Query 033646
Match_columns 114
No_of_seqs 189 out of 802
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:40:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033646.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033646hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1603 Copper chaperone [Inor 98.9 3.1E-09 6.8E-14 69.1 5.5 45 2-46 24-70 (73)
2 PF00403 HMA: Heavy-metal-asso 98.3 1.2E-06 2.6E-11 54.1 4.3 40 2-41 18-60 (62)
3 COG2608 CopZ Copper chaperone 97.3 0.00039 8.5E-09 44.9 4.2 44 2-45 22-69 (71)
4 KOG4656 Copper chaperone for s 97.0 0.0015 3.2E-08 51.6 5.0 48 2-49 26-74 (247)
5 PLN02957 copper, zinc superoxi 95.6 0.037 7.9E-07 43.2 6.0 50 3-52 26-76 (238)
6 PF02680 DUF211: Uncharacteriz 92.7 0.13 2.9E-06 35.7 3.0 40 2-41 24-71 (95)
7 COG1888 Uncharacterized protei 91.1 0.36 7.8E-06 33.5 3.7 40 2-41 26-73 (97)
8 PRK10671 copA copper exporting 90.0 0.41 8.9E-06 43.3 4.2 44 2-47 23-67 (834)
9 PF13732 DUF4162: Domain of un 77.8 8.3 0.00018 24.4 5.1 40 3-42 25-65 (84)
10 TIGR00003 copper ion binding p 63.2 21 0.00045 18.9 4.6 39 3-41 23-64 (68)
11 COG1432 Uncharacterized conser 62.5 6.5 0.00014 29.4 2.2 35 16-50 109-144 (181)
12 PF04972 BON: BON domain; Int 62.1 9.7 0.00021 22.9 2.7 31 7-38 14-44 (64)
13 KOG0207 Cation transport ATPas 61.3 12 0.00026 35.3 4.1 48 2-49 14-64 (951)
14 COG4004 Uncharacterized protei 58.8 18 0.00039 25.1 3.7 24 3-26 35-58 (96)
15 cd06471 ACD_LpsHSP_like Group 57.5 9.4 0.0002 24.9 2.1 26 4-29 15-42 (93)
16 cd06167 LabA_like LabA_like pr 55.2 18 0.0004 25.0 3.4 29 21-49 103-132 (149)
17 COG2217 ZntA Cation transport 54.9 20 0.00044 32.6 4.4 43 3-45 22-69 (713)
18 PRK10671 copA copper exporting 54.5 18 0.0004 32.8 4.1 44 3-46 120-164 (834)
19 COG0071 IbpA Molecular chapero 49.9 12 0.00027 26.6 1.9 28 3-30 54-83 (146)
20 PHA00514 dsDNA binding protein 49.7 43 0.00092 23.2 4.4 31 21-51 33-66 (98)
21 cd06482 ACD_HspB10 Alpha cryst 49.1 17 0.00036 24.3 2.3 24 5-28 14-39 (87)
22 smart00653 eIF2B_5 domain pres 48.0 34 0.00074 23.9 3.8 28 13-41 50-77 (110)
23 PF01936 NYN: NYN domain; Int 48.0 21 0.00046 24.2 2.8 29 20-48 98-127 (146)
24 cd06475 ACD_HspB1_like Alpha c 47.5 20 0.00044 23.5 2.5 24 5-28 16-41 (86)
25 TIGR00288 conserved hypothetic 47.4 27 0.00059 26.1 3.4 29 20-48 108-137 (160)
26 cd06464 ACD_sHsps-like Alpha-c 46.5 17 0.00038 22.4 2.0 27 4-30 12-40 (88)
27 PRK10743 heat shock protein Ib 42.8 23 0.00049 25.6 2.3 24 5-28 51-76 (137)
28 cd06470 ACD_IbpA-B_like Alpha- 42.6 26 0.00056 22.9 2.5 24 5-28 17-42 (90)
29 cd06477 ACD_HspB3_Like Alpha c 41.9 26 0.00056 23.1 2.4 24 5-28 13-38 (83)
30 PRK11597 heat shock chaperone 40.9 25 0.00053 25.7 2.3 25 4-28 48-74 (142)
31 cd06497 ACD_alphaA-crystallin_ 40.4 30 0.00064 22.7 2.5 24 5-28 16-41 (86)
32 KOG0207 Cation transport ATPas 40.0 53 0.0011 31.1 4.7 46 3-48 167-216 (951)
33 TIGR01676 GLDHase galactonolac 39.6 46 0.001 29.4 4.1 36 4-41 110-145 (541)
34 cd06478 ACD_HspB4-5-6 Alpha-cr 39.0 33 0.00072 22.2 2.5 23 5-27 13-37 (83)
35 cd06476 ACD_HspB2_like Alpha c 38.9 31 0.00068 22.6 2.4 25 5-29 13-39 (83)
36 cd00298 ACD_sHsps_p23-like Thi 38.4 29 0.00062 20.2 2.0 23 6-28 13-37 (80)
37 cd06481 ACD_HspB9_like Alpha c 37.5 35 0.00075 22.4 2.4 24 5-28 13-38 (87)
38 PRK11198 LysM domain/BON super 37.4 40 0.00087 24.3 3.0 35 10-44 42-77 (147)
39 PRK10553 assembly protein for 36.9 82 0.0018 21.2 4.2 46 2-47 24-76 (87)
40 cd04910 ACT_AK-Ectoine_1 ACT d 36.6 42 0.00091 21.8 2.6 42 3-45 24-69 (71)
41 PF13241 NAD_binding_7: Putati 36.4 56 0.0012 21.7 3.4 38 13-50 1-40 (103)
42 cd06479 ACD_HspB7_like Alpha c 36.3 37 0.00081 22.2 2.4 24 5-28 14-39 (81)
43 PF01873 eIF-5_eIF-2B: Domain 35.0 55 0.0012 23.4 3.3 27 13-40 63-89 (125)
44 PF02107 FlgH: Flagellar L-rin 34.7 22 0.00047 26.7 1.2 28 7-34 111-138 (179)
45 cd06498 ACD_alphaB-crystallin_ 34.7 42 0.0009 21.9 2.5 23 5-27 13-37 (84)
46 PF00013 KH_1: KH domain syndr 34.6 21 0.00045 21.2 0.9 32 4-38 25-58 (60)
47 COG1094 Predicted RNA-binding 33.9 60 0.0013 25.2 3.5 32 4-36 33-67 (194)
48 PF05193 Peptidase_M16_C: Pept 33.8 48 0.001 22.3 2.8 21 20-40 20-40 (184)
49 PF13362 Toprim_3: Toprim doma 33.6 81 0.0018 20.4 3.8 40 9-48 31-79 (96)
50 cd06526 metazoan_ACD Alpha-cry 32.0 44 0.00095 21.3 2.2 24 5-28 13-38 (83)
51 PF09358 UBA_e1_C: Ubiquitin-a 31.4 78 0.0017 22.4 3.6 31 20-50 35-67 (125)
52 PF03958 Secretin_N: Bacterial 31.2 87 0.0019 19.4 3.5 26 12-37 47-72 (82)
53 PF07744 SPOC: SPOC domain; I 30.8 65 0.0014 21.4 3.0 23 19-41 38-60 (119)
54 PF00352 TBP: Transcription fa 30.3 96 0.0021 20.1 3.7 23 18-40 56-78 (86)
55 cd06472 ACD_ScHsp26_like Alpha 30.1 60 0.0013 21.0 2.7 25 4-28 14-41 (92)
56 PTZ00423 glideosome-associated 29.1 20 0.00043 27.3 0.2 11 104-114 171-181 (193)
57 COG2072 TrkA Predicted flavopr 28.3 87 0.0019 26.4 3.9 35 15-49 171-207 (443)
58 PF05309 TraE: TraE protein; 28.1 63 0.0014 24.0 2.7 19 10-28 130-148 (187)
59 PF07338 DUF1471: Protein of u 28.0 84 0.0018 19.2 2.9 20 20-39 6-26 (56)
60 PRK06719 precorrin-2 dehydroge 27.8 1.2E+02 0.0025 22.0 4.1 38 12-49 6-45 (157)
61 PRK12342 hypothetical protein; 27.8 95 0.0021 24.7 3.8 46 6-52 9-63 (254)
62 PF04312 DUF460: Protein of un 27.7 2.5E+02 0.0055 20.7 6.0 41 8-48 39-83 (138)
63 TIGR01470 cysG_Nterm siroheme 27.2 1.2E+02 0.0027 22.9 4.3 39 13-51 3-43 (205)
64 PRK11023 outer membrane lipopr 27.1 95 0.0021 23.3 3.6 28 12-39 69-96 (191)
65 PF12971 NAGLU_N: Alpha-N-acet 26.5 62 0.0013 21.3 2.2 45 4-49 25-74 (86)
66 PF03927 NapD: NapD protein; 26.4 1.8E+02 0.0039 18.8 4.4 37 2-39 22-59 (79)
67 PRK03988 translation initiatio 25.8 1.2E+02 0.0027 22.0 3.8 24 18-41 76-99 (138)
68 TIGR02761 TraE_TIGR type IV co 25.8 69 0.0015 23.9 2.6 19 10-28 130-148 (181)
69 TIGR00311 aIF-2beta translatio 25.4 1.2E+02 0.0025 22.0 3.6 23 19-41 72-94 (133)
70 PF01565 FAD_binding_4: FAD bi 24.4 1.5E+02 0.0034 20.0 4.0 29 13-41 57-85 (139)
71 TIGR00411 redox_disulf_1 small 24.0 1.7E+02 0.0037 17.5 4.3 31 7-40 51-81 (82)
72 cd02991 UAS_ETEA UAS family, E 23.8 1.3E+02 0.0029 20.7 3.6 28 14-41 82-113 (116)
73 PF13465 zf-H2C2_2: Zinc-finge 23.7 27 0.00058 17.9 0.0 12 103-114 9-20 (26)
74 PRK06718 precorrin-2 dehydroge 23.4 1.6E+02 0.0034 22.2 4.2 37 13-49 4-42 (202)
75 PRK12698 flgH flagellar basal 23.0 48 0.001 26.0 1.3 28 7-34 154-181 (224)
76 PF04468 PSP1: PSP1 C-terminal 23.0 2.3E+02 0.0049 18.6 4.5 35 11-45 45-85 (88)
77 TIGR00735 hisF imidazoleglycer 22.4 2.1E+02 0.0046 22.0 4.8 37 13-50 8-54 (254)
78 PRK14114 1-(5-phosphoribosyl)- 21.4 2.1E+02 0.0046 22.2 4.7 35 12-46 123-163 (241)
79 PRK13726 conjugal transfer pil 21.3 94 0.002 23.7 2.6 18 11-28 131-148 (188)
80 PF00988 CPSase_sm_chain: Carb 21.3 62 0.0013 23.5 1.5 28 18-45 101-130 (131)
81 PF13738 Pyr_redox_3: Pyridine 21.1 1.1E+02 0.0023 21.7 2.7 35 16-50 164-200 (203)
82 COG0277 GlcD FAD/FMN-containin 20.7 1.1E+02 0.0023 25.0 3.0 36 4-41 81-116 (459)
83 KOG2768 Translation initiation 20.6 1.1E+02 0.0023 24.5 2.8 29 12-41 150-178 (231)
84 PRK12788 flgH flagellar basal 20.4 57 0.0012 25.9 1.3 28 7-34 165-192 (234)
85 PF08712 Nfu_N: Scaffold prote 20.3 1.2E+02 0.0025 20.1 2.6 36 3-40 42-79 (87)
86 PF05188 MutS_II: MutS domain 20.3 2.7E+02 0.0058 18.4 4.7 37 13-49 18-54 (137)
No 1
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.91 E-value=3.1e-09 Score=69.12 Aligned_cols=45 Identities=38% Similarity=0.735 Sum_probs=40.5
Q ss_pred ccccCCCCccEEEEecCCCeEEEEeeCCHHHHHHHHHhcC--CeEEe
Q 033646 2 KTVSGLAGVDSISMDMKEKKLTVIGDIDPVSIVSKLRKLC--HTEIL 46 (114)
Q Consensus 2 Kal~~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g--~aeiv 46 (114)
+.|+.+.||.++.+|+++++|||.|++||..|+++|++.+ ++.+|
T Consensus 24 ~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 24 RVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred HHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEe
Confidence 5789999999999999999999999999999999999877 44444
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=98.29 E-value=1.2e-06 Score=54.11 Aligned_cols=40 Identities=35% Similarity=0.468 Sum_probs=36.7
Q ss_pred ccccCCCCccEEEEecCCCeEEEEeeCC---HHHHHHHHHhcC
Q 033646 2 KTVSGLAGVDSISMDMKEKKLTVIGDID---PVSIVSKLRKLC 41 (114)
Q Consensus 2 Kal~~l~GV~sV~vD~~~~kvtV~G~vD---p~~lv~~LrK~g 41 (114)
++|++++||.++.+|+..++++|+++.+ +.+|.++|+++|
T Consensus 18 ~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~G 60 (62)
T PF00403_consen 18 KALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAG 60 (62)
T ss_dssp HHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTT
T ss_pred HHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhC
Confidence 5799999999999999999999999854 599999999987
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=97.32 E-value=0.00039 Score=44.87 Aligned_cols=44 Identities=20% Similarity=0.337 Sum_probs=36.7
Q ss_pred ccccCCCCccEEEEecCCCeE--EEEe-eCCHHHHHHHHHhcC-CeEE
Q 033646 2 KTVSGLAGVDSISMDMKEKKL--TVIG-DIDPVSIVSKLRKLC-HTEI 45 (114)
Q Consensus 2 Kal~~l~GV~sV~vD~~~~kv--tV~G-~vDp~~lv~~LrK~g-~aei 45 (114)
++|.+++||.+|++|+..+.+ ++.+ .++..+|+++|.++| .+..
T Consensus 22 ~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~ 69 (71)
T COG2608 22 KALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEE 69 (71)
T ss_pred HHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeee
Confidence 578999999999999999554 4456 589999999999999 5543
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=96.97 E-value=0.0015 Score=51.56 Aligned_cols=48 Identities=19% Similarity=0.441 Sum_probs=44.3
Q ss_pred ccccCCCCccEEEEecCCCeEEEEeeCCHHHHHHHHHhcC-CeEEeecC
Q 033646 2 KTVSGLAGVDSISMDMKEKKLTVIGDIDPVSIVSKLRKLC-HTEILSVG 49 (114)
Q Consensus 2 Kal~~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g-~aeivsv~ 49 (114)
+.|.+++||++|++|+.++.|.|.+.+-+..+...|+-+| +|.|.-.|
T Consensus 26 ~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G 74 (247)
T KOG4656|consen 26 ACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAG 74 (247)
T ss_pred HHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCC
Confidence 3578899999999999999999999999999999999999 89988765
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=95.61 E-value=0.037 Score=43.22 Aligned_cols=50 Identities=16% Similarity=0.395 Sum_probs=44.8
Q ss_pred cccCCCCccEEEEecCCCeEEEEeeCCHHHHHHHHHhcC-CeEEeecCCCC
Q 033646 3 TVSGLAGVDSISMDMKEKKLTVIGDIDPVSIVSKLRKLC-HTEILSVGPAK 52 (114)
Q Consensus 3 al~~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g-~aeivsv~p~k 52 (114)
+|.+++||.++.+|+..++++|.+.+++..++..|++.| .+++++.+.+.
T Consensus 26 ~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 26 KLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred HHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 578899999999999999999999899999999999999 88888886654
No 6
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=92.68 E-value=0.13 Score=35.68 Aligned_cols=40 Identities=38% Similarity=0.594 Sum_probs=30.7
Q ss_pred ccccCCCCccEEE-----EecCCC--eEEEEee-CCHHHHHHHHHhcC
Q 033646 2 KTVSGLAGVDSIS-----MDMKEK--KLTVIGD-IDPVSIVSKLRKLC 41 (114)
Q Consensus 2 Kal~~l~GV~sV~-----vD~~~~--kvtV~G~-vDp~~lv~~LrK~g 41 (114)
++|++++||+.|. +|.... ++||.|+ +|-..|.++|++.|
T Consensus 24 ~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~G 71 (95)
T PF02680_consen 24 KALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELG 71 (95)
T ss_dssp HHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT
T ss_pred HHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcC
Confidence 3678899998874 455553 7788897 99999999999988
No 7
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=91.14 E-value=0.36 Score=33.54 Aligned_cols=40 Identities=28% Similarity=0.449 Sum_probs=31.2
Q ss_pred ccccCCCCccEEE-----EecCC--CeEEEEee-CCHHHHHHHHHhcC
Q 033646 2 KTVSGLAGVDSIS-----MDMKE--KKLTVIGD-IDPVSIVSKLRKLC 41 (114)
Q Consensus 2 Kal~~l~GV~sV~-----vD~~~--~kvtV~G~-vDp~~lv~~LrK~g 41 (114)
+.|++++||+.|. +|.+. =++||.|+ +|=..|.+.|++.|
T Consensus 26 ~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~G 73 (97)
T COG1888 26 LELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELG 73 (97)
T ss_pred HHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcC
Confidence 3577888887764 35444 48889996 99999999999988
No 8
>PRK10671 copA copper exporting ATPase; Provisional
Probab=90.05 E-value=0.41 Score=43.26 Aligned_cols=44 Identities=7% Similarity=0.251 Sum_probs=38.8
Q ss_pred ccccCCCCccEEEEecCCCeEEEEeeCCHHHHHHHHHhcC-CeEEee
Q 033646 2 KTVSGLAGVDSISMDMKEKKLTVIGDIDPVSIVSKLRKLC-HTEILS 47 (114)
Q Consensus 2 Kal~~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g-~aeivs 47 (114)
++|.+++||.++.+|+ ++.+|++.+++..+...++..| .+++.+
T Consensus 23 ~al~~~~gv~~v~v~~--~~~~v~~~~~~~~i~~~i~~~Gy~~~~~~ 67 (834)
T PRK10671 23 ESLEQRPDVEQADVSI--TEAHVTGTASAEALIETIKQAGYDASVSH 67 (834)
T ss_pred HHHhcCCCcceEEEee--eEEEEEecCCHHHHHHHHHhcCCcccccc
Confidence 4688999999999999 4677788899999999999999 888865
No 9
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=77.78 E-value=8.3 Score=24.39 Aligned_cols=40 Identities=15% Similarity=0.227 Sum_probs=31.1
Q ss_pred cccCCCCccEEEEecCC-CeEEEEeeCCHHHHHHHHHhcCC
Q 033646 3 TVSGLAGVDSISMDMKE-KKLTVIGDIDPVSIVSKLRKLCH 42 (114)
Q Consensus 3 al~~l~GV~sV~vD~~~-~kvtV~G~vDp~~lv~~LrK~g~ 42 (114)
.|..++||.++..+... =.+.|.+..+...|+..|...|.
T Consensus 25 ~l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~~~g~ 65 (84)
T PF13732_consen 25 ELEELPGVESVEQDGDGKLRIKLEDEETANELLQELIEKGI 65 (84)
T ss_pred HHhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHHhCCC
Confidence 36778999999876544 36666777899999999988774
No 10
>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=63.19 E-value=21 Score=18.88 Aligned_cols=39 Identities=15% Similarity=0.239 Sum_probs=29.7
Q ss_pred cccCCCCccEEEEecCCCeEEEEe---eCCHHHHHHHHHhcC
Q 033646 3 TVSGLAGVDSISMDMKEKKLTVIG---DIDPVSIVSKLRKLC 41 (114)
Q Consensus 3 al~~l~GV~sV~vD~~~~kvtV~G---~vDp~~lv~~LrK~g 41 (114)
.+..+.|+.+..+++..+.+++.. .++...+...+...|
T Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 64 (68)
T TIGR00003 23 FVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAG 64 (68)
T ss_pred HHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcC
Confidence 356788999999999999988863 357777777666555
No 11
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=62.46 E-value=6.5 Score=29.41 Aligned_cols=35 Identities=20% Similarity=0.284 Sum_probs=29.4
Q ss_pred ecCCCeEEEEeeCCHHHHHHHHHhcC-CeEEeecCC
Q 033646 16 DMKEKKLTVIGDIDPVSIVSKLRKLC-HTEILSVGP 50 (114)
Q Consensus 16 D~~~~kvtV~G~vDp~~lv~~LrK~g-~aeivsv~p 50 (114)
+.-+.-+.++|+-|=.-++++++..| ++++++.++
T Consensus 109 ~~~D~ivl~SgD~DF~p~v~~~~~~G~rv~v~~~~~ 144 (181)
T COG1432 109 KNVDTIVLFSGDGDFIPLVEAARDKGKRVEVAGIEP 144 (181)
T ss_pred cCCCEEEEEcCCccHHHHHHHHHHcCCEEEEEecCC
Confidence 34445667789999999999999989 999999987
No 12
>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=62.14 E-value=9.7 Score=22.90 Aligned_cols=31 Identities=16% Similarity=0.260 Sum_probs=22.4
Q ss_pred CCCccEEEEecCCCeEEEEeeCCHHHHHHHHH
Q 033646 7 LAGVDSISMDMKEKKLTVIGDIDPVSIVSKLR 38 (114)
Q Consensus 7 l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~Lr 38 (114)
+++- +|.+...++.|+++|.++-.....++.
T Consensus 14 ~~~~-~i~v~v~~g~v~L~G~v~s~~~~~~a~ 44 (64)
T PF04972_consen 14 LPDS-NISVSVENGVVTLSGEVPSQEQRDAAE 44 (64)
T ss_dssp TT-T-TEEEEEECTEEEEEEEESSCHHHHHHH
T ss_pred cCCC-eEEEEEECCEEEEEeeCcHHHHHHhHH
Confidence 5555 688888999999999985555554443
No 13
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=61.32 E-value=12 Score=35.25 Aligned_cols=48 Identities=25% Similarity=0.400 Sum_probs=41.4
Q ss_pred ccccCCCCccEEEEecCCCeEEEE--eeCCHHHHHHHHHhcC-CeEEeecC
Q 033646 2 KTVSGLAGVDSISMDMKEKKLTVI--GDIDPVSIVSKLRKLC-HTEILSVG 49 (114)
Q Consensus 2 Kal~~l~GV~sV~vD~~~~kvtV~--G~vDp~~lv~~LrK~g-~aeivsv~ 49 (114)
+++++.+||.++++++..+..+|. ..++++.+.+.+...| .+++++-.
T Consensus 14 ~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~ 64 (951)
T KOG0207|consen 14 KAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGFEASLLSDS 64 (951)
T ss_pred HHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccceeeecccC
Confidence 468899999999999999888875 4589999999999999 89887653
No 14
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.82 E-value=18 Score=25.14 Aligned_cols=24 Identities=29% Similarity=0.390 Sum_probs=22.1
Q ss_pred cccCCCCccEEEEecCCCeEEEEe
Q 033646 3 TVSGLAGVDSISMDMKEKKLTVIG 26 (114)
Q Consensus 3 al~~l~GV~sV~vD~~~~kvtV~G 26 (114)
.+..++|++.|++..+++++-|.|
T Consensus 35 ivas~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 35 IVASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EEEecCCceEEEEecccceEEEec
Confidence 567899999999999999999987
No 15
>cd06471 ACD_LpsHSP_like Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Transcription of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is regulated by a variety of stresses including heat, cold and ethanol. Early growing L. plantarum cells contain elevated levels of these mRNAs which rapidly fall of as the cells enter stationary phase. Also belonging to this group is Bifidobacterium breve (Bb) HSP20 and Oenococcus oenis (syn. Leuconostoc oenos) (Oo) HSP18. Transcription of the gene encoding BbHSP20 is strongly induced following heat or osmotic shock, and that of the gene encoding OoHSP18 following heat, ethanol or acid shock. OoHSP18 is peripherally associated with the cytoplasmic me
Probab=57.46 E-value=9.4 Score=24.86 Aligned_cols=26 Identities=31% Similarity=0.497 Sum_probs=20.9
Q ss_pred ccCCCCc--cEEEEecCCCeEEEEeeCC
Q 033646 4 VSGLAGV--DSISMDMKEKKLTVIGDID 29 (114)
Q Consensus 4 l~~l~GV--~sV~vD~~~~kvtV~G~vD 29 (114)
...|+|| +.|+|+..++.++|.|.-.
T Consensus 15 ~~~lPGv~~edi~v~~~~~~L~I~g~~~ 42 (93)
T cd06471 15 EADLPGFKKEDIKLDYKDGYLTISAKRD 42 (93)
T ss_pred EEECCCCCHHHeEEEEECCEEEEEEEEc
Confidence 3468899 5589999999999999753
No 16
>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=55.25 E-value=18 Score=25.00 Aligned_cols=29 Identities=31% Similarity=0.434 Sum_probs=25.5
Q ss_pred eEEEEeeCCHHHHHHHHHhcC-CeEEeecC
Q 033646 21 KLTVIGDIDPVSIVSKLRKLC-HTEILSVG 49 (114)
Q Consensus 21 kvtV~G~vDp~~lv~~LrK~g-~aeivsv~ 49 (114)
-+.|+|+-|=.-++..||..| ++.+++..
T Consensus 103 ivLvSgD~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 103 IVLVSGDSDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEEECCccHHHHHHHHHHcCCEEEEEccC
Confidence 456689999999999999999 99998885
No 17
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=54.92 E-value=20 Score=32.61 Aligned_cols=43 Identities=26% Similarity=0.519 Sum_probs=37.4
Q ss_pred cccCCCCccEEEEecCCCeEEEEee---CC-HHHHHHHHHhcC-CeEE
Q 033646 3 TVSGLAGVDSISMDMKEKKLTVIGD---ID-PVSIVSKLRKLC-HTEI 45 (114)
Q Consensus 3 al~~l~GV~sV~vD~~~~kvtV~G~---vD-p~~lv~~LrK~g-~aei 45 (114)
+|.+++||.++.+++...+++|..+ .+ +..+..++++.| .+..
T Consensus 22 ~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 22 ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 5788999999999999999999854 56 789999999999 6665
No 18
>PRK10671 copA copper exporting ATPase; Provisional
Probab=54.52 E-value=18 Score=32.82 Aligned_cols=44 Identities=20% Similarity=0.431 Sum_probs=37.4
Q ss_pred cccCCCCccEEEEecCCCeEEEEeeCCHHHHHHHHHhcC-CeEEe
Q 033646 3 TVSGLAGVDSISMDMKEKKLTVIGDIDPVSIVSKLRKLC-HTEIL 46 (114)
Q Consensus 3 al~~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g-~aeiv 46 (114)
.+..++||.++.+++..+++.|.+..++..+...++..| .+.++
T Consensus 120 ~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~ 164 (834)
T PRK10671 120 ALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAI 164 (834)
T ss_pred HHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCcccc
Confidence 467889999999999999999987789999988898888 66543
No 19
>COG0071 IbpA Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=49.88 E-value=12 Score=26.62 Aligned_cols=28 Identities=29% Similarity=0.533 Sum_probs=22.8
Q ss_pred cccCCCCccE--EEEecCCCeEEEEeeCCH
Q 033646 3 TVSGLAGVDS--ISMDMKEKKLTVIGDIDP 30 (114)
Q Consensus 3 al~~l~GV~s--V~vD~~~~kvtV~G~vDp 30 (114)
.+..|+||.. |+|...++.|||+|....
T Consensus 54 I~~elPG~~kedI~I~~~~~~l~I~g~~~~ 83 (146)
T COG0071 54 ITAELPGVDKEDIEITVEGNTLTIRGEREE 83 (146)
T ss_pred EEEEcCCCChHHeEEEEECCEEEEEEEecc
Confidence 4567889875 888999999999998654
No 20
>PHA00514 dsDNA binding protein
Probab=49.68 E-value=43 Score=23.21 Aligned_cols=31 Identities=23% Similarity=0.374 Sum_probs=25.2
Q ss_pred eEEEEeeCCHHHHHHHHHhc--C-CeEEeecCCC
Q 033646 21 KLTVIGDIDPVSIVSKLRKL--C-HTEILSVGPA 51 (114)
Q Consensus 21 kvtV~G~vDp~~lv~~LrK~--g-~aeivsv~p~ 51 (114)
..|..|++.-+..-..|.|. + .+.++|++|-
T Consensus 33 ~~Tl~GNLtiEqAQ~e~~k~~k~~pvqVvsVEpn 66 (98)
T PHA00514 33 EQTLLGNLTIEQAQKELSKQYKHGPVQVVSVEPN 66 (98)
T ss_pred cceeecceeHHHHHHHHhhcccCCCeeEEEecCC
Confidence 34667999999999999865 4 8999999764
No 21
>cd06482 ACD_HspB10 Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB10, also known as sperm outer dense fiber protein (ODFP), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB10 occurs exclusively in the axoneme of sperm cells and may have a cytoskeletal role.
Probab=49.09 E-value=17 Score=24.30 Aligned_cols=24 Identities=17% Similarity=0.422 Sum_probs=19.4
Q ss_pred cCCCCccE--EEEecCCCeEEEEeeC
Q 033646 5 SGLAGVDS--ISMDMKEKKLTVIGDI 28 (114)
Q Consensus 5 ~~l~GV~s--V~vD~~~~kvtV~G~v 28 (114)
..|+|+.. |+|...++.|||.|.-
T Consensus 14 adlPG~~kedI~V~v~~~~L~I~ger 39 (87)
T cd06482 14 VDVCGFEPDQVKVKVKDGKVQVSAER 39 (87)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEEE
Confidence 45788865 8888889999999974
No 22
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=47.99 E-value=34 Score=23.95 Aligned_cols=28 Identities=32% Similarity=0.400 Sum_probs=23.3
Q ss_pred EEEecCCCeEEEEeeCCHHHHHHHHHhcC
Q 033646 13 ISMDMKEKKLTVIGDIDPVSIVSKLRKLC 41 (114)
Q Consensus 13 V~vD~~~~kvtV~G~vDp~~lv~~LrK~g 41 (114)
.++|.+ +++++.|.+++..|-+.|++.-
T Consensus 50 g~id~~-~rlii~G~~~~~~i~~~l~~yI 77 (110)
T smart00653 50 GSIDGK-GRLIVNGRFTPKKLQDLLRRYI 77 (110)
T ss_pred eeECCC-CeEEEEEeeCHHHHHHHHHHHH
Confidence 366755 8999999999999999998643
No 23
>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=47.99 E-value=21 Score=24.22 Aligned_cols=29 Identities=28% Similarity=0.337 Sum_probs=20.9
Q ss_pred CeEEEEeeCCHHHHHHHHHhcC-CeEEeec
Q 033646 20 KKLTVIGDIDPVSIVSKLRKLC-HTEILSV 48 (114)
Q Consensus 20 ~kvtV~G~vDp~~lv~~LrK~g-~aeivsv 48 (114)
.=+.|+|+-|=..++.+||..| ++.++..
T Consensus 98 ~ivLvSgD~Df~~~v~~l~~~g~~V~v~~~ 127 (146)
T PF01936_consen 98 TIVLVSGDSDFAPLVRKLRERGKRVIVVGA 127 (146)
T ss_dssp EEEEE---GGGHHHHHHHHHH--EEEEEE-
T ss_pred EEEEEECcHHHHHHHHHHHHcCCEEEEEEe
Confidence 3566789999999999999999 8998884
No 24
>cd06475 ACD_HspB1_like Alpha crystallin domain (ACD) found in mammalian small (s)heat shock protein (Hsp)-27 (also denoted HspB1 in human) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Hsp27 shows enhanced synthesis in response to stress. It is a molecular chaperone which interacts with a large number of different proteins. It is found in many types of human cells including breast, uterus, cervix, platelets and cancer cells. Hsp27 has diverse cellular functions including, chaperoning, regulation of actin polymerization, keratinocyte differentiation, regulation of inflammatory pathways in keratinocytes, and protection from oxidative stress through modulating glutathione levels. It is also a subunit of AUF1-containing protein complexes. It has been linked to several transduction pathways regulating cellular functions including differentiat
Probab=47.48 E-value=20 Score=23.53 Aligned_cols=24 Identities=8% Similarity=0.194 Sum_probs=19.2
Q ss_pred cCCCCccE--EEEecCCCeEEEEeeC
Q 033646 5 SGLAGVDS--ISMDMKEKKLTVIGDI 28 (114)
Q Consensus 5 ~~l~GV~s--V~vD~~~~kvtV~G~v 28 (114)
..|+|+.. ++|+..++.+||+|.-
T Consensus 16 ~dlPG~~~edi~V~v~~~~L~I~g~~ 41 (86)
T cd06475 16 LDVNHFAPEELVVKTKDGVVEITGKH 41 (86)
T ss_pred EECCCCCHHHEEEEEECCEEEEEEEE
Confidence 45778864 8888888999999973
No 25
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=47.39 E-value=27 Score=26.13 Aligned_cols=29 Identities=17% Similarity=0.218 Sum_probs=25.4
Q ss_pred CeEEEEeeCCHHHHHHHHHhcC-CeEEeec
Q 033646 20 KKLTVIGDIDPVSIVSKLRKLC-HTEILSV 48 (114)
Q Consensus 20 ~kvtV~G~vDp~~lv~~LrK~g-~aeivsv 48 (114)
.=+.|+|+-|=..|+.+||..| .+..+++
T Consensus 108 ~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~ 137 (160)
T TIGR00288 108 AVALVTRDADFLPVINKAKENGKETIVIGA 137 (160)
T ss_pred EEEEEeccHhHHHHHHHHHHCCCEEEEEeC
Confidence 3567789999999999999989 8998886
No 26
>cd06464 ACD_sHsps-like Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
Probab=46.54 E-value=17 Score=22.44 Aligned_cols=27 Identities=22% Similarity=0.513 Sum_probs=21.2
Q ss_pred ccCCCCc--cEEEEecCCCeEEEEeeCCH
Q 033646 4 VSGLAGV--DSISMDMKEKKLTVIGDIDP 30 (114)
Q Consensus 4 l~~l~GV--~sV~vD~~~~kvtV~G~vDp 30 (114)
...|+|| ++|+|...++.|+|.|....
T Consensus 12 ~~~lpg~~~~~i~V~v~~~~l~I~g~~~~ 40 (88)
T cd06464 12 EADLPGFKKEDIKVEVEDGVLTISGEREE 40 (88)
T ss_pred EEECCCCCHHHeEEEEECCEEEEEEEEec
Confidence 3467888 66888888899999997543
No 27
>PRK10743 heat shock protein IbpA; Provisional
Probab=42.79 E-value=23 Score=25.57 Aligned_cols=24 Identities=21% Similarity=0.371 Sum_probs=19.0
Q ss_pred cCCCCcc--EEEEecCCCeEEEEeeC
Q 033646 5 SGLAGVD--SISMDMKEKKLTVIGDI 28 (114)
Q Consensus 5 ~~l~GV~--sV~vD~~~~kvtV~G~v 28 (114)
..|+||. +|+|+..++.|||.|.-
T Consensus 51 aelPGv~kedi~V~v~~~~LtI~ge~ 76 (137)
T PRK10743 51 IAVAGFAESELEITAQDNLLVVKGAH 76 (137)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEEE
Confidence 4678885 48888888999999974
No 28
>cd06470 ACD_IbpA-B_like Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. IbpA and IbpB are produced during high-level production of various heterologous proteins, specifically human prorenin, renin and bovine insulin-like growth factor 2 (bIGF-2), and are strongly associated with inclusion bodies containing these heterologous proteins. IbpA and IbpB work as an integrated system to stabilize thermally aggregated proteins in a disaggregation competent state. The chaperone activity of IbpB is also significantly elevated as the temperature increases from normal to heat shock. The high temperature results in the disassociation of 2-3-MDa IbpB oligomers into smaller approximately 6
Probab=42.64 E-value=26 Score=22.91 Aligned_cols=24 Identities=25% Similarity=0.535 Sum_probs=19.2
Q ss_pred cCCCCccE--EEEecCCCeEEEEeeC
Q 033646 5 SGLAGVDS--ISMDMKEKKLTVIGDI 28 (114)
Q Consensus 5 ~~l~GV~s--V~vD~~~~kvtV~G~v 28 (114)
..|+||.. |+|...++.|+|.|.-
T Consensus 17 ~~lPG~~kedi~v~~~~~~L~I~g~~ 42 (90)
T cd06470 17 LAVAGFSEDDLEIEVENNQLTVTGKK 42 (90)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEEE
Confidence 45788864 8888888999999974
No 29
>cd06477 ACD_HspB3_Like Alpha crystallin domain (ACD) found in mammalian HspB3, also known as heat-shock protein 27-like protein (HSPL27, 17-kDa) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB3 is expressed in adult skeletal muscle, smooth muscle, and heart, and in several other fetal tissues. In muscle cells HspB3 forms an oligomeric 150 kDa complex with myotonic dystrophy protein kinase-binding protein (MKBP/ HspB2), this complex may comprise one of two independent muscle-cell specific chaperone systems. The expression of HspB3 is induced during muscle differentiation controlled by the myogenic factor MyoD. HspB3 may also interact with Hsp22 (HspB8).
Probab=41.93 E-value=26 Score=23.13 Aligned_cols=24 Identities=17% Similarity=0.156 Sum_probs=19.7
Q ss_pred cCCCCcc--EEEEecCCCeEEEEeeC
Q 033646 5 SGLAGVD--SISMDMKEKKLTVIGDI 28 (114)
Q Consensus 5 ~~l~GV~--sV~vD~~~~kvtV~G~v 28 (114)
..|+|+. .|+|+..++.|+|.|.-
T Consensus 13 ~dlpG~~~edI~V~v~~~~L~I~ge~ 38 (83)
T cd06477 13 LDVVQFRPEDIIIQVFEGWLLIKGQH 38 (83)
T ss_pred EEcCCCCHHHeEEEEECCEEEEEEEE
Confidence 4567775 48999999999999974
No 30
>PRK11597 heat shock chaperone IbpB; Provisional
Probab=40.91 E-value=25 Score=25.66 Aligned_cols=25 Identities=28% Similarity=0.484 Sum_probs=20.4
Q ss_pred ccCCCCcc--EEEEecCCCeEEEEeeC
Q 033646 4 VSGLAGVD--SISMDMKEKKLTVIGDI 28 (114)
Q Consensus 4 l~~l~GV~--sV~vD~~~~kvtV~G~v 28 (114)
...|+||. +|+|+..++.|||.|.-
T Consensus 48 ~adlPGv~kedi~V~v~~~~LtI~ge~ 74 (142)
T PRK11597 48 TLALAGFRQEDLDIQLEGTRLTVKGTP 74 (142)
T ss_pred EEEeCCCCHHHeEEEEECCEEEEEEEE
Confidence 34678985 48999999999999974
No 31
>cd06497 ACD_alphaA-crystallin_HspB4 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaA-crystallin (HspB4, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 does not belong to this group. Mutations inHspB4 have been associated with Autosomal Dominant Congenital Cataract (ADCC). The chaperone-like functions of HspB4 are considered important for maintaining lens transparency and preventing cataract.
Probab=40.35 E-value=30 Score=22.71 Aligned_cols=24 Identities=4% Similarity=0.191 Sum_probs=18.7
Q ss_pred cCCCCcc--EEEEecCCCeEEEEeeC
Q 033646 5 SGLAGVD--SISMDMKEKKLTVIGDI 28 (114)
Q Consensus 5 ~~l~GV~--sV~vD~~~~kvtV~G~v 28 (114)
..++||. +|+|+..++.|+|.|.-
T Consensus 16 ~dlpG~~~edi~V~v~~~~L~I~g~~ 41 (86)
T cd06497 16 LDVKHFSPEDLTVKVLDDYVEIHGKH 41 (86)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEEE
Confidence 3567775 48888889999999973
No 32
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=40.00 E-value=53 Score=31.14 Aligned_cols=46 Identities=17% Similarity=0.266 Sum_probs=39.3
Q ss_pred cccCCCCccEEEEecCCCeEEEEe---eCCHHHHHHHHHhcC-CeEEeec
Q 033646 3 TVSGLAGVDSISMDMKEKKLTVIG---DIDPVSIVSKLRKLC-HTEILSV 48 (114)
Q Consensus 3 al~~l~GV~sV~vD~~~~kvtV~G---~vDp~~lv~~LrK~g-~aeivsv 48 (114)
.|.+++||.++++|+..+++.|.= ..-|-++++.|...+ .+.+...
T Consensus 167 ~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~ 216 (951)
T KOG0207|consen 167 ILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPY 216 (951)
T ss_pred HHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeec
Confidence 577899999999999999999964 378999999999888 7776664
No 33
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=39.60 E-value=46 Score=29.44 Aligned_cols=36 Identities=17% Similarity=0.318 Sum_probs=29.8
Q ss_pred ccCCCCccEEEEecCCCeEEEEeeCCHHHHHHHHHhcC
Q 033646 4 VSGLAGVDSISMDMKEKKLTVIGDIDPVSIVSKLRKLC 41 (114)
Q Consensus 4 l~~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g 41 (114)
|++|.|| +++|..++.|||.+-+.-.+|...|...|
T Consensus 110 L~~ln~V--l~vD~~~~tVtV~AG~~l~~L~~~L~~~G 145 (541)
T TIGR01676 110 LALMDKV--LEVDEEKKRVRVQAGIRVQQLVDAIKEYG 145 (541)
T ss_pred hhhCCCC--EEEcCCCCEEEEcCCCCHHHHHHHHHHcC
Confidence 4456665 46788899999999999999999999877
No 34
>cd06478 ACD_HspB4-5-6 Alpha-crystallin domain found in alphaA-crystallin (HspB4), alphaB-crystallin (HspB5), and the small heat shock protein (sHsp) HspB6, also known as Hsp20. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 on the other hand is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. HspB5's functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its ol
Probab=38.95 E-value=33 Score=22.23 Aligned_cols=23 Identities=9% Similarity=0.172 Sum_probs=18.3
Q ss_pred cCCCCccE--EEEecCCCeEEEEee
Q 033646 5 SGLAGVDS--ISMDMKEKKLTVIGD 27 (114)
Q Consensus 5 ~~l~GV~s--V~vD~~~~kvtV~G~ 27 (114)
..|+|+.. |+|+..++.|+|.|.
T Consensus 13 ~dlpG~~~edI~V~v~~~~L~I~g~ 37 (83)
T cd06478 13 LDVKHFSPEELSVKVLGDFVEIHGK 37 (83)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEE
Confidence 45677754 888888999999996
No 35
>cd06476 ACD_HspB2_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB2/heat shock 27kDa protein 2 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB2 is preferentially and constitutively expressed in skeletal muscle and heart. HspB2 shows homooligomeric activity and forms aggregates in muscle cytosol. Although its expression is not induced by heat shock, it redistributes to the insoluble fraction in response to heat shock. In the mouse heart, HspB2 plays a role in maintaining energetic balance, by protecting cardiac energetics during ischemia/reperfusion, and allowing for increased work during acute inotropic challenge. hHspB2 [previously also known as myotonic dystrophy protein kinase (DMPK) binding protein (MKBP)] is selectively up-regulated in skeletal muscles from myotonic dystrophy patients.
Probab=38.88 E-value=31 Score=22.58 Aligned_cols=25 Identities=12% Similarity=0.108 Sum_probs=19.2
Q ss_pred cCCCCcc--EEEEecCCCeEEEEeeCC
Q 033646 5 SGLAGVD--SISMDMKEKKLTVIGDID 29 (114)
Q Consensus 5 ~~l~GV~--sV~vD~~~~kvtV~G~vD 29 (114)
..++|+. .|+|+..++.|+|.|.-.
T Consensus 13 ~dlpG~~~edi~V~v~~~~L~I~g~~~ 39 (83)
T cd06476 13 LDVCHFTPDEITVRTVDNLLEVSARHP 39 (83)
T ss_pred EEcCCCCHHHeEEEEECCEEEEEEEEc
Confidence 3466775 488889999999999753
No 36
>cd00298 ACD_sHsps_p23-like This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this family is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind
Probab=38.40 E-value=29 Score=20.24 Aligned_cols=23 Identities=30% Similarity=0.625 Sum_probs=18.3
Q ss_pred CCCCc--cEEEEecCCCeEEEEeeC
Q 033646 6 GLAGV--DSISMDMKEKKLTVIGDI 28 (114)
Q Consensus 6 ~l~GV--~sV~vD~~~~kvtV~G~v 28 (114)
.++|+ +.+.|+...+.++|.|..
T Consensus 13 ~~~~~~~~~i~v~~~~~~l~v~~~~ 37 (80)
T cd00298 13 DLPGVKKEDIKVEVEDNVLTISGKR 37 (80)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEEE
Confidence 45677 778888888999998864
No 37
>cd06481 ACD_HspB9_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB9 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB9 is expressed exclusively in the normal testis and in various tumor samples and is a cancer/testis antigen. hHspB9 interacts with TCTEL1 (T-complex testis expressed protein -1), a subunit of dynein. hHspB9 and TCTEL1 are co-expressed in similar cells within the testis and in tumor cells. Included in this group is Xenopus Hsp30, a developmentally-regulated heat-inducible molecular chaperone.
Probab=37.48 E-value=35 Score=22.44 Aligned_cols=24 Identities=25% Similarity=0.444 Sum_probs=18.7
Q ss_pred cCCCCcc--EEEEecCCCeEEEEeeC
Q 033646 5 SGLAGVD--SISMDMKEKKLTVIGDI 28 (114)
Q Consensus 5 ~~l~GV~--sV~vD~~~~kvtV~G~v 28 (114)
..++|+. +|+|...++.|+|.|.-
T Consensus 13 ~dlpG~~~edI~V~v~~~~L~I~g~~ 38 (87)
T cd06481 13 LDVRGFSPEDLSVRVDGRKLVVTGKR 38 (87)
T ss_pred EECCCCChHHeEEEEECCEEEEEEEE
Confidence 4567874 48888889999999963
No 38
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=37.44 E-value=40 Score=24.30 Aligned_cols=35 Identities=17% Similarity=0.241 Sum_probs=25.8
Q ss_pred ccEEEEecCCCeEEEEeeCCHHHHHHHHHh-cCCeE
Q 033646 10 VDSISMDMKEKKLTVIGDIDPVSIVSKLRK-LCHTE 44 (114)
Q Consensus 10 V~sV~vD~~~~kvtV~G~vDp~~lv~~LrK-~g~ae 44 (114)
...+.|...++.||+.|.+.......++.. .+.+.
T Consensus 42 ~~~i~V~v~~G~v~l~G~v~s~~~~~~~~~aa~~v~ 77 (147)
T PRK11198 42 DADVNVQVEDGKATVSGDAASQEAKEKILLAVGNIQ 77 (147)
T ss_pred cCCceEEEeCCEEEEEEEeCCHHHHHHHHHHhccCC
Confidence 344566667999999999988888888874 34433
No 39
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=36.90 E-value=82 Score=21.17 Aligned_cols=46 Identities=13% Similarity=0.268 Sum_probs=29.9
Q ss_pred ccccCCCCccEEEEecCCCeEEEEee-CCHH---HHHHHHHhc-C--CeEEee
Q 033646 2 KTVSGLAGVDSISMDMKEKKLTVIGD-IDPV---SIVSKLRKL-C--HTEILS 47 (114)
Q Consensus 2 Kal~~l~GV~sV~vD~~~~kvtV~G~-vDp~---~lv~~LrK~-g--~aeivs 47 (114)
++|..++|++=-..|...||++|+=. -+.. +.+..|+.. | .|.++-
T Consensus 24 ~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~I~~l~GVlsa~lVY 76 (87)
T PRK10553 24 TQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIESVRNVEGVLAVSLVY 76 (87)
T ss_pred HHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHHHHcCCCceEEEEEE
Confidence 46788999987778888888888632 3334 444555543 4 566654
No 40
>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=36.58 E-value=42 Score=21.75 Aligned_cols=42 Identities=19% Similarity=0.281 Sum_probs=29.6
Q ss_pred cccCCCCccEEEEecCCCeEEE--EeeC-CHHHHHHHHHhcC-CeEE
Q 033646 3 TVSGLAGVDSISMDMKEKKLTV--IGDI-DPVSIVSKLRKLC-HTEI 45 (114)
Q Consensus 3 al~~l~GV~sV~vD~~~~kvtV--~G~v-Dp~~lv~~LrK~g-~aei 45 (114)
+|.+. +|.=|..|...+.+|. .|.. +...++..|++.. .++|
T Consensus 24 ~l~~~-~v~ii~K~~nANtit~yl~~~~k~~~r~~~~Le~~~p~a~i 69 (71)
T cd04910 24 LLQRF-KVSIIAKDTNANTITHYLAGSLKTIKRLTEDLENRFPNAEI 69 (71)
T ss_pred HHHHc-CCeEEEEecCCCeEEEEEEcCHHHHHHHHHHHHHhCccCcc
Confidence 34444 7777888999998887 4553 6678888888766 5554
No 41
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=36.41 E-value=56 Score=21.69 Aligned_cols=38 Identities=18% Similarity=0.229 Sum_probs=23.5
Q ss_pred EEEecCCCeEEEEee-CCHHHHHHHHHhcC-CeEEeecCC
Q 033646 13 ISMDMKEKKLTVIGD-IDPVSIVSKLRKLC-HTEILSVGP 50 (114)
Q Consensus 13 V~vD~~~~kvtV~G~-vDp~~lv~~LrK~g-~aeivsv~p 50 (114)
+-+|+++.++.|.|. --...-+..|.+.| ++.+++...
T Consensus 1 l~l~l~~~~vlVvGgG~va~~k~~~Ll~~gA~v~vis~~~ 40 (103)
T PF13241_consen 1 LFLDLKGKRVLVVGGGPVAARKARLLLEAGAKVTVISPEI 40 (103)
T ss_dssp EEE--TT-EEEEEEESHHHHHHHHHHCCCTBEEEEEESSE
T ss_pred CEEEcCCCEEEEECCCHHHHHHHHHHHhCCCEEEEECCch
Confidence 457899999999987 22233344445677 888888865
No 42
>cd06479 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging. Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies.
Probab=36.34 E-value=37 Score=22.23 Aligned_cols=24 Identities=8% Similarity=0.206 Sum_probs=18.8
Q ss_pred cCCCCcc--EEEEecCCCeEEEEeeC
Q 033646 5 SGLAGVD--SISMDMKEKKLTVIGDI 28 (114)
Q Consensus 5 ~~l~GV~--sV~vD~~~~kvtV~G~v 28 (114)
..++|+. +|+|...++.|+|.|.-
T Consensus 14 ~dlpG~~pedi~V~v~~~~L~I~ger 39 (81)
T cd06479 14 VDVSDFSPEDIIVTTSNNQIEVHAEK 39 (81)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEEE
Confidence 3467775 48888889999999973
No 43
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=34.95 E-value=55 Score=23.36 Aligned_cols=27 Identities=30% Similarity=0.327 Sum_probs=23.2
Q ss_pred EEEecCCCeEEEEeeCCHHHHHHHHHhc
Q 033646 13 ISMDMKEKKLTVIGDIDPVSIVSKLRKL 40 (114)
Q Consensus 13 V~vD~~~~kvtV~G~vDp~~lv~~LrK~ 40 (114)
.++|.+ ++++|.|.+++..|-+.|++.
T Consensus 63 ~~id~~-~~lii~G~~~~~~i~~~L~~f 89 (125)
T PF01873_consen 63 GSIDGK-GRLIINGRFSSKQIQDLLDKF 89 (125)
T ss_dssp EEEETT-TEEEEESSSSCCHHHHHHHHH
T ss_pred eEECCC-CEEEEEEecCHHHHHHHHHHH
Confidence 467776 999999999999999999763
No 44
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=34.74 E-value=22 Score=26.72 Aligned_cols=28 Identities=21% Similarity=0.382 Sum_probs=25.0
Q ss_pred CCCccEEEEecCCCeEEEEeeCCHHHHH
Q 033646 7 LAGVDSISMDMKEKKLTVIGDIDPVSIV 34 (114)
Q Consensus 7 l~GV~sV~vD~~~~kvtV~G~vDp~~lv 34 (114)
+.|=..|.++-..+.++|.|.|.|.+|-
T Consensus 111 I~G~k~i~vn~e~~~i~lsGiVRp~DI~ 138 (179)
T PF02107_consen 111 IEGEKQIRVNGEEQYIRLSGIVRPEDID 138 (179)
T ss_pred EEEEEEEEECCCEEEEEEEEEECHHHCC
Confidence 5677889999999999999999999976
No 45
>cd06498 ACD_alphaB-crystallin_HspB5 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaB-crystallin (HspB5, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. HspB4 does not belong to this group. HspB5 shows increased synthesis in response to stress. HspB5 is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. Its functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its oligomerization and anti-apoptotic activ
Probab=34.69 E-value=42 Score=21.94 Aligned_cols=23 Identities=4% Similarity=0.153 Sum_probs=18.3
Q ss_pred cCCCCcc--EEEEecCCCeEEEEee
Q 033646 5 SGLAGVD--SISMDMKEKKLTVIGD 27 (114)
Q Consensus 5 ~~l~GV~--sV~vD~~~~kvtV~G~ 27 (114)
..++|+. .|+|+..++.|+|.|.
T Consensus 13 ~dlpG~~~edi~V~v~~~~L~I~g~ 37 (84)
T cd06498 13 LDVKHFSPEELKVKVLGDFIEIHGK 37 (84)
T ss_pred EECCCCCHHHeEEEEECCEEEEEEE
Confidence 