11198 25 EDAADALKEHISKQGLGDADVNVQV-EDGKATVSGD-AASQEAKEKILLAVGNIQGIA 80 (147)
T ss_pred HHHHHHHHHHHHhcCCCcCCceEEE-eCCEEEEEEE-eCCHHHHHHHHHHhccCCCcc
Confidence 44566777777542 1333344444 5689999999 877777777776566554443
No 73
>PF14006 YqzL: YqzL-like protein
Probab=26.26 E-value=40 Score=19.89 Aligned_cols=40 Identities=23% Similarity=0.273 Sum_probs=24.8
Q ss_pred EEEccccCHHHHHHHHHhhcCceEEEeccCCcccCccCCccccce
Q 048349 44 EVTGDGMDAIVLFMSLRKKLRYATFIASKLRRKVFLSDRSLVSHH 88 (94)
Q Consensus 44 tV~G~~vDp~~l~~~LrKk~~~aeivsv~p~k~~~~~~~~~~~~~ 88 (94)
..+|+ ||.--|.+.+.+... -...+..++...++.+.|+|
T Consensus 8 ~~TG~-i~aYllyke~E~~~~----~~~~~~eeel~~~e~d~~~h 47 (47)
T PF14006_consen 8 EQTGS-IDAYLLYKELEEESE----DEPEEEEEELALDEVDSPIH 47 (47)
T ss_pred hhcCC-HHHHHHHHHHHhhcc----ccccccchhhHHhhcccCCC
Confidence 45898 999999988876332 12233333334566777766
No 74
>cd06464 ACD_sHsps-like Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
Probab=26.15 E-value=30 Score=20.48 Aligned_cols=23 Identities=17% Similarity=0.586 Sum_probs=18.4
Q ss_pred cCCCCe--eEEEecCCCCCcEEEEcc
Q 048349 25 GGMPGV--ESVAFKGDDRSQIEVTGD 48 (94)
Q Consensus 25 ~~~~GV--~sV~id~~~~~kvtV~G~ 48 (94)
..+||+ +++.+.. ..+.|.|.|.
T Consensus 13 ~~lpg~~~~~i~V~v-~~~~l~I~g~ 37 (88)
T cd06464 13 ADLPGFKKEDIKVEV-EDGVLTISGE 37 (88)
T ss_pred EECCCCCHHHeEEEE-ECCEEEEEEE
Confidence 467888 6777777 6699999998
No 75
>PRK11597 heat shock chaperone IbpB; Provisional
Probab=25.65 E-value=25 Score=24.68 Aligned_cols=24 Identities=17% Similarity=0.378 Sum_probs=17.9
Q ss_pred hcCCCCe--eEEEecCCCCCcEEEEcc
Q 048349 24 VGGMPGV--ESVAFKGDDRSQIEVTGD 48 (94)
Q Consensus 24 i~~~~GV--~sV~id~~~~~kvtV~G~ 48 (94)
-+.+||| +.|+++. +.+.|||.|+
T Consensus 48 ~adlPGv~kedi~V~v-~~~~LtI~ge 73 (142)
T PRK11597 48 TLALAGFRQEDLDIQL-EGTRLTVKGT 73 (142)
T ss_pred EEEeCCCCHHHeEEEE-ECCEEEEEEE
Confidence 3567888 3466666 6789999997
No 76
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=25.40 E-value=1.6e+02 Score=26.76 Aligned_cols=46 Identities=15% Similarity=0.325 Sum_probs=34.5
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCcEEEE-------ccccCHHHHHHHHHhh
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQIEVT-------GDGMDAIVLFMSLRKK 62 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~kvtV~-------G~~vDp~~l~~~LrKk 62 (94)
.+.++..+.+++||.+|++.+.....+.|. ..|+++.++.+.|+..
T Consensus 168 ~~~l~~~L~~i~gV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~~v~~ai~~~ 220 (1040)
T PRK10503 168 ETRVAQKISQVSGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETVRTAITGA 220 (1040)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 356888999999999999998544566663 3357788888888753
No 77
>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=24.97 E-value=1.6e+02 Score=26.78 Aligned_cols=44 Identities=11% Similarity=0.223 Sum_probs=35.5
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCcEEEE-------ccccCHHHHHHHHHh
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQIEVT-------GDGMDAIVLFMSLRK 61 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~kvtV~-------G~~vDp~~l~~~LrK 61 (94)
...+...+.+++||.+|++.+. ..++.|. ..|+++.++.+.|+.
