Query 041984
Match_columns 98
No_of_seqs 106 out of 605
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 12:48:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041984.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041984hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 99.7 1.8E-17 3.9E-22 105.7 8.7 68 20-89 3-71 (73)
2 PF00403 HMA: Heavy-metal-asso 99.2 4.4E-11 9.5E-16 72.4 7.2 57 25-83 1-60 (62)
3 COG2608 CopZ Copper chaperone 98.5 7.2E-07 1.6E-11 56.5 7.3 60 22-83 2-64 (71)
4 KOG4656 Copper chaperone for s 98.2 1.2E-05 2.5E-10 62.1 7.9 67 22-91 7-74 (247)
5 PLN02957 copper, zinc superoxi 98.0 7.1E-05 1.5E-09 56.9 9.4 71 21-94 5-76 (238)
6 PRK10671 copA copper exporting 97.7 0.00014 3.1E-09 63.3 7.4 65 20-89 1-67 (834)
7 TIGR00003 copper ion binding p 94.6 0.34 7.4E-06 25.7 7.6 58 22-80 2-62 (68)
8 COG2217 ZntA Cation transport 92.9 0.38 8.2E-06 42.4 6.8 63 22-86 2-68 (713)
9 PRK10671 copA copper exporting 92.0 0.63 1.4E-05 40.9 7.0 63 23-88 100-164 (834)
10 KOG0207 Cation transport ATPas 89.7 0.94 2E-05 41.3 6.1 58 22-80 146-206 (951)
11 PF02680 DUF211: Uncharacteriz 88.7 2.8 6E-05 28.6 6.5 62 22-83 5-72 (95)
12 COG1888 Uncharacterized protei 84.8 2.6 5.7E-05 28.8 4.7 47 37-83 22-74 (97)
13 PRK11033 zntA zinc/cadmium/mer 80.8 7.5 0.00016 34.1 7.2 61 21-83 52-113 (741)
14 KOG0207 Cation transport ATPas 73.1 8.4 0.00018 35.4 5.4 63 29-92 2-65 (951)
15 PF13291 ACT_4: ACT domain; PD 69.9 16 0.00034 22.3 4.8 32 22-53 48-79 (80)
16 TIGR02052 MerP mercuric transp 67.2 17 0.00036 21.3 4.4 74 6-80 7-83 (92)
17 PF03927 NapD: NapD protein; 66.0 22 0.00049 22.7 5.0 34 22-55 39-72 (79)
18 PF01883 DUF59: Domain of unkn 64.6 13 0.00028 22.5 3.6 33 22-54 34-72 (72)
19 PF13732 DUF4162: Domain of un 63.9 28 0.00061 21.3 5.1 38 43-81 26-63 (84)
20 PF05180 zf-DNL: DNL zinc fing 60.3 4.9 0.00011 25.6 1.0 8 6-13 1-8 (66)
21 cd04910 ACT_AK-Ectoine_1 ACT d 59.7 25 0.00053 22.4 4.3 54 32-87 14-69 (71)
22 cd04888 ACT_PheB-BS C-terminal 55.8 40 0.00088 19.8 6.4 33 22-54 41-74 (76)
23 PF08712 Nfu_N: Scaffold prote 53.5 43 0.00092 21.8 4.7 42 37-81 37-79 (87)
24 cd04877 ACT_TyrR N-terminal AC 52.9 37 0.00081 20.5 4.2 31 24-54 39-69 (74)
25 PRK10553 assembly protein for 50.5 71 0.0015 21.0 5.5 45 34-79 17-61 (87)
26 TIGR00489 aEF-1_beta translati 49.5 35 0.00075 22.6 3.8 42 15-56 42-84 (88)
27 PF09358 UBA_e1_C: Ubiquitin-a 48.7 35 0.00075 23.6 3.9 60 5-92 7-67 (125)
28 COG1432 Uncharacterized conser 47.1 31 0.00068 25.1 3.7 31 61-92 114-144 (181)
29 PRK10553 assembly protein for 46.3 56 0.0012 21.5 4.4 35 22-56 42-76 (87)
30 KOG3411 40S ribosomal protein 46.2 16 0.00035 26.5 2.0 43 34-80 98-140 (143)
31 cd06167 LabA_like LabA_like pr 45.0 38 0.00083 22.7 3.6 30 61-91 103-132 (149)
32 PF03927 NapD: NapD protein; 44.1 83 0.0018 20.0 5.9 45 34-80 15-59 (79)
33 KOG3277 Uncharacterized conser 43.9 21 0.00045 26.6 2.3 28 5-36 75-111 (165)
34 PRK00435 ef1B elongation facto 42.4 46 0.00099 22.0 3.6 43 14-56 41-84 (88)
35 cd04878 ACT_AHAS N-terminal AC 40.7 59 0.0013 18.2 3.6 31 22-53 42-72 (72)
36 TIGR00288 conserved hypothetic 40.3 47 0.001 24.3 3.7 31 61-92 109-139 (160)
37 PHA00514 dsDNA binding protein 38.2 58 0.0013 22.2 3.6 33 60-93 32-66 (98)
38 PF14492 EFG_II: Elongation Fa 38.0 86 0.0019 19.4 4.2 51 35-86 20-72 (75)
39 PF04972 BON: BON domain; Int 36.7 83 0.0018 18.2 3.8 31 23-53 27-57 (64)
40 PF05922 Inhibitor_I9: Peptida 35.6 42 0.0009 20.1 2.4 20 37-56 58-77 (82)
41 PF05193 Peptidase_M16_C: Pept 34.9 35 0.00077 22.3 2.2 22 61-83 21-42 (184)
42 PRK09577 multidrug efflux prot 33.4 79 0.0017 28.9 4.7 47 35-82 157-210 (1032)
43 COG2092 EFB1 Translation elong 33.3 75 0.0016 21.4 3.5 42 15-56 42-84 (88)
44 PF10369 ALS_ss_C: Small subun 33.3 1.2E+02 0.0027 18.9 4.7 64 24-91 5-68 (75)
45 PF08478 POTRA_1: POTRA domain 33.2 67 0.0014 18.8 3.0 30 36-65 36-65 (69)
46 PF01936 NYN: NYN domain; Int 33.1 58 0.0013 21.4 3.0 29 61-90 99-127 (146)
47 cd04887 ACT_MalLac-Enz ACT_Mal 32.9 1.1E+02 0.0023 17.9 4.6 32 23-54 41-72 (74)
48 PF07683 CobW_C: Cobalamin syn 32.3 48 0.001 20.6 2.4 22 59-80 71-92 (94)
49 KOG1651 Glutathione peroxidase 31.1 51 0.0011 24.7 2.7 54 6-80 69-123 (171)
50 PF14437 MafB19-deam: MafB19-l 31.1 1.1E+02 0.0024 22.3 4.3 42 21-63 99-141 (146)
51 COG2177 FtsX Cell division pro 30.6 51 0.0011 26.2 2.8 33 23-56 62-94 (297)
52 PF05137 PilN: Fimbrial assemb 30.2 1.2E+02 0.0027 17.9 4.2 42 50-94 17-63 (78)
53 PF00736 EF1_GNE: EF-1 guanine 29.3 1.7E+02 0.0036 19.2 4.9 45 12-56 39-85 (89)
54 PF00919 UPF0004: Uncharacteri 28.4 1.2E+02 0.0027 19.9 3.9 58 4-88 37-96 (98)
55 PRK13760 putative RNA-associat 28.2 2E+02 0.0042 22.4 5.5 66 16-87 158-227 (231)
56 PF12164 SporV_AA: Stage V spo 27.9 64 0.0014 21.3 2.5 53 30-93 29-81 (93)
57 PF07338 DUF1471: Protein of u 27.6 72 0.0016 19.1 2.5 23 60-82 6-28 (56)
58 PHA01634 hypothetical protein 27.6 25 0.00053 25.8 0.4 12 29-40 97-108 (156)
59 PF12971 NAGLU_N: Alpha-N-acet 27.5 1.3E+02 0.0029 19.2 3.9 29 48-79 30-59 (86)
60 PRK10555 aminoglycoside/multid 27.2 1.3E+02 0.0028 27.6 5.0 46 35-81 158-210 (1037)
61 PRK11023 outer membrane lipopr 26.9 1.5E+02 0.0033 21.6 4.6 47 29-77 44-93 (191)
62 smart00833 CobW_C Cobalamin sy 26.1 1.1E+02 0.0023 18.7 3.2 22 59-80 69-90 (92)
63 PF01981 PTH2: Peptidyl-tRNA h 26.0 2.1E+02 0.0045 19.1 5.6 56 22-81 51-112 (116)
64 PRK13748 putative mercuric red 25.7 3.2E+02 0.0069 22.5 6.7 60 29-90 8-69 (561)
65 PF01424 R3H: R3H domain; Int 25.6 1.2E+02 0.0027 17.6 3.3 33 33-65 29-61 (63)
66 cd02643 R3H_NF-X1 R3H domain o 25.5 1.3E+02 0.0028 18.9 3.5 30 35-64 43-72 (74)
67 smart00653 eIF2B_5 domain pres 25.4 1.2E+02 0.0026 20.7 3.6 40 39-82 38-77 (110)
68 cd03309 CmuC_like CmuC_like. P 24.8 1.2E+02 0.0026 24.1 3.9 46 27-74 214-269 (321)
69 cd04879 ACT_3PGDH-like ACT_3PG 23.7 92 0.002 17.2 2.4 19 36-54 52-70 (71)
70 PRK15127 multidrug efflux syst 22.8 1.6E+02 0.0034 27.1 4.7 45 35-80 158-209 (1049)
71 COG0612 PqqL Predicted Zn-depe 22.7 78 0.0017 25.2 2.5 23 60-83 199-221 (438)
72 PF15174 PRNT: Prion-related p 22.4 14 0.0003 22.4 -1.4 18 25-42 32-49 (51)
73 TIGR00915 2A0602 The (Largely 22.3 1.7E+02 0.0037 26.8 4.9 45 35-80 158-209 (1044)
74 cd00292 EF1B Elongation factor 22.3 1.7E+02 0.0037 19.1 3.7 43 14-56 41-84 (88)
75 TIGR02945 SUF_assoc FeS assemb 21.6 1.4E+02 0.0031 19.0 3.2 21 36-56 57-77 (99)
76 PF01876 RNase_P_p30: RNase P 20.8 90 0.0019 21.6 2.2 34 61-96 3-36 (150)
77 TIGR03406 FeS_long_SufT probab 20.2 1.6E+02 0.0034 21.7 3.5 34 23-56 114-153 (174)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.74 E-value=1.8e-17 Score=105.67 Aligned_cols=68 Identities=31% Similarity=0.412 Sum_probs=61.8
Q ss_pred cceeEEEEEeecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcCC-ceEEEE
Q 041984 20 LNGKVVIKLSLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTMR-FAELLT 89 (98)
Q Consensus 20 m~qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~~-~aeivs 89 (98)
..+..+++|+|||+||++++.+.+..++||+++.+|.++ +++||.|+ +||..|+++|+|.++ ++++|.
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~-~kvtV~g~-~~p~~vl~~l~k~~~k~~~~~~ 71 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKK-QKVTVKGN-VDPVKLLKKLKKTGGKRAELWK 71 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCC-CEEEEEEe-cCHHHHHHHHHhcCCCceEEec
Confidence 348899999999999999999999999999999999987 69999999 999999999999774 566653
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=99.24 E-value=4.4e-11 Score=72.43 Aligned_cols=57 Identities=19% Similarity=0.212 Sum_probs=50.2
Q ss_pred EEEE-eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecc--cCHHHHHHHHHhcCC
Q 041984 25 VIKL-SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDG--MDPVLLTSLLRKTMR 83 (98)
Q Consensus 25 VlKV-~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~--vDp~~lv~kLrKk~~ 83 (98)
+|+| +|+|++|++++.+++.+++||.++.+|... ++++|.++. +++..+.++|++ .|
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~-~~v~v~~~~~~~~~~~i~~~i~~-~G 60 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLET-KTVTVTYDPDKTSIEKIIEAIEK-AG 60 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTT-TEEEEEESTTTSCHHHHHHHHHH-TT
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCC-CEEEEEEecCCCCHHHHHHHHHH-hC
Confidence 4677 799999999999999999999999999976 799999982 345999999998 44
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.51 E-value=7.2e-07 Score=56.50 Aligned_cols=60 Identities=20% Similarity=0.174 Sum_probs=50.4
Q ss_pred eeEEEEE-eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEec--ccCHHHHHHHHHhcCC
Q 041984 22 GKVVIKL-SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGD--GMDPVLLTSLLRKTMR 83 (98)
Q Consensus 22 qkvVlKV-~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~--~vDp~~lv~kLrKk~~ 83 (98)
++..|++ +|+|++|...+.++|.+++||.++.+|.+. +..+|.-+ .++...+...+.. .|
T Consensus 2 ~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~-~~~~V~~d~~~~~~~~i~~ai~~-aG 64 (71)
T COG2608 2 MKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEK-GTATVTFDSNKVDIEAIIEAIED-AG 64 (71)
T ss_pred ceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEccc-CeEEEEEcCCcCCHHHHHHHHHH-cC
Confidence 5677888 699999999999999999999999999975 34555544 3899999999988 55
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.15 E-value=1.2e-05 Score=62.06 Aligned_cols=67 Identities=13% Similarity=0.098 Sum_probs=59.1
Q ss_pred eeEEEEEeecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcCC-ceEEEEcc
Q 041984 22 GKVVIKLSLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTMR-FAELLTVI 91 (98)
Q Consensus 22 qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~~-~aeivsv~ 91 (98)
-++.+-|+|+||.|..-+++.+..++||+++++|.++ +.+.|-+. +-|..+...|+. +| .|-|.-.+
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~-q~v~v~ts-~p~s~i~~~le~-tGr~Avl~G~G 74 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQ-QIVSVETS-VPPSEIQNTLEN-TGRDAVLRGAG 74 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhh-cEEEEEcc-CChHHHHHHHHh-hChheEEecCC
Confidence 4678889999999999999999999999999999976 58889998 999999999998 55 77765544
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=97.99 E-value=7.1e-05 Score=56.94 Aligned_cols=71 Identities=13% Similarity=0.099 Sum_probs=62.5
Q ss_pred ceeEEEEEeecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcCC-ceEEEEccCCC
Q 041984 21 NGKVVIKLSLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTMR-FAELLTVINLK 94 (98)
Q Consensus 21 ~qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~~-~aeivsv~p~k 94 (98)
.+++.+.+.|+|+.|..++.+.+.+++||.++.++... ++++|.+. .++..+...+++ .+ .+++++.++..
T Consensus 5 ~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~-~~v~V~~~-~~~~~I~~aIe~-~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 5 ELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSN-QVVRVLGS-SPVKAMTAALEQ-TGRKARLIGQGDPE 76 (238)
T ss_pred cEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCC-CEEEEEec-CCHHHHHHHHHH-cCCcEEEecCCCcc
Confidence 37788999999999999999999999999999999976 69999987 899999999997 56 68888876665
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.68 E-value=0.00014 Score=63.33 Aligned_cols=65 Identities=14% Similarity=0.142 Sum_probs=56.6
Q ss_pred cceeEEEEE-eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcCC-ceEEEE
Q 041984 20 LNGKVVIKL-SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTMR-FAELLT 89 (98)
Q Consensus 20 m~qkvVlKV-~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~~-~aeivs 89 (98)
|++++.++| .|+|..|.+++.+.+.+++||.++.++.+ +.+|.++ .++..+...++. .| .+++.+
T Consensus 1 ~~~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~---~~~v~~~-~~~~~i~~~i~~-~Gy~~~~~~ 67 (834)
T PRK10671 1 MSQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT---EAHVTGT-ASAEALIETIKQ-AGYDASVSH 67 (834)
T ss_pred CCeEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee---EEEEEec-CCHHHHHHHHHh-cCCcccccc
Confidence 558899999 59999999999999999999999999983 6678887 899999999997 56 777754
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=94.55 E-value=0.34 Score=25.71 Aligned_cols=58 Identities=17% Similarity=0.252 Sum_probs=43.8
Q ss_pred eeEEEEE-eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEec--ccCHHHHHHHHHh
Q 041984 22 GKVVIKL-SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGD--GMDPVLLTSLLRK 80 (98)
Q Consensus 22 qkvVlKV-~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~--~vDp~~lv~kLrK 80 (98)
++..+.+ .++|..|...+.+.+...+|+.+..++... +.+.+..+ ..+...+...+..
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 62 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEK-ASVKVEFDAPQATEICIAEAILD 62 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCC-CEEEEEeCCCCCCHHHHHHHHHH
Confidence 3455677 578999999999999999999999998865 57777642 2466776665543
No 8
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=92.89 E-value=0.38 Score=42.43 Aligned_cols=63 Identities=16% Similarity=0.178 Sum_probs=50.5
Q ss_pred eeEEEEE-eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecc--cC-HHHHHHHHHhcCCceE
Q 041984 22 GKVVIKL-SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDG--MD-PVLLTSLLRKTMRFAE 86 (98)
Q Consensus 22 qkvVlKV-~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~--vD-p~~lv~kLrKk~~~ae 86 (98)
++..|.+ .|||..|.+++. .+.+++||++..++.-. ++++|..+. .+ +..+...+++..-.+.
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t-~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~ 68 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLAT-ERATVVYDPEEVDLPADIVAAVEKAGYSAR 68 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeeccc-ceEEEEecccccccHHHHHHHHHhcCcccc
Confidence 3456677 599999999999 99999999999999966 699998762 56 7889999887332443
No 9
>PRK10671 copA copper exporting ATPase; Provisional
Probab=91.95 E-value=0.63 Score=40.91 Aligned_cols=63 Identities=19% Similarity=0.172 Sum_probs=51.6
Q ss_pred eEEEEE-eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcCC-ceEEE
Q 041984 23 KVVIKL-SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTMR-FAELL 88 (98)
Q Consensus 23 kvVlKV-~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~~-~aeiv 88 (98)
.+.+.+ .|+|..|...+.+.+.+.+||.+..++... ++..+.+. .++..+...++. .| .+.++
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t-~~~~V~~~-~s~~~I~~~I~~-~Gy~a~~~ 164 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAE-RTALVMGS-ASPQDLVQAVEK-AGYGAEAI 164 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCC-CeEEEEcc-CCHHHHHHHHHh-cCCCcccc
Confidence 556666 699999999999999999999999999865 57888775 889998888876 55 45443
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=89.74 E-value=0.94 Score=41.31 Aligned_cols=58 Identities=19% Similarity=0.185 Sum_probs=49.5
Q ss_pred eeEEEEE-eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEec--ccCHHHHHHHHHh
Q 041984 22 GKVVIKL-SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGD--GMDPVLLTSLLRK 80 (98)
Q Consensus 22 qkvVlKV-~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~--~vDp~~lv~kLrK 80 (98)
++++|.| .|.|+.|..++.+.+.+++||.+++++... +++.|.=+ ..-|..+++.+..
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t-~~~~V~~~~~~~~pr~i~k~ie~ 206 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLAT-DTAIVVYDPEITGPRDIIKAIEE 206 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccC-CceEEEecccccChHHHHHHHHh
Confidence 7888888 699999999999999999999999999966 68887665 3567778887765
No 11
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=88.73 E-value=2.8 Score=28.61 Aligned_cols=62 Identities=16% Similarity=0.239 Sum_probs=41.1
Q ss_pred eeEEEEEeecchhhHHHHHHHhcCCCceeEEEe-----cCCCCC-eEEEEecccCHHHHHHHHHhcCC
Q 041984 22 GKVVIKLSLEGHKSRSKALKIAVRVSGVESVAL-----KGDDRS-QIEVTGDGMDPVLLTSLLRKTMR 83 (98)
Q Consensus 22 qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~i-----d~~~k~-kvtV~G~~vDp~~lv~kLrKk~~ 83 (98)
.++||-|--.-+=---..-+.+++++||+.|.+ |.+..+ ++|+.|+.+|...+.+.+.+-++
T Consensus 5 rRlVLDVlKP~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg 72 (95)
T PF02680_consen 5 RRLVLDVLKPHEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGG 72 (95)
T ss_dssp EEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-
T ss_pred eEEEEEeecCCCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCC
Confidence 455666643333344455677889999998865 433222 78999999999999999998554
No 12
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=84.79 E-value=2.6 Score=28.77 Aligned_cols=47 Identities=15% Similarity=0.222 Sum_probs=34.7
Q ss_pred HHHHHHhcCCCceeEEEe-----cCCCC-CeEEEEecccCHHHHHHHHHhcCC
Q 041984 37 SKALKIAVRVSGVESVAL-----KGDDR-SQIEVTGDGMDPVLLTSLLRKTMR 83 (98)
Q Consensus 37 ~Kv~k~i~~~~GV~SV~i-----d~~~k-~kvtV~G~~vDp~~lv~kLrKk~~ 83 (98)
-..-+.+++++||+.|.+ |.+.- =++|+-|..+|-..+.+.|.+-.|
T Consensus 22 ve~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg 74 (97)
T COG1888 22 VELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGG 74 (97)
T ss_pred HHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCC
Confidence 345567788888887754 33222 289999999999999999998544
No 13
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=80.75 E-value=7.5 Score=34.12 Aligned_cols=61 Identities=15% Similarity=0.148 Sum_probs=44.3
Q ss_pred ceeEEEEE-eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcCC
Q 041984 21 NGKVVIKL-SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTMR 83 (98)
Q Consensus 21 ~qkvVlKV-~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~~ 83 (98)
.+++.+++ .|+|..|..++.+.+.+.+||.++.++... +++.+..+.-....+...++. .|
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at-~k~~V~~d~~~~~~I~~aI~~-~G 113 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFAT-EKLVVDADNDIRAQVESAVQK-AG 113 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCC-CeEEEEecccchHHHHHHHHh-cc
Confidence 46777777 499999999999999999999999999765 576665331112455555555 44
No 14
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=73.12 E-value=8.4 Score=35.42 Aligned_cols=63 Identities=16% Similarity=0.139 Sum_probs=50.1
Q ss_pred eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEec-ccCHHHHHHHHHhcCCceEEEEccC
Q 041984 29 SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGD-GMDPVLLTSLLRKTMRFAELLTVIN 92 (98)
Q Consensus 29 ~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~-~vDp~~lv~kLrKk~~~aeivsv~p 92 (98)
.|.|..|...+.+.+++.+||.+++++..+ +..+|.=+ .++|..+.+.+.--+..+++.+.+.
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~-~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~~ 65 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQ-KRANVSYDNIVSPESIKETIEDMGFEASLLSDSE 65 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEecc-ccceEEEeeccCHHHHHHHhhcccceeeecccCc
Confidence 588999999999999999999999999866 45554433 4899999999887333788776543
No 15
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=69.92 E-value=16 Score=22.32 Aligned_cols=32 Identities=13% Similarity=0.323 Sum_probs=28.4
Q ss_pred eeEEEEEeecchhhHHHHHHHhcCCCceeEEE
Q 041984 22 GKVVIKLSLEGHKSRSKALKIAVRVSGVESVA 53 (98)
Q Consensus 22 qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~ 53 (98)
-.+.|.+.+..-.--..+++.+.+++||.+|.
T Consensus 48 ~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 48 ARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 56778888888889999999999999999985
No 16
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=67.17 E-value=17 Score=21.33 Aligned_cols=74 Identities=16% Similarity=0.099 Sum_probs=44.6
Q ss_pred eEEEEEeecCCccccceeEEEEE-eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEE--ecccCHHHHHHHHHh
Q 041984 6 LELVFTCTYGPMSFLNGKVVIKL-SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVT--GDGMDPVLLTSLLRK 80 (98)
Q Consensus 6 ~~~~~~~~~~p~~~m~qkvVlKV-~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~--G~~vDp~~lv~kLrK 80 (98)
|-+.|+-+|.|--....++.+.+ .++|..|...+.......+|+.+...+... ....+. +...++..+...+..
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 83 (92)
T TIGR02052 7 LLALFVLTSLPAWAATQTVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKT-KLAVVTFDDEKTNVKALTEATTD 83 (92)
T ss_pred HHHHHHHhcchhhhcceEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecC-CEEEEEECCCCCCHHHHHHHHHh
Confidence 33445555555544334444544 467999999999999999998877776543 343332 212455555555443
No 17
>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=65.99 E-value=22 Score=22.67 Aligned_cols=34 Identities=24% Similarity=0.386 Sum_probs=29.9
Q ss_pred eeEEEEEeecchhhHHHHHHHhcCCCceeEEEec
Q 041984 22 GKVVIKLSLEGHKSRSKALKIAVRVSGVESVALK 55 (98)
Q Consensus 22 qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id 55 (98)
-++|+=+.-...+-....++.+..++||-|+++=
T Consensus 39 GKiVVtiE~~~~~~~~~~~~~i~~l~GVlsa~lv 72 (79)
T PF03927_consen 39 GKIVVTIEAESSEEEVDLIDAINALPGVLSASLV 72 (79)
T ss_dssp TEEEEEEEESSHHHHHHHHHHHCCSTTEEEEEES
T ss_pred CeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEE
Confidence 4788888888889999999999999999999874
No 18
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=64.64 E-value=13 Score=22.55 Aligned_cols=33 Identities=30% Similarity=0.415 Sum_probs=22.2
Q ss_pred eeEEEEEeecchhh------HHHHHHHhcCCCceeEEEe
Q 041984 22 GKVVIKLSLEGHKS------RSKALKIAVRVSGVESVAL 54 (98)
Q Consensus 22 qkvVlKV~m~ce~C------~~Kv~k~i~~~~GV~SV~i 54 (98)
.++.+.+.+...+| +..+.+++..++||.++++
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 45566666655444 5788899999999999975
No 19
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=63.86 E-value=28 Score=21.31 Aligned_cols=38 Identities=26% Similarity=0.327 Sum_probs=29.6
Q ss_pred hcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhc
Q 041984 43 AVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKT 81 (98)
Q Consensus 43 i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk 81 (98)
+..++||.++..+.+..-.+.+..+ .++..|++.|...
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~-~~~~~ll~~l~~~ 63 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDE-ETANELLQELIEK 63 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCc-ccHHHHHHHHHhC
Confidence 6678999999986543236777776 8999999999874
No 20
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=60.32 E-value=4.9 Score=25.61 Aligned_cols=8 Identities=50% Similarity=1.132 Sum_probs=6.3
Q ss_pred eEEEEEee
Q 041984 6 LELVFTCT 13 (98)
Q Consensus 6 ~~~~~~~~ 13 (98)
+.|.|||+
T Consensus 1 ~~l~FTC~ 8 (66)
T PF05180_consen 1 YQLTFTCN 8 (66)
T ss_dssp EEEEEEET
T ss_pred CeEEEEcC
Confidence 36889997
No 21
>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=59.67 E-value=25 Score=22.39 Aligned_cols=54 Identities=20% Similarity=0.149 Sum_probs=40.9
Q ss_pred chhhHHHHHHHhcCCCceeEEEecCCCCCeEE--EEecccCHHHHHHHHHhcCCceEE
Q 041984 32 GHKSRSKALKIAVRVSGVESVALKGDDRSQIE--VTGDGMDPVLLTSLLRKTMRFAEL 87 (98)
Q Consensus 32 ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvt--V~G~~vDp~~lv~kLrKk~~~aei 87 (98)
.-+=..++++++.+. +|.=|.-+... |.+| +.|..-+...+...|++.++.|++
T Consensus 14 ~~g~d~~i~~~l~~~-~v~ii~K~~nA-Ntit~yl~~~~k~~~r~~~~Le~~~p~a~i 69 (71)
T cd04910 14 EVGYDLEILELLQRF-KVSIIAKDTNA-NTITHYLAGSLKTIKRLTEDLENRFPNAEI 69 (71)
T ss_pred ChhHHHHHHHHHHHc-CCeEEEEecCC-CeEEEEEEcCHHHHHHHHHHHHHhCccCcc
Confidence 345678888888876 88888888877 6888 445423568889999888888776
No 22
>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=55.82 E-value=40 Score=19.81 Aligned_cols=33 Identities=24% Similarity=0.329 Sum_probs=26.5
Q ss_pred eeEEEEEeecchh-hHHHHHHHhcCCCceeEEEe
Q 041984 22 GKVVIKLSLEGHK-SRSKALKIAVRVSGVESVAL 54 (98)
Q Consensus 22 qkvVlKV~m~ce~-C~~Kv~k~i~~~~GV~SV~i 54 (98)
..+.+-+...... .-..+++.+.+++||.+|.+
T Consensus 41 ~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 41 ANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 4566666666665 77999999999999999976
No 23
>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=53.48 E-value=43 Score=21.76 Aligned_cols=42 Identities=26% Similarity=0.243 Sum_probs=30.5
Q ss_pred HHHHHHhcCCCceeEEEecCCCCCeEEEEec-ccCHHHHHHHHHhc
Q 041984 37 SKALKIAVRVSGVESVALKGDDRSQIEVTGD-GMDPVLLTSLLRKT 81 (98)
Q Consensus 37 ~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~-~vDp~~lv~kLrKk 81 (98)
+-.-+.|-.++||.||-+.. |=+||+-+ .+|-..|...++..
T Consensus 37 spLA~~Lf~i~gV~~Vf~~~---dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIGD---DFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEET---TEEEEEE-TTS-HHHHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEEC---CEEEEeeCCCCCHHHHHHHHHHH
Confidence 44455566899999999976 68888876 38888888888753
No 24
>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=52.88 E-value=37 Score=20.50 Aligned_cols=31 Identities=16% Similarity=0.239 Sum_probs=25.6
Q ss_pred EEEEEeecchhhHHHHHHHhcCCCceeEEEe
Q 041984 24 VVIKLSLEGHKSRSKALKIAVRVSGVESVAL 54 (98)
Q Consensus 24 vVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~i 54 (98)
+-+.+....-.--..+++.+.+++||.+|+-
T Consensus 39 i~l~i~v~~~~~L~~li~~L~~i~gV~~V~R 69 (74)
T cd04877 39 IYLNFPTIEFEKLQTLMPEIRRIDGVEDVKT 69 (74)
T ss_pred EEEEeEecCHHHHHHHHHHHhCCCCceEEEE
Confidence 6677777777777999999999999999863
No 25
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=50.47 E-value=71 Score=21.03 Aligned_cols=45 Identities=16% Similarity=0.094 Sum_probs=33.0
Q ss_pred hhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHH
Q 041984 34 KSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLR 79 (98)
Q Consensus 34 ~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLr 79 (98)
.-...+.+.+..++|++=-..|.+. +|+.|+=++-+...+++.+.
T Consensus 17 e~~~~V~~~l~~ipg~Evh~~d~~~-GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 17 ERISDISTQLNAFPGCEVAVSDAPS-GQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHHHcCCCcEEEeecCCC-CeEEEEEEeCChHHHHHHHH
Confidence 3467788999999999988887654 78888877555665555444
No 26
>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=49.47 E-value=35 Score=22.63 Aligned_cols=42 Identities=19% Similarity=0.241 Sum_probs=30.7
Q ss_pred CCccccceeEEEEEeecch-hhHHHHHHHhcCCCceeEEEecC
Q 041984 15 GPMSFLNGKVVIKLSLEGH-KSRSKALKIAVRVSGVESVALKG 56 (98)
Q Consensus 15 ~p~~~m~qkvVlKV~m~ce-~C~~Kv~k~i~~~~GV~SV~id~ 56 (98)
.|.+.--+.+.+-+-|.++ +--..+-..+++++||+|+++..
T Consensus 42 ePiaFGLkaL~~~~vv~D~~g~td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 42 EPIAFGLVAINVMVVMGDAEGGTEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred EeeeccceeeEEEEEEecCCcChHHHHHHHhcCCCccEEEEEE
Confidence 3444444555566666554 66789999999999999999864
No 27
>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=48.66 E-value=35 Score=23.65 Aligned_cols=60 Identities=23% Similarity=0.194 Sum_probs=38.7
Q ss_pred ceEEEEEeecCCccccceeEEEEEeecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcCC-
Q 041984 5 NLELVFTCTYGPMSFLNGKVVIKLSLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTMR- 83 (98)
Q Consensus 5 ~~~~~~~~~~~p~~~m~qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~~- 83 (98)
||-|-|+.+.-|...-..++ ...+.... |++.|.|+ +....+++.+++++|
T Consensus 7 NLAlP~~~fsEP~~~~k~k~-------------------------~~~~~T~W--Dr~~v~~~-~Tl~~li~~~~~~~~l 58 (125)
T PF09358_consen 7 NLALPFFSFSEPIPAPKTKY-------------------------NDKEWTLW--DRIEVNGD-MTLQELIDYFKEKYGL 58 (125)
T ss_dssp ETTTTEEEEE---B--EEEE-------------------------TTEEETTT---EEEEES---BHHHHHHHHHHTTS-
T ss_pred EcCccceeeeeccCCCceEe-------------------------cCccccce--eEEEEcCC-CCHHHHHHHHHHHhCc
Confidence 66666777788877733322 11233556 69999997 999999999999988
Q ss_pred ceEEEEccC
Q 041984 84 FAELLTVIN 92 (98)
Q Consensus 84 ~aeivsv~p 92 (98)
.+.+++.+.
T Consensus 59 ev~ml~~g~ 67 (125)
T PF09358_consen 59 EVTMLSQGV 67 (125)
T ss_dssp EEEEEEETT
T ss_pred eEEEEEeCC
Confidence 888888764
No 28
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=47.13 E-value=31 Score=25.07 Aligned_cols=31 Identities=19% Similarity=0.166 Sum_probs=26.8
Q ss_pred eEEEEecccCHHHHHHHHHhcCCceEEEEccC
Q 041984 61 QIEVTGDGMDPVLLTSLLRKTMRFAELLTVIN 92 (98)
Q Consensus 61 kvtV~G~~vDp~~lv~kLrKk~~~aeivsv~p 92 (98)
-+.++|+ -|-.-++++++.+++++++++.+|
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 4557798 898889999999888999999887
No 29
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=46.30 E-value=56 Score=21.53 Aligned_cols=35 Identities=20% Similarity=0.330 Sum_probs=30.3
Q ss_pred eeEEEEEeecchhhHHHHHHHhcCCCceeEEEecC
Q 041984 22 GKVVIKLSLEGHKSRSKALKIAVRVSGVESVALKG 56 (98)
Q Consensus 22 qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~ 56 (98)
-|+|+-+.-.+.+-.-...+.+..++||-|+++=.
T Consensus 42 GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVY 76 (87)
T PRK10553 42 GQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVY 76 (87)
T ss_pred CeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEE
Confidence 47888888888888889999999999999998844
No 30
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=46.21 E-value=16 Score=26.51 Aligned_cols=43 Identities=14% Similarity=0.149 Sum_probs=30.6
Q ss_pred hhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHh
Q 041984 34 KSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRK 80 (98)
Q Consensus 34 ~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrK 80 (98)
+|.++|+..+.++ .-|+.+.+..-++|=.|. =|...++.+++.
T Consensus 98 ~i~rkvlQ~Le~~---~~ve~hp~gGR~lt~~Gq-rdldrIa~~i~~ 140 (143)
T KOG3411|consen 98 GIARKVLQALEKM---GIVEKHPKGGRRLTEQGQ-RDLDRIAGQIRE 140 (143)
T ss_pred HHHHHHHHHHHhC---CceeeCCCCcceeCcccc-hhHHHHHHHHHh
Confidence 5666666666555 445555543349999998 899999999875
No 31
>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=44.97 E-value=38 Score=22.72 Aligned_cols=30 Identities=27% Similarity=0.214 Sum_probs=25.3
Q ss_pred eEEEEecccCHHHHHHHHHhcCCceEEEEcc
Q 041984 61 QIEVTGDGMDPVLLTSLLRKTMRFAELLTVI 91 (98)
Q Consensus 61 kvtV~G~~vDp~~lv~kLrKk~~~aeivsv~ 91 (98)
=+.|+|+ -|-.-++++||.....+.++++.
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 5568898 89999999999975589988876
No 32
>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=44.11 E-value=83 Score=20.00 Aligned_cols=45 Identities=20% Similarity=0.203 Sum_probs=34.5
Q ss_pred hhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHh
Q 041984 34 KSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRK 80 (98)
Q Consensus 34 ~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrK 80 (98)
+-...+.+.+..++|++=-..+. + +|+.|+=+.-+...+.+.+..
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 45678999999999997666665 3 699988886677777777665
No 33
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.90 E-value=21 Score=26.55 Aligned_cols=28 Identities=21% Similarity=0.498 Sum_probs=16.6
Q ss_pred ceEEEEEeec---------CCccccceeEEEEEeecchhhH
Q 041984 5 NLELVFTCTY---------GPMSFLNGKVVIKLSLEGHKSR 36 (98)
Q Consensus 5 ~~~~~~~~~~---------~p~~~m~qkvVlKV~m~ce~C~ 36 (98)
.+.|+|||.+ ++++--. -+|| +.|+||.
T Consensus 75 ~m~l~yTCkvCntRs~ktisk~AY~~-GvVi---vqC~gC~ 111 (165)
T KOG3277|consen 75 RMQLAYTCKVCNTRSTKTISKQAYEK-GVVI---VQCPGCK 111 (165)
T ss_pred ceEEEEEeeccCCccccccChhhhhC-ceEE---EECCCCc
Confidence 3689999983 3333322 2332 4699996
No 34
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=42.35 E-value=46 Score=22.04 Aligned_cols=43 Identities=19% Similarity=0.226 Sum_probs=32.5
Q ss_pred cCCccccceeEEEEEeecch-hhHHHHHHHhcCCCceeEEEecC
Q 041984 14 YGPMSFLNGKVVIKLSLEGH-KSRSKALKIAVRVSGVESVALKG 56 (98)
Q Consensus 14 ~~p~~~m~qkvVlKV~m~ce-~C~~Kv~k~i~~~~GV~SV~id~ 56 (98)
..|.+.--+++-+-+-+.++ +--..+-..+++++||.|+++..
T Consensus 41 ~ePIaFGLkaL~i~~vv~D~~~~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 41 EEPIAFGLKALKLYVIMPDEEGGTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred EEEeeccceeEEEEEEEEcCCcCcHHHHHHHhccCCCcEEEEEE
Confidence 44555555666666666664 77889999999999999999864
No 35
>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=40.67 E-value=59 Score=18.21 Aligned_cols=31 Identities=13% Similarity=0.168 Sum_probs=23.2
Q ss_pred eeEEEEEeecchhhHHHHHHHhcCCCceeEEE
Q 041984 22 GKVVIKLSLEGHKSRSKALKIAVRVSGVESVA 53 (98)
Q Consensus 22 qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~ 53 (98)
..+++.+.... .--..+.+.+.+++||.+|+
T Consensus 42 ~~~~~~~~~~~-~~~~~l~~~l~~~~~v~~v~ 72 (72)
T cd04878 42 SRITIVVEGDD-DVIEQIVKQLNKLVDVLKVS 72 (72)
T ss_pred EEEEEEEECCH-HHHHHHHHHHhCCccEEEeC
Confidence 45677776543 55688889999999999874
No 36
>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=40.28 E-value=47 Score=24.30 Aligned_cols=31 Identities=13% Similarity=0.009 Sum_probs=25.6
Q ss_pred eEEEEecccCHHHHHHHHHhcCCceEEEEccC
Q 041984 61 QIEVTGDGMDPVLLTSLLRKTMRFAELLTVIN 92 (98)
Q Consensus 61 kvtV~G~~vDp~~lv~kLrKk~~~aeivsv~p 92 (98)
=+-|+|+ -|-.-|+.+||..+..+..+++++
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 4668998 999999999999755888888654
No 37
>PHA00514 dsDNA binding protein
Probab=38.18 E-value=58 Score=22.17 Aligned_cols=33 Identities=12% Similarity=0.087 Sum_probs=27.5
Q ss_pred CeEEEEecccCHHHHHHHHHhcC--CceEEEEccCC
Q 041984 60 SQIEVTGDGMDPVLLTSLLRKTM--RFAELLTVINL 93 (98)
Q Consensus 60 ~kvtV~G~~vDp~~lv~kLrKk~--~~aeivsv~p~ 93 (98)
+..|..|+ .....--+.|.|+. +.+.++|++|-
T Consensus 32 ~~~Tl~GN-LtiEqAQ~e~~k~~k~~pvqVvsVEpn 66 (98)
T PHA00514 32 NEQTLLGN-LTIEQAQKELSKQYKHGPVQVVSVEPN 66 (98)
T ss_pred Ccceeecc-eeHHHHHHHHhhcccCCCeeEEEecCC
Confidence 35589999 99888889998875 47999999985
No 38
>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=37.96 E-value=86 Score=19.44 Aligned_cols=51 Identities=18% Similarity=0.190 Sum_probs=34.3
Q ss_pred hHHHHHHHhcCCCceeEEEecCCCCCeEEEEecc-cCHHHHHHHHHhcCC-ceE
Q 041984 35 SRSKALKIAVRVSGVESVALKGDDRSQIEVTGDG-MDPVLLTSLLRKTMR-FAE 86 (98)
Q Consensus 35 C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~-vDp~~lv~kLrKk~~-~ae 86 (98)
.-..+++.+..-+=--.+..|.+. +.+.+.|-| +=-.-++++|+++++ .++
T Consensus 20 kl~~aL~~l~~eDP~l~~~~d~et-~e~~l~g~Gelhlev~~~~L~~~~~v~v~ 72 (75)
T PF14492_consen 20 KLSEALQKLSEEDPSLRVERDEET-GELILSGMGELHLEVLLERLKRRFGVEVE 72 (75)
T ss_dssp HHHHHHHHHHHH-TTSEEEEETTT-SEEEEEESSHHHHHHHHHHHHHTTCEBEE
T ss_pred HHHHHHHHHHhcCCeEEEEEcchh-ceEEEEECCHHHHHHHHHHHHHHHCCeeE
Confidence 334555555555545578888765 687777664 778889999999887 554
No 39
>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=36.73 E-value=83 Score=18.17 Aligned_cols=31 Identities=26% Similarity=0.360 Sum_probs=25.6
Q ss_pred eEEEEEeecchhhHHHHHHHhcCCCceeEEE
Q 041984 23 KVVIKLSLEGHKSRSKALKIAVRVSGVESVA 53 (98)
Q Consensus 23 kvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~ 53 (98)
.+.|.=....+..+.++.+++..+.||.+|.
T Consensus 27 ~v~L~G~v~s~~~~~~a~~~a~~v~gv~~V~ 57 (64)
T PF04972_consen 27 VVTLSGEVPSQEQRDAAERLARSVAGVREVV 57 (64)
T ss_dssp EEEEEEEESSCHHHHHHHHHHHCC-STSEEE
T ss_pred EEEEEeeCcHHHHHHhHHhhhccCCCcCEEE
Confidence 5666666778899999999999999999986
No 40
>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=35.64 E-value=42 Score=20.13 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=16.3
Q ss_pred HHHHHHhcCCCceeEEEecC
Q 041984 37 SKALKIAVRVSGVESVALKG 56 (98)
Q Consensus 37 ~Kv~k~i~~~~GV~SV~id~ 56 (98)
....+.+.+.+||.+|+.|.
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 34557888999999999985
No 41
>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=34.90 E-value=35 Score=22.30 Aligned_cols=22 Identities=32% Similarity=0.569 Sum_probs=19.0
Q ss_pred eEEEEecccCHHHHHHHHHhcCC
Q 041984 61 QIEVTGDGMDPVLLTSLLRKTMR 83 (98)
Q Consensus 61 kvtV~G~~vDp~~lv~kLrKk~~ 83 (98)
.+.++|+ +|+..+.+.+++.++
T Consensus 21 ~l~i~Gd-~~~~~~~~~i~~~~~ 42 (184)
T PF05193_consen 21 TLVIVGD-IDPDELEKLIEKYFG 42 (184)
T ss_dssp EEEEEES-SGHHHHHHHHHHHHT
T ss_pred EEEEEcC-ccHHHHHHHHHhhhh
Confidence 7889998 999999999887665
No 42
>PRK09577 multidrug efflux protein; Reviewed
Probab=33.38 E-value=79 Score=28.92 Aligned_cols=47 Identities=21% Similarity=0.302 Sum_probs=35.8
Q ss_pred hHHHHHHHhcCCCceeEEEecCCCCCeEEEE-------ecccCHHHHHHHHHhcC
Q 041984 35 SRSKALKIAVRVSGVESVALKGDDRSQIEVT-------GDGMDPVLLTSLLRKTM 82 (98)
Q Consensus 35 C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~-------G~~vDp~~lv~kLrKk~ 82 (98)
-+.++...+.+++||.+|++.+.+ .++.|. ..|+++..+.+.|+...
T Consensus 157 ~~~~l~~~L~~v~GV~~V~~~G~e-~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n 210 (1032)
T PRK09577 157 ASANVLQALRRVEGVGKVQFWGAE-YAMRIWPDPVKLAALGLTASDIASAVRAHN 210 (1032)
T ss_pred HHHHHHHHHhcCCCcEEEEecCCc-eEEEEEeCHHHHHHcCCCHHHHHHHHHHhC
Confidence 356788999999999999999854 466663 23567778888998743
No 43
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=33.34 E-value=75 Score=21.35 Aligned_cols=42 Identities=21% Similarity=0.280 Sum_probs=30.4
Q ss_pred CCccccceeEEEEEeecc-hhhHHHHHHHhcCCCceeEEEecC
Q 041984 15 GPMSFLNGKVVIKLSLEG-HKSRSKALKIAVRVSGVESVALKG 56 (98)
Q Consensus 15 ~p~~~m~qkvVlKV~m~c-e~C~~Kv~k~i~~~~GV~SV~id~ 56 (98)
-|.+.--+.+.+.+-|.+ +|---.+-..+..++||+|+++..
T Consensus 42 epIaFGLkal~l~vvv~D~Eg~td~~ee~l~~vegV~sveve~ 84 (88)
T COG2092 42 EPIAFGLKALKLYVVVEDKEGGTDALEEALEEVEGVESVEVEN 84 (88)
T ss_pred EeeeeeeeeEEEEEEEcccccCcHHHHHHHhhccCcceEEEEE
Confidence 344444456666666654 566788999999999999999853
No 44
>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=33.29 E-value=1.2e+02 Score=18.89 Aligned_cols=64 Identities=23% Similarity=0.254 Sum_probs=44.2
Q ss_pred EEEEEeecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcCCceEEEEcc
Q 041984 24 VVIKLSLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTMRFAELLTVI 91 (98)
Q Consensus 24 vVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~~~aeivsv~ 91 (98)
+.+||.. ...-+..+.+.+..+.| .=+++..+. =.+.++|+.-....+++.|++ ++-.|+..-|
T Consensus 5 ~LiKV~~-~~~~r~ei~~l~~~f~a-~ivd~~~~~-~iie~tG~~~kid~fi~~l~~-~gi~Ei~RtG 68 (75)
T PF10369_consen 5 ALIKVKA-TPENRSEILQLAEIFRA-RIVDVSPDS-IIIELTGTPEKIDAFIKLLKP-FGILEIARTG 68 (75)
T ss_dssp EEEEEE--SCHHHHHHHHHHHHTT--EEEEEETTE-EEEEEEE-HHHHHHHHHHSTG-GGEEEEEEEE
T ss_pred EEEEEEC-CccCHHHHHHHHHHhCC-EEEEECCCE-EEEEEcCCHHHHHHHHHHhhh-cCCEEEEccc
Confidence 5678877 56788888888888766 666776644 477789985556777888887 7777776543
No 45
>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=33.19 E-value=67 Score=18.80 Aligned_cols=30 Identities=17% Similarity=0.129 Sum_probs=23.1
Q ss_pred HHHHHHHhcCCCceeEEEecCCCCCeEEEE
Q 041984 36 RSKALKIAVRVSGVESVALKGDDRSQIEVT 65 (98)
Q Consensus 36 ~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~ 65 (98)
..++.+.+.+++.|.++++...--|++.|.
T Consensus 36 ~~~~~~~l~~~p~V~~v~V~r~~P~~l~I~ 65 (69)
T PF08478_consen 36 LKKIEQRLEKLPWVKSVSVSRRFPNTLEIK 65 (69)
T ss_dssp HHHHHHCCCCTTTEEEEEEEEETTTEEEEE
T ss_pred HHHHHHHHHcCCCEEEEEEEEeCCCEEEEE
Confidence 456778888999999999976555677653
No 46
>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=33.09 E-value=58 Score=21.38 Aligned_cols=29 Identities=24% Similarity=0.224 Sum_probs=20.2
Q ss_pred eEEEEecccCHHHHHHHHHhcCCceEEEEc
Q 041984 61 QIEVTGDGMDPVLLTSLLRKTMRFAELLTV 90 (98)
Q Consensus 61 kvtV~G~~vDp~~lv~kLrKk~~~aeivsv 90 (98)
=+.|+|+ -|-..++++||.+..++.++..
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 5678898 9999999999986558888884
No 47
>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=32.89 E-value=1.1e+02 Score=17.94 Aligned_cols=32 Identities=6% Similarity=0.071 Sum_probs=25.3
Q ss_pred eEEEEEeecchhhHHHHHHHhcCCCceeEEEe
Q 041984 23 KVVIKLSLEGHKSRSKALKIAVRVSGVESVAL 54 (98)
Q Consensus 23 kvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~i 54 (98)
.+-+.+......--..+++.+.+++||...++
T Consensus 41 ~~~~~vev~~~~~l~~i~~~L~~i~gV~~~~~ 72 (74)
T cd04887 41 VRDITVDAPSEEHAETIVAAVRALPEVKVLSV 72 (74)
T ss_pred EEEEEEEcCCHHHHHHHHHHHhcCCCeEEEEe
Confidence 34556666777788899999999999988766
No 48
>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=32.30 E-value=48 Score=20.58 Aligned_cols=22 Identities=23% Similarity=0.323 Sum_probs=16.7
Q ss_pred CCeEEEEecccCHHHHHHHHHh
Q 041984 59 RSQIEVTGDGMDPVLLTSLLRK 80 (98)
Q Consensus 59 k~kvtV~G~~vDp~~lv~kLrK 80 (98)
.++++++|.++|...|-+.|..
T Consensus 71 ~~~lV~IG~~ld~~~l~~~l~~ 92 (94)
T PF07683_consen 71 DSRLVFIGKNLDKEALREALDA 92 (94)
T ss_dssp -EEEEEEEES--HHHHHHHHHT
T ss_pred CeEEEEEECCCCHHHHHHHHHc
Confidence 4699999999999999888764
No 49
>KOG1651 consensus Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones]
Probab=31.14 E-value=51 Score=24.66 Aligned_cols=54 Identities=28% Similarity=0.370 Sum_probs=38.3
Q ss_pred eEEEEEee-cCCccccceeEEEEEeecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHh
Q 041984 6 LELVFTCT-YGPMSFLNGKVVIKLSLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRK 80 (98)
Q Consensus 6 ~~~~~~~~-~~p~~~m~qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrK 80 (98)
.+|+|-|+ |+-+- .++...++.-+....|++- ..- +|+.|.|+ .+.-|-+.|++
T Consensus 69 ~ILaFPCNQFg~QE--------------p~~n~Ei~~f~~~r~~~~f---~if--~KidVNG~--~~~PlykfLK~ 123 (171)
T KOG1651|consen 69 EILAFPCNQFGNQE--------------PGSNEEILNFVKVRYGAEF---PIF--QKIDVNGD--NADPLYKFLKK 123 (171)
T ss_pred EEEEeccccccCcC--------------CCCcHHHHHHHHhccCCCC---ccE--eEEecCCC--CCchHHHHHhh
Confidence 47899998 55333 3778888888887778765 444 49999998 44446666665
No 50
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=31.09 E-value=1.1e+02 Score=22.26 Aligned_cols=42 Identities=10% Similarity=0.159 Sum_probs=29.0
Q ss_pred ceeEEEEEe-ecchhhHHHHHHHhcCCCceeEEEecCCCCCeEE
Q 041984 21 NGKVVIKLS-LEGHKSRSKALKIAVRVSGVESVALKGDDRSQIE 63 (98)
Q Consensus 21 ~qkvVlKV~-m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvt 63 (98)
...+.+.|+ --|.-|+.-+.+.+.++ |+++++|-..+.+++.
T Consensus 99 g~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 99 GRSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred CCeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 467788887 33999996666555554 9999999765334443
No 51
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=30.58 E-value=51 Score=26.19 Aligned_cols=33 Identities=15% Similarity=0.258 Sum_probs=26.4
Q ss_pred eEEEEEeecchhhHHHHHHHhcCCCceeEEEecC
Q 041984 23 KVVIKLSLEGHKSRSKALKIAVRVSGVESVALKG 56 (98)
Q Consensus 23 kvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~ 56 (98)
.+-|..+.+ +.|+..+...+..++||.|+..-.
T Consensus 62 ~vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~~s 94 (297)
T COG2177 62 TVYLQIDAD-QDDAALVREKIEGIPGVKSVRFIS 94 (297)
T ss_pred EEEEecCCC-hHHHHHHHHHHhcCCCcceEEEeC
Confidence 455555555 888999999999999999998743
No 52
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating [].
Probab=30.24 E-value=1.2e+02 Score=17.93 Aligned_cols=42 Identities=12% Similarity=0.186 Sum_probs=24.3
Q ss_pred eEEEecCCCCCeEEEEecccCHHHHH---HHHHhcC--CceEEEEccCCC
Q 041984 50 ESVALKGDDRSQIEVTGDGMDPVLLT---SLLRKTM--RFAELLTVINLK 94 (98)
Q Consensus 50 ~SV~id~~~k~kvtV~G~~vDp~~lv---~kLrKk~--~~aeivsv~p~k 94 (98)
++++++. +++++.|..-+...+. ..|++.- ..+++.++....
T Consensus 17 ~~l~~~~---~~l~i~G~a~~~~~v~~f~~~L~~~~~f~~v~l~~~~~~~ 63 (78)
T PF05137_consen 17 TSLSING---NTLSISGYADSYQSVAAFLRNLEQSPFFSDVSLSSISRQE 63 (78)
T ss_pred EEEEEeC---CEEEEEEEECCHHHHHHHHHHHhhCCCccceEEEEEEeec
Confidence 4555543 6999999965555554 4454311 256666655443
No 53
>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=29.30 E-value=1.7e+02 Score=19.16 Aligned_cols=45 Identities=18% Similarity=0.196 Sum_probs=34.6
Q ss_pred eecCCccccceeEEEEEeecch-hhHHHHHHHh-cCCCceeEEEecC
Q 041984 12 CTYGPMSFLNGKVVIKLSLEGH-KSRSKALKIA-VRVSGVESVALKG 56 (98)
Q Consensus 12 ~~~~p~~~m~qkvVlKV~m~ce-~C~~Kv~k~i-~~~~GV~SV~id~ 56 (98)
+-.-|.+.-.+...+.+-+.++ +--..+-..+ +..+||.|+++..
T Consensus 39 ~~~epIaFGlk~L~v~~vv~D~~~~~d~lee~i~~~~e~Vqsvei~~ 85 (89)
T PF00736_consen 39 SKEEPIAFGLKALQVSCVVEDDEGSTDDLEEAIESFEEGVQSVEIES 85 (89)
T ss_dssp EEEEEECTTEEEEEEEEEECTTTCGHHHHHHHHTTCTTTEEEEEEEE
T ss_pred eeeeeecccEEEEEEEEEEEcCccChHHHHHHHHhcCCCccEEEEEE
Confidence 4455666656777777777775 6678888899 9999999999864
No 54
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=28.41 E-value=1.2e+02 Score=19.91 Aligned_cols=58 Identities=21% Similarity=0.259 Sum_probs=38.9
Q ss_pred eceEEEEEeecCCccccceeEEEEEeecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecc--cCHHHHHHHHHhc
Q 041984 4 SNLELVFTCTYGPMSFLNGKVVIKLSLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDG--MDPVLLTSLLRKT 81 (98)
Q Consensus 4 ~~~~~~~~~~~~p~~~m~qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~--vDp~~lv~kLrKk 81 (98)
.++++.-||++. +...+++++.+.++.... .. . -++.|+|=- .++ +.|++.
T Consensus 37 AD~iiiNTC~V~-----------------~~Ae~k~~~~i~~l~~~~----~~-~-~~ivv~GC~aq~~~----~~l~~~ 89 (98)
T PF00919_consen 37 ADVIIINTCTVR-----------------ESAEQKSRNRIRKLKKLK----KP-G-AKIVVTGCMAQRYG----EELKKE 89 (98)
T ss_pred CCEEEEEcCCCC-----------------cHHHHHHHHHHHHHHHhc----CC-C-CEEEEEeCccccCh----HHHHhh
Confidence 367777888877 567777777777766555 22 2 489999962 344 556666
Q ss_pred CCceEEE
Q 041984 82 MRFAELL 88 (98)
Q Consensus 82 ~~~aeiv 88 (98)
.+++++|
T Consensus 90 ~p~vd~v 96 (98)
T PF00919_consen 90 FPEVDLV 96 (98)
T ss_pred CCCeEEE
Confidence 6777776
No 55
>PRK13760 putative RNA-associated protein; Provisional
Probab=28.16 E-value=2e+02 Score=22.36 Aligned_cols=66 Identities=17% Similarity=0.154 Sum_probs=41.7
Q ss_pred CccccceeEEEEEeecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCH---HHHHHHHHhcCC-ceEE
Q 041984 16 PMSFLNGKVVIKLSLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDP---VLLTSLLRKTMR-FAEL 87 (98)
Q Consensus 16 p~~~m~qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp---~~lv~kLrKk~~-~aei 87 (98)
|...+ ++.++|.+. .....++...+.++-.+.+-+.+.+ +.++.++. +|| ..+.+.|++.++ .+++
T Consensus 158 Pi~~~--~~~~~v~iP-~~~~~~~~~~l~~~~~i~~eew~~d--gs~~~v~~-Ip~G~~~~~~~~~~~~tkG~~~~ 227 (231)
T PRK13760 158 PIKFE--KARIAVKIP-PEYAGKAYGELRKFGEIKKEEWQSD--GSWIAVLE-IPAGLQNEFYDKLNKLTKGEAET 227 (231)
T ss_pred Cccee--eEEEEEEEC-HHHHHHHHHHHHhhcccchhhccCC--CcEEEEEE-ECCccHHHHHHHHHHhcCCcEEE
Confidence 55553 344444443 2336677777777766776666553 47888888 887 677777777663 5543
No 56
>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=27.90 E-value=64 Score=21.33 Aligned_cols=53 Identities=4% Similarity=0.057 Sum_probs=30.7
Q ss_pred ecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcCCceEEEEccCC
Q 041984 30 LEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTMRFAELLTVINL 93 (98)
Q Consensus 30 m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~~~aeivsv~p~ 93 (98)
+.|+. .+...+..+ =+.+ ++.++++.+. +|.-++++.+++.++++++-..||.
T Consensus 29 i~~~~---~~~~klk~l-~i~~--~~~~d~~r~V-----isvm~II~~I~~~~p~l~I~~iGe~ 81 (93)
T PF12164_consen 29 IYCDD---EIENKLKAL-PIYK--IKKKDKNRYV-----ISVMKIIEKIQEEYPNLDIQNIGET 81 (93)
T ss_dssp EEESS---HHHHHHHTS-EEEE---BTTT--EEE-----EEHHHHHHHHHHH-SSEEEEE-S-S
T ss_pred EEeCH---HHHHHhhcc-Eeee--ecCCCCCEEE-----EEHHHHHHHHHHHCCCcEEEEcCCC
Confidence 44555 444444444 2333 3444443333 5788999999999999999998875
No 57
>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=27.60 E-value=72 Score=19.10 Aligned_cols=23 Identities=26% Similarity=0.212 Sum_probs=18.8
Q ss_pred CeEEEEecccCHHHHHHHHHhcC
Q 041984 60 SQIEVTGDGMDPVLLTSLLRKTM 82 (98)
Q Consensus 60 ~kvtV~G~~vDp~~lv~kLrKk~ 82 (98)
+.++|.|..-.|.++.++|.+|.
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 47889997678999999998765
No 58
>PHA01634 hypothetical protein
Probab=27.55 E-value=25 Score=25.85 Aligned_cols=12 Identities=8% Similarity=0.044 Sum_probs=9.7
Q ss_pred eecchhhHHHHH
Q 041984 29 SLEGHKSRSKAL 40 (98)
Q Consensus 29 ~m~ce~C~~Kv~ 40 (98)
-|+||||++++-
T Consensus 97 ~iDCeGCE~~l~ 108 (156)
T PHA01634 97 VMDCEGCEEKLN 108 (156)
T ss_pred EEEccchHHhcC
Confidence 478999998764
No 59
>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=27.48 E-value=1.3e+02 Score=19.22 Aligned_cols=29 Identities=31% Similarity=0.479 Sum_probs=23.1
Q ss_pred ceeEEEecC-CCCCeEEEEecccCHHHHHHHHH
Q 041984 48 GVESVALKG-DDRSQIEVTGDGMDPVLLTSLLR 79 (98)
Q Consensus 48 GV~SV~id~-~~k~kvtV~G~~vDp~~lv~kLr 79 (98)
|-+.+++.. .. ++++|.|. ++..+..-|.
T Consensus 30 ~~d~F~l~~~~~-gki~I~G~--s~vala~Gl~ 59 (86)
T PF12971_consen 30 GKDVFELSSADN-GKIVIRGN--SGVALASGLN 59 (86)
T ss_dssp TBEEEEEEE-SS-S-EEEEES--SHHHHHHHHH
T ss_pred CCCEEEEEeCCC-CeEEEEeC--CHHHHHHHHH
Confidence 888888886 55 79999998 8888887765
No 60
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=27.18 E-value=1.3e+02 Score=27.56 Aligned_cols=46 Identities=17% Similarity=0.128 Sum_probs=34.7
Q ss_pred hHHHHHHHhcCCCceeEEEecCCCCCeEEEEe-------cccCHHHHHHHHHhc
Q 041984 35 SRSKALKIAVRVSGVESVALKGDDRSQIEVTG-------DGMDPVLLTSLLRKT 81 (98)
Q Consensus 35 C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G-------~~vDp~~lv~kLrKk 81 (98)
-+..++..+.+++||.+|++.+.+ .++.|.= .++++..+.+.|+..
T Consensus 158 ~~~~l~~~L~~v~GV~~V~~~G~~-~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 158 VASNIQDPLSRVNGVGDIDAYGSQ-YSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHHhhcCCCeEEEEEcCCc-eEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 456788899999999999999864 4565542 256778888888863
No 61
>PRK11023 outer membrane lipoprotein; Provisional
Probab=26.93 E-value=1.5e+02 Score=21.59 Aligned_cols=47 Identities=6% Similarity=0.112 Sum_probs=31.1
Q ss_pred eecchhhHHHHHHHhcCCCcee---EEEecCCCCCeEEEEecccCHHHHHHH
Q 041984 29 SLEGHKSRSKALKIAVRVSGVE---SVALKGDDRSQIEVTGDGMDPVLLTSL 77 (98)
Q Consensus 29 ~m~ce~C~~Kv~k~i~~~~GV~---SV~id~~~k~kvtV~G~~vDp~~lv~k 77 (98)
.+.+..-+.++...+..-+++. .+.+.-.. +.++.+|+ ++....-.+
T Consensus 44 ~~dD~~i~~~V~~aL~~~~~l~~~~~I~V~v~~-G~V~L~G~-V~~~~~k~~ 93 (191)
T PRK11023 44 QVDDGTLELRVNNALSKDEQIKKEARINVTAYQ-GKVLLTGQ-SPNAELSER 93 (191)
T ss_pred eehhHHHHHHHHHHHhhCcccCcCceEEEEEEC-CEEEEEEE-eCCHHHHHH
Confidence 3456667788888887666663 46666654 68888888 765544333
No 62
>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=26.10 E-value=1.1e+02 Score=18.72 Aligned_cols=22 Identities=18% Similarity=0.368 Sum_probs=18.5
Q ss_pred CCeEEEEecccCHHHHHHHHHh
Q 041984 59 RSQIEVTGDGMDPVLLTSLLRK 80 (98)
Q Consensus 59 k~kvtV~G~~vDp~~lv~kLrK 80 (98)
.++++++|.++|...|-+.|..
T Consensus 69 ~~~lV~IG~~l~~~~l~~~l~~ 90 (92)
T smart00833 69 RTRLVFIGRDLDEEAIRAALDA 90 (92)
T ss_pred ceEEEEEeCCCCHHHHHHHHHH
Confidence 3689999999999988887764
No 63
>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=25.99 E-value=2.1e+02 Score=19.10 Aligned_cols=56 Identities=16% Similarity=0.182 Sum_probs=35.8
Q ss_pred eeEEEEEeecchhhHHHHHHHhcCCCceeEEEe-cC-----CCCCeEEEEecccCHHHHHHHHHhc
Q 041984 22 GKVVIKLSLEGHKSRSKALKIAVRVSGVESVAL-KG-----DDRSQIEVTGDGMDPVLLTSLLRKT 81 (98)
Q Consensus 22 qkvVlKV~m~ce~C~~Kv~k~i~~~~GV~SV~i-d~-----~~k~kvtV~G~~vDp~~lv~kLrKk 81 (98)
.+|||+++ .+.--..+.+.+.. .|+....+ |- .. |..||.|-|-.|...++++-++
T Consensus 51 ~Kivlkv~--~e~~L~~l~~~a~~-~gl~~~~i~Dag~Tei~p-gs~TvlaigP~~~~~i~~it~~ 112 (116)
T PF01981_consen 51 KKIVLKVP--SEEELLELAKKAKE-AGLPHYLIRDAGRTEIPP-GSVTVLAIGPAPKEEIDKITGH 112 (116)
T ss_dssp SEEEEEES--SHHHHHHHHHHHHH-TT-SEEEEEETSSSSSST-TCEEEEEEEEEEHHHHHHHHTT
T ss_pred ceEEEEeC--CHHHHHHHHHHHHH-CCCCEEEEEECCCCcCCC-CCeEEEEECcCCHHHHHHHhCc
Confidence 78999987 34444444444443 45554444 32 22 5789999888999999888654
No 64
>PRK13748 putative mercuric reductase; Provisional
Probab=25.73 E-value=3.2e+02 Score=22.55 Aligned_cols=60 Identities=17% Similarity=0.211 Sum_probs=41.8
Q ss_pred eecchhhHHHHHHHhcCCCceeEEEecCCCCCeEEEEec-ccCHHHHHHHHHhcCC-ceEEEEc
Q 041984 29 SLEGHKSRSKALKIAVRVSGVESVALKGDDRSQIEVTGD-GMDPVLLTSLLRKTMR-FAELLTV 90 (98)
Q Consensus 29 ~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G~-~vDp~~lv~kLrKk~~-~aeivsv 90 (98)
.++|..|..++...+...+|+.+...+... +...+... ..++..+...+.. .+ .++....
T Consensus 8 g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~-~~~~v~~~~~~~~~~i~~~i~~-~g~~~~~~~~ 69 (561)
T PRK13748 8 GMTCDSCAAHVKDALEKVPGVQSADVSYPK-GSAQLAIEVGTSPDALTAAVAG-LGYRATLADA 69 (561)
T ss_pred CeecHHHHHHHHHHHhcCCCeeEEEEEcCC-CEEEEEECCCCCHHHHHHHHHH-cCCeeeccCc
Confidence 578999999999999999999988887755 46555531 2466666666654 44 4554444
No 65
>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=25.55 E-value=1.2e+02 Score=17.64 Aligned_cols=33 Identities=12% Similarity=0.116 Sum_probs=23.2
Q ss_pred hhhHHHHHHHhcCCCceeEEEecCCCCCeEEEE
Q 041984 33 HKSRSKALKIAVRVSGVESVALKGDDRSQIEVT 65 (98)
Q Consensus 33 e~C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~ 65 (98)
..=.|++...++...|+.|-+.+.+.+-.|+|.
T Consensus 29 ~~~~R~~iH~~a~~~gL~s~S~g~~~~R~vvv~ 61 (63)
T PF01424_consen 29 NSFERKLIHELAEYYGLKSKSEGEGPNRRVVVS 61 (63)
T ss_dssp -SHHHHHHHHHHHHCTEEEEEESSSSSSEEEEE
T ss_pred CHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEE
Confidence 466677777777799999999986543245553
No 66
>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=25.48 E-value=1.3e+02 Score=18.88 Aligned_cols=30 Identities=13% Similarity=0.277 Sum_probs=21.8
Q ss_pred hHHHHHHHhcCCCceeEEEecCCCCCeEEE
Q 041984 35 SRSKALKIAVRVSGVESVALKGDDRSQIEV 64 (98)
Q Consensus 35 C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV 64 (98)
=.|++...++...|++|.+.|.+.+-.|.|
T Consensus 43 ~eR~iIH~la~~~~l~S~S~G~ep~R~VvI 72 (74)
T cd02643 43 EKRRIVHELAEHFGIESVSYDQEPKRNVVA 72 (74)
T ss_pred HHHHHHHHHHhhCCCEEEecCCCCCceEEE
Confidence 456666678889999999998766434433
No 67
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=25.42 E-value=1.2e+02 Score=20.70 Aligned_cols=40 Identities=28% Similarity=0.479 Sum_probs=27.6
Q ss_pred HHHHhcCCCceeEEEecCCCCCeEEEEecccCHHHHHHHHHhcC
Q 041984 39 ALKIAVRVSGVESVALKGDDRSQIEVTGDGMDPVLLTSLLRKTM 82 (98)
Q Consensus 39 v~k~i~~~~GV~SV~id~~~k~kvtV~G~~vDp~~lv~kLrKk~ 82 (98)
+++.+..==|. +.++|++ +++++.|. +++..+-+.|++..
T Consensus 38 v~kyl~~ELgt-~g~id~~--~rlii~G~-~~~~~i~~~l~~yI 77 (110)
T smart00653 38 VLKFLLAELGT-QGSIDGK--GRLIVNGR-FTPKKLQDLLRRYI 77 (110)
T ss_pred HHHHHHHHhCC-ceeECCC--CeEEEEEe-eCHHHHHHHHHHHH
Confidence 34444432233 3466764 69999998 99999999998743
No 68
>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=24.83 E-value=1.2e+02 Score=24.10 Aligned_cols=46 Identities=15% Similarity=0.215 Sum_probs=33.4
Q ss_pred EEeecchhhHHHHHHHhcCCCceeEEEecCCC----------CCeEEEEecccCHHHH
Q 041984 27 KLSLEGHKSRSKALKIAVRVSGVESVALKGDD----------RSQIEVTGDGMDPVLL 74 (98)
Q Consensus 27 KV~m~ce~C~~Kv~k~i~~~~GV~SV~id~~~----------k~kvtV~G~~vDp~~l 74 (98)
.+-+|..|........+... |++.+.+|... .+++++-|+ +||.-|
T Consensus 214 piilH~cG~~~~~l~~~~e~-g~dvl~~d~~~~dl~eak~~~g~k~~l~GN-lDp~~L 269 (321)
T cd03309 214 LIVHHSCGAAASLVPSMAEM-GVDSWNVVMTANNTAELRRLLGDKVVLAGA-IDDVAL 269 (321)
T ss_pred ceEEEeCCCcHHHHHHHHHc-CCCEEEecCCCCCHHHHHHHhCCCeEEEcC-CChHHh
Confidence 45567777766677777766 88888887643 247999998 998544
No 69
>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=23.72 E-value=92 Score=17.24 Aligned_cols=19 Identities=21% Similarity=0.272 Sum_probs=16.5
Q ss_pred HHHHHHHhcCCCceeEEEe
Q 041984 36 RSKALKIAVRVSGVESVAL 54 (98)
Q Consensus 36 ~~Kv~k~i~~~~GV~SV~i 54 (98)
-..+++.+.+++||.++..
T Consensus 52 ~~~l~~~l~~~~~V~~v~~ 70 (71)
T cd04879 52 PEEVLEELKALPGIIRVRL 70 (71)
T ss_pred CHHHHHHHHcCCCeEEEEE
Confidence 5689999999999999863
No 70
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=22.82 E-value=1.6e+02 Score=27.14 Aligned_cols=45 Identities=20% Similarity=0.219 Sum_probs=33.2
Q ss_pred hHHHHHHHhcCCCceeEEEecCCCCCeEEEEe-------cccCHHHHHHHHHh
Q 041984 35 SRSKALKIAVRVSGVESVALKGDDRSQIEVTG-------DGMDPVLLTSLLRK 80 (98)
Q Consensus 35 C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G-------~~vDp~~lv~kLrK 80 (98)
-+..++..+.+++||.+|++.+.+ .++.|.= .++++.++.+.|+.
T Consensus 158 ~~~~l~~~L~~v~GV~~V~~~G~~-~ei~V~vDp~kl~~~gls~~~V~~~l~~ 209 (1049)
T PRK15127 158 VAANMKDPISRTSGVGDVQLFGSQ-YAMRIWMNPNELNKFQLTPVDVINAIKA 209 (1049)
T ss_pred HHHHHHHHHhcCCCceEEEEcCCc-eEEEEEeCHHHHHHcCCCHHHHHHHHHH
Confidence 345688999999999999999864 4566542 24566777788884
No 71
>COG0612 PqqL Predicted Zn-dependent peptidases [General function prediction only]
Probab=22.67 E-value=78 Score=25.25 Aligned_cols=23 Identities=26% Similarity=0.374 Sum_probs=20.7
Q ss_pred CeEEEEecccCHHHHHHHHHhcCC
Q 041984 60 SQIEVTGDGMDPVLLTSLLRKTMR 83 (98)
Q Consensus 60 ~kvtV~G~~vDp~~lv~kLrKk~~ 83 (98)
=.|.|+|+ +|+..+...+.+.++
T Consensus 199 ~~l~vvGd-i~~~~v~~~~~~~f~ 221 (438)
T COG0612 199 MVLVVVGD-VDAEEVVELIEKYFG 221 (438)
T ss_pred eEEEEecC-CCHHHHHHHHHHHHc
Confidence 37889998 999999999999887
No 72
>PF15174 PRNT: Prion-related protein testis-specific
Probab=22.38 E-value=14 Score=22.35 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=14.8
Q ss_pred EEEEeecchhhHHHHHHH
Q 041984 25 VIKLSLEGHKSRSKALKI 42 (98)
Q Consensus 25 VlKV~m~ce~C~~Kv~k~ 42 (98)
.|..+.+|+.|.||.+|+
T Consensus 32 ~LqiPvDcQACnRkskki 49 (51)
T PF15174_consen 32 HLQIPVDCQACNRKSKKI 49 (51)
T ss_pred hhcCCcchhhhcccccee
Confidence 477889999999987764
No 73
>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=22.34 E-value=1.7e+02 Score=26.84 Aligned_cols=45 Identities=20% Similarity=0.235 Sum_probs=35.2
Q ss_pred hHHHHHHHhcCCCceeEEEecCCCCCeEEEEe-------cccCHHHHHHHHHh
Q 041984 35 SRSKALKIAVRVSGVESVALKGDDRSQIEVTG-------DGMDPVLLTSLLRK 80 (98)
Q Consensus 35 C~~Kv~k~i~~~~GV~SV~id~~~k~kvtV~G-------~~vDp~~lv~kLrK 80 (98)
-+..++..+.+++||..|++.+. +.++.|.= .++++.++.+.|+.
T Consensus 158 ~~~~l~~~L~~v~GV~~V~~~G~-~~ei~V~vD~~kl~~~gls~~dV~~~i~~ 209 (1044)
T TIGR00915 158 IASNMVDPISRLEGVGDVQLFGS-QYAMRIWLDPAKLNSYQLTPADVISAIQA 209 (1044)
T ss_pred HHHHHHHHHhCCCCceEEEecCC-ceEEEEEECHHHHHHcCCCHHHHHHHHHH
Confidence 44678899999999999999987 45666652 25677888888886
No 74
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=22.33 E-value=1.7e+02 Score=19.14 Aligned_cols=43 Identities=19% Similarity=0.227 Sum_probs=31.5
Q ss_pred cCCccccceeEEEEEeecch-hhHHHHHHHhcCCCceeEEEecC
Q 041984 14 YGPMSFLNGKVVIKLSLEGH-KSRSKALKIAVRVSGVESVALKG 56 (98)
Q Consensus 14 ~~p~~~m~qkvVlKV~m~ce-~C~~Kv~k~i~~~~GV~SV~id~ 56 (98)
..|.+.--++.-+.+-+.++ +--..+-..++..+||.|+++..
T Consensus 41 ~epiaFGlk~L~i~~vv~D~~~~td~lee~i~~~d~VqsveI~~ 84 (88)
T cd00292 41 LEPIAFGLKALQIYCVVEDDEGGTDELEEAISEEDGVQSVDVEA 84 (88)
T ss_pred EEEeeeEeeEEEEEEEEEeCCcCcHHHHHHHhccCCceEEEEEE
Confidence 44555555666666666655 55578888899999999999865
No 75
>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=21.61 E-value=1.4e+02 Score=19.01 Aligned_cols=21 Identities=24% Similarity=0.213 Sum_probs=17.3
Q ss_pred HHHHHHHhcCCCceeEEEecC
Q 041984 36 RSKALKIAVRVSGVESVALKG 56 (98)
Q Consensus 36 ~~Kv~k~i~~~~GV~SV~id~ 56 (98)
+..+..++..++|++++.++.
T Consensus 57 ~~~i~~al~~l~gv~~v~v~i 77 (99)
T TIGR02945 57 PGEVENAVRAVPGVGSVTVEL 77 (99)
T ss_pred HHHHHHHHHhCCCCceEEEEE
Confidence 355788889999999999865
No 76
>PF01876 RNase_P_p30: RNase P subunit p30; InterPro: IPR002738 Members of this protein family are part of the ribonuclease P complex () that takes part in endonucleolytic cleavage of RNA, removing 5'-extra-nucleotide from tRNA precursor. This process is essential for tRNA processing.; GO: 0004540 ribonuclease activity, 0008033 tRNA processing; PDB: 1V77_A 2CZV_A.
Probab=20.82 E-value=90 Score=21.58 Aligned_cols=34 Identities=21% Similarity=0.254 Sum_probs=20.4
Q ss_pred eEEEEecccCHHHHHHHHHhcCCceEEEEccCCCCC
Q 041984 61 QIEVTGDGMDPVLLTSLLRKTMRFAELLTVINLKPK 96 (98)
Q Consensus 61 kvtV~G~~vDp~~lv~kLrKk~~~aeivsv~p~kek 96 (98)
++|+.=+ |+..+...+++.....+|+++.|..++
T Consensus 3 R~ti~~~--d~~~~~~~~~~~~~~~divav~p~~~~ 36 (150)
T PF01876_consen 3 RLTIVAS--DPSSLRRSLSKFRKKYDIVAVRPGSEK 36 (150)
T ss_dssp SEEEEEE--S--HHHHHHHHTTT--SEEEEE-S-HH
T ss_pred cEEEEEc--CHHHHHHHhhcccCCceEEEEEcCCHH
Confidence 5677766 665677788876668999999887653
No 77
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=20.22 E-value=1.6e+02 Score=21.67 Aligned_cols=34 Identities=18% Similarity=0.239 Sum_probs=25.6
Q ss_pred eEEEEEeecchhhH------HHHHHHhcCCCceeEEEecC
Q 041984 23 KVVIKLSLEGHKSR------SKALKIAVRVSGVESVALKG 56 (98)
Q Consensus 23 kvVlKV~m~ce~C~------~Kv~k~i~~~~GV~SV~id~ 56 (98)
++.+.+.+...+|. ..+..++..++||+++.++.
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 56677766655554 45888899999999988864
Done!