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 4568889999999999999994 6666664 346788889999987
No 78
>PRK04435 hypothetical protein; Provisional
Probab=24.90 E-value=2e+02 Score=19.95 Aligned_cols=20 Identities=25% Similarity=0.403 Sum_probs=12.3
Q ss_pred hHHHHHHHhcCCCCeeEEEe
Q 048349 16 SRSKALKIVGGMPGVESVAF 35 (94)
Q Consensus 16 C~~K~~k~i~~~~GV~sV~i 35 (94)
.-..++..+..++||.+|.+
T Consensus 124 ~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 124 DIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred HHHHHHHHHHcCCCcEEEEE
Confidence 55566666666666666654
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=24.89 E-value=49 Score=20.66 Aligned_cols=24 Identities=25% Similarity=0.616 Sum_probs=16.7
Q ss_pred cCCCCee--EEEecCCCCCcEEEEcc
Q 048349 25 GGMPGVE--SVAFKGDDRSQIEVTGD 48 (94)
Q Consensus 25 ~~~~GV~--sV~id~~~~~kvtV~G~ 48 (94)
..+|||. .++++.++.+.|+|.|+
T Consensus 15 ~~lPGv~~edi~i~v~~~~~L~I~g~ 40 (92)
T cd06472 15 ADVPGVKKEDVKVEVEDGRVLRISGE 40 (92)
T ss_pred EECCCCChHhEEEEEeCCCEEEEEEE
Confidence 4678885 56666523358999997
No 80
>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=24.84 E-value=89 Score=17.11 Aligned_cols=18 Identities=22% Similarity=0.451 Sum_probs=15.6
Q ss_pred HHHHHHHhcCCCCeeEEE
Q 048349 17 RSKALKIVGGMPGVESVA 34 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~ 34 (94)
-..+++.+..++||.++.
T Consensus 52 ~~~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 52 PEEVLEELKALPGIIRVR 69 (71)
T ss_pred CHHHHHHHHcCCCeEEEE
Confidence 458999999999999986
No 81
>PLN02625 uroporphyrin-III C-methyltransferase
Probab=24.50 E-value=76 Score=23.74 Aligned_cols=33 Identities=18% Similarity=0.235 Sum_probs=28.2
Q ss_pred CCCcEEEEcccc-CHHHHHHHHHhhcCceEEEec
Q 048349 39 DRSQIEVTGDGM-DAIVLFMSLRKKLRYATFIAS 71 (94)
Q Consensus 39 ~~~kvtV~G~~v-Dp~~l~~~LrKk~~~aeivsv 71 (94)
..++++++|.|. ||.-|+-+-.+....|++|-.
T Consensus 13 ~~g~l~vVG~GpGdp~~LTl~a~~~l~~ADvI~~ 46 (263)
T PLN02625 13 GPGNVFLVGTGPGDPDLLTLKALRLLQTADVVLY 46 (263)
T ss_pred CCCEEEEEEeCCCChHHhHHHHHHHHhcCCEEEE
Confidence 357899999987 999999999888888998875
No 82
>COG4687 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.23 E-value=1.7e+02 Score=20.47 Aligned_cols=36 Identities=11% Similarity=0.224 Sum_probs=28.7
Q ss_pred EEEecCCCCCcEEEEccccCHHHHHHHHHhhcCceEEEec
Q 048349 32 SVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLRYATFIAS 71 (94)
Q Consensus 32 sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv 71 (94)
++-+| .+++++-.-. |+.++++.+|...++..+|..
T Consensus 70 ~i~td--~~gk~~FaSk--dsg~iLk~ir~yvg~~~vV~s 105 (122)
T COG4687 70 SIFTD--TQGKVRFASK--DSGKILKKIREYVGNEKVVKS 105 (122)
T ss_pred EEEEc--CCceEEEEeC--CchhHHHHHHHHhCccceecc
Confidence 45554 5778888776 999999999999998877753
No 83
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=24.15 E-value=1.7e+02 Score=26.53 Aligned_cols=47 Identities=13% Similarity=0.212 Sum_probs=34.7
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCcEEEE-------ccccCHHHHHHHHHhhc
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQIEVT-------GDGMDAIVLFMSLRKKL 63 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~kvtV~-------G~~vDp~~l~~~LrKk~ 63 (94)
+..++..+.+++||.+|.+.+....++.|. ..|+.+.++...|+...
T Consensus 159 ~~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~~ 212 (1025)
T PRK10614 159 STQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQAISNAN 212 (1025)
T ss_pred HHHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 457888999999999999998444566663 22467777888887644
No 84
>PHA01634 hypothetical protein
Probab=24.07 E-value=27 Score=25.27 Aligned_cols=12 Identities=8% Similarity=0.091 Sum_probs=9.7
Q ss_pred eCcchhhHHHHH
Q 048349 10 PLENDKSRSKAL 21 (94)
Q Consensus 10 ~m~c~~C~~K~~ 21 (94)
-|+|+||.+++-
T Consensus 97 ~iDCeGCE~~l~ 108 (156)
T PHA01634 97 VMDCEGCEEKLN 108 (156)
T ss_pred EEEccchHHhcC
Confidence 388999998764
No 85
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 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 EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=23.96 E-value=2.1e+02 Score=18.44 Aligned_cols=33 Identities=21% Similarity=0.266 Sum_probs=24.3
Q ss_pred EEEEEeCcch-hhHHHHHHHh-cCCCCeeEEEecC
Q 048349 5 VGIEQPLEND-KSRSKALKIV-GGMPGVESVAFKG 37 (94)
Q Consensus 5 vVlKV~m~c~-~C~~K~~k~i-~~~~GV~sV~id~ 37 (94)
+.+.+-+..+ +.-..+...+ ...+||+|+++..
T Consensus 51 L~v~~vv~D~~~~~d~lee~i~~~~e~Vqsvei~~ 85 (89)
T PF00736_consen 51 LQVSCVVEDDEGSTDDLEEAIESFEEGVQSVEIES 85 (89)
T ss_dssp EEEEEEECTTTCGHHHHHHHHTTCTTTEEEEEEEE
T ss_pred EEEEEEEEcCccChHHHHHHHHhcCCCccEEEEEE
Confidence 3444455554 6677888888 9999999999863
No 86
>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=23.92 E-value=47 Score=23.98 Aligned_cols=29 Identities=14% Similarity=0.245 Sum_probs=25.5
Q ss_pred CCCCeeEEEecCCCCCcEEEEccccCHHHHH
Q 048349 26 GMPGVESVAFKGDDRSQIEVTGDGMDAIVLF 56 (94)
Q Consensus 26 ~~~GV~sV~id~~~~~kvtV~G~~vDp~~l~ 56 (94)
.++|=..+.++. +.+.+++.|. |.|.++-
T Consensus 110 ~I~G~k~i~vn~-e~~~i~lsGi-VRp~DI~ 138 (179)
T PF02107_consen 110 VIEGEKQIRVNG-EEQYIRLSGI-VRPEDID 138 (179)
T ss_pred EEEEEEEEEECC-CEEEEEEEEE-ECHHHCC
Confidence 467889999997 9999999999 9998875
No 87
>PF03990 DUF348: Domain of unknown function (DUF348) ; InterPro: IPR007137 This domain normally occurs as tandem repeats; however it is found as a single copy in the Saccharomyces cerevisiae (Baker's yeast) DNA-binding nuclear protein YCR593 (P25357 from SWISSPROT).
Probab=23.85 E-value=1.2e+02 Score=16.56 Aligned_cols=39 Identities=15% Similarity=0.128 Sum_probs=24.9
Q ss_pred EEEecCCCCCcEEEEccccCHHHHHHHHHhhcCceEEEeccC
Q 048349 32 SVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKLRYATFIASKL 73 (94)
Q Consensus 32 sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~p 73 (94)
.|.+|+ +...+.... -+..++++.+.-..+..+.++|..
T Consensus 3 tv~~dG-~~~~v~T~a--~tV~~~L~~~gI~l~~~D~v~p~~ 41 (43)
T PF03990_consen 3 TVTVDG-KEKTVYTTA--STVGDALKELGITLGEEDKVSPSL 41 (43)
T ss_pred EEEECC-EEEEEEeCC--CCHHHHHHhCCCCCCCCCEEecCC
Confidence 356666 444444333 488888888876667667776643
No 88
>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=23.82 E-value=1.6e+02 Score=16.95 Aligned_cols=29 Identities=14% Similarity=0.268 Sum_probs=19.4
Q ss_pred EEEeCcchhhHHHHHHHhcCCCCeeEEEe
Q 048349 7 IEQPLENDKSRSKALKIVGGMPGVESVAF 35 (94)
Q Consensus 7 lKV~m~c~~C~~K~~k~i~~~~GV~sV~i 35 (94)
+.+......--..+++.+.+++||...++
T Consensus 44 ~~vev~~~~~l~~i~~~L~~i~gV~~~~~ 72 (74)
T cd04887 44 ITVDAPSEEHAETIVAAVRALPEVKVLSV 72 (74)
T ss_pred EEEEcCCHHHHHHHHHHHhcCCCeEEEEe
Confidence 44455555666777888888888776554
No 89
>COG0612 PqqL Predicted Zn-dependent peptidases [General function prediction only]
Probab=23.72 E-value=84 Score=24.76 Aligned_cols=25 Identities=28% Similarity=0.333 Sum_probs=21.7
Q ss_pred CCCcEEEEccccCHHHHHHHHHhhcC
Q 048349 39 DRSQIEVTGDGMDAIVLFMSLRKKLR 64 (94)
Q Consensus 39 ~~~kvtV~G~~vDp~~l~~~LrKk~~ 64 (94)
++=.|.|+|+ +|+.++...+.+.++
T Consensus 197 ~n~~l~vvGd-i~~~~v~~~~~~~f~ 221 (438)
T COG0612 197 DNMVLVVVGD-VDAEEVVELIEKYFG 221 (438)
T ss_pred CceEEEEecC-CCHHHHHHHHHHHHc
Confidence 4457889999 999999999999887
No 90
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=22.15 E-value=1.2e+02 Score=18.08 Aligned_cols=23 Identities=13% Similarity=0.138 Sum_probs=17.3
Q ss_pred EEEecCCCCCcEEEEccccCHHHH
Q 048349 32 SVAFKGDDRSQIEVTGDGMDAIVL 55 (94)
Q Consensus 32 sV~id~~~~~kvtV~G~~vDp~~l 55 (94)
+|..|. ..|.|.|.|..-+...+
T Consensus 47 ~i~~d~-~tNsliv~g~~~~~~~i 69 (82)
T PF03958_consen 47 RIVADE-RTNSLIVRGTPEDLEQI 69 (82)
T ss_dssp EEEEEC-TTTEEEEEEEHHHHHHH
T ss_pred EEEEEC-CCCEEEEEeCHHHHHHH
Confidence 899996 99999999983333333
No 91
>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=21.53 E-value=1.9e+02 Score=17.10 Aligned_cols=35 Identities=26% Similarity=0.221 Sum_probs=22.0
Q ss_pred cEEEEccccCHHHHHHHHHhhcCceEEEeccCCcc
Q 048349 42 QIEVTGDGMDAIVLFMSLRKKLRYATFIASKLRRK 76 (94)
Q Consensus 42 kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~p~k~ 76 (94)
+++|.|-|.-..++...|++....+.++...|..-
T Consensus 1 ~vvViGgG~ig~E~A~~l~~~g~~vtli~~~~~~~ 35 (80)
T PF00070_consen 1 RVVVIGGGFIGIELAEALAELGKEVTLIERSDRLL 35 (80)
T ss_dssp EEEEESSSHHHHHHHHHHHHTTSEEEEEESSSSSS
T ss_pred CEEEECcCHHHHHHHHHHHHhCcEEEEEeccchhh
Confidence 35677766666777777766444677766555433
No 92
>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=21.44 E-value=1.1e+02 Score=27.39 Aligned_cols=48 Identities=17% Similarity=0.295 Sum_probs=34.0
Q ss_pred hHHHHHHHhcCCCCeeEEEecCCCCCcEEEE-------ccccCHHHHHHHHHhhc
Q 048349 16 SRSKALKIVGGMPGVESVAFKGDDRSQIEVT-------GDGMDAIVLFMSLRKKL 63 (94)
Q Consensus 16 C~~K~~k~i~~~~GV~sV~id~~~~~kvtV~-------G~~vDp~~l~~~LrKk~ 63 (94)
.+..++..+.+++||.+|++.|....++.|. ..++++.++...|+...
T Consensus 157 ~~~~l~~~L~~i~gV~~v~~~G~~~~ei~i~~d~~kl~~~gls~~~v~~~l~~~n 211 (1021)
T PF00873_consen 157 AEEQLKPRLERIPGVARVDISGGREREIQIELDPEKLAAYGLSLSDVAQALQANN 211 (1021)
T ss_dssp HHHCTHHHHHTSTTEEEEEESSS--EEEEEEE-HHHHHHTT--HHHHHHHHHHHS
T ss_pred HHHHHHHhccceeEEEEEEeccchhhhhhheechhhhhhhCCCHHHHHHHHHHhh
Confidence 3456888899999999999999566666663 34577888888888744
No 93
>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=21.35 E-value=85 Score=19.57 Aligned_cols=32 Identities=25% Similarity=0.336 Sum_probs=21.8
Q ss_pred CCcEEEE-cc---ccCHHHHHHHHHhhcC-ceEEEec
Q 048349 40 RSQIEVT-GD---GMDAIVLFMSLRKKLR-YATFIAS 71 (94)
Q Consensus 40 ~~kvtV~-G~---~vDp~~l~~~LrKk~~-~aeivsv 71 (94)
+..||++ |- ++|+.++++.|+++++ .+.+...
T Consensus 17 ~K~vT~V~gl~~~~~d~~~lak~lkk~~ac~~sv~~~ 53 (83)
T PF01253_consen 17 RKFVTIVSGLELFGIDLKELAKELKKKFACGGSVTKD 53 (83)
T ss_dssp SEEEEEEES--STTSHHHHHHHHHHHHHTS-EEEEE-
T ss_pred CeEEEEEECCcccccCHHHHHHHHHHhccCceEEeec
Confidence 3456654 32 4799999999999997 6666554
No 94
>PRK04021 hypothetical protein; Reviewed
Probab=20.92 E-value=2.5e+02 Score=18.29 Aligned_cols=48 Identities=19% Similarity=0.279 Sum_probs=33.1
Q ss_pred eCcchhhHHHHHHHhcCCCCeeEEEecCCCCC---cEEEEccccCHHHHHHHHH
Q 048349 10 PLENDKSRSKALKIVGGMPGVESVAFKGDDRS---QIEVTGDGMDAIVLFMSLR 60 (94)
Q Consensus 10 ~m~c~~C~~K~~k~i~~~~GV~sV~id~~~~~---kvtV~G~~vDp~~l~~~Lr 60 (94)
.....++...+.+.+++.=|+ +|++.....+ .+.+.| +|+..+..+|+
T Consensus 41 pP~~GkAN~ali~~LAk~l~~-~I~I~~G~~sr~K~v~i~g--~~~e~l~~~L~ 91 (92)
T PRK04021 41 PPVKGKANKELVKFFSKLLGA-EVEIIRGETSREKDLLVKG--ISLEEVKKKLK 91 (92)
T ss_pred CCCCChHHHHHHHHHHHHhCC-CEEEEecCCcCceEEEEec--CCHHHHHHHhc
Confidence 344667888888888888888 6887432333 334445 69999988874
No 95
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=20.76 E-value=1.6e+02 Score=18.73 Aligned_cols=39 Identities=18% Similarity=0.068 Sum_probs=23.1
Q ss_pred EecCCCCCcEEEEccccCHHHHHHHHHhhcCceEEEeccC
Q 048349 34 AFKGDDRSQIEVTGDGMDAIVLFMSLRKKLRYATFIASKL 73 (94)
Q Consensus 34 ~id~~~~~kvtV~G~~vDp~~l~~~LrKk~~~aeivsv~p 73 (94)
-+|. +..++.|+|.|=-...=+..|.+...++.++++..
T Consensus 2 ~l~l-~~~~vlVvGgG~va~~k~~~Ll~~gA~v~vis~~~ 40 (103)
T PF13241_consen 2 FLDL-KGKRVLVVGGGPVAARKARLLLEAGAKVTVISPEI 40 (103)
T ss_dssp EE---TT-EEEEEEESHHHHHHHHHHCCCTBEEEEEESSE
T ss_pred EEEc-CCCEEEEECCCHHHHHHHHHHHhCCCEEEEECCch
Confidence 3565 67899999986444444455555334778888774
No 96
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=20.63 E-value=1.2e+02 Score=23.55 Aligned_cols=29 Identities=17% Similarity=0.336 Sum_probs=24.1
Q ss_pred eEEEecCCCCCcEEEEccccCHHHHHHHHHhhc
Q 048349 31 ESVAFKGDDRSQIEVTGDGMDAIVLFMSLRKKL 63 (94)
Q Consensus 31 ~sV~id~~~~~kvtV~G~~vDp~~l~~~LrKk~ 63 (94)
+.|..|. .+++||++|- |..|.+.|++..
T Consensus 303 ~~i~yd~-~~~~ltI~~~---p~~l~~ql~r~~ 331 (334)
T PRK00378 303 ERIFYDP-ATDTLTIKGT---PPNLRDQLQRRL 331 (334)
T ss_pred CceEEcC-CCCEEEEeCC---CHHHHHHHHHHh
Confidence 4889996 9999999996 888888887644
No 97
>PRK09579 multidrug efflux protein; Reviewed
Probab=20.37 E-value=2.9e+02 Score=25.09 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=35.3
Q ss_pred HHHHHHHhcCCCCeeEEEecCCCCCcEEEE-------ccccCHHHHHHHHHhh
Q 048349 17 RSKALKIVGGMPGVESVAFKGDDRSQIEVT-------GDGMDAIVLFMSLRKK 62 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~id~~~~~kvtV~-------G~~vDp~~l~~~LrKk 62 (94)
++.++..+.+++||..|++.+....++.|. ..|+++.++.+.|+..
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 456788899999999999998555566663 2257888899999874
No 98
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 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 Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the 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 site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=20.34 E-value=1.2e+02 Score=17.01 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=14.8
Q ss_pred HHHHHHHhcCCCCeeEEEe
Q 048349 17 RSKALKIVGGMPGVESVAF 35 (94)
Q Consensus 17 ~~K~~k~i~~~~GV~sV~i 35 (94)
-..+++.+.+++||.+|..
T Consensus 50 l~~li~~l~~~~~V~~v~~ 68 (69)
T cd04901 50 SEELLEALRAIPGTIRVRL 68 (69)
T ss_pred CHHHHHHHHcCCCeEEEEE
Confidence 3467788889999998864
No 99
>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=20.23 E-value=1.2e+02 Score=16.72 Aligned_cols=20 Identities=10% Similarity=0.341 Sum_probs=15.9
Q ss_pred hHHHHHHHhcCCCCeeEEEe
Q 048349 16 SRSKALKIVGGMPGVESVAF 35 (94)
Q Consensus 16 C~~K~~k~i~~~~GV~sV~i 35 (94)
--.++.+.+.+++||.++..
T Consensus 51 ~~~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 51 IDEEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred CCHHHHHHHHcCCCceEEEE
Confidence 35578888999999998863
No 100
>PF01981 PTH2: Peptidyl-tRNA hydrolase PTH2; InterPro: IPR002833 Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.; GO: 0004045 aminoacyl-tRNA hydrolase activity; PDB: 1RLK_A 1XTY_C 2ZV3_I 2D3K_A 1WN2_A 1Q7S_A 3ERJ_B 1RZW_A.
Probab=20.11 E-value=2.7e+02 Score=18.28 Aligned_cols=58 Identities=10% Similarity=0.111 Sum_probs=33.3
Q ss_pred eeEEEEEeCcchhhHHHHHHHhcCCCCeeEEEe-cCC----CCCcEEEEccccCHHHHHHHHHhhc
Q 048349 3 RMVGIEQPLENDKSRSKALKIVGGMPGVESVAF-KGD----DRSQIEVTGDGMDAIVLFMSLRKKL 63 (94)
Q Consensus 3 q~vVlKV~m~c~~C~~K~~k~i~~~~GV~sV~i-d~~----~~~kvtV~G~~vDp~~l~~~LrKk~ 63 (94)
.+|||+++ .+.--..+.+.+. -.|+....+ |.. ..+..||.|-|-.|.+.++.+-++.
T Consensus 51 ~Kivlkv~--~e~~L~~l~~~a~-~~gl~~~~i~Dag~Tei~pgs~TvlaigP~~~~~i~~it~~L 113 (116)
T PF01981_consen 51 KKIVLKVP--SEEELLELAKKAK-EAGLPHYLIRDAGRTEIPPGSVTVLAIGPAPKEEIDKITGHL 113 (116)
T ss_dssp SEEEEEES--SHHHHHHHHHHHH-HTT-SEEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTS
T ss_pred ceEEEEeC--CHHHHHHHHHHHH-HCCCCEEEEEECCCCcCCCCCeEEEEECcCCHHHHHHHhCcC
Confidence 47888876 2333333333333 245444333 320 2457888887778988888886643
Done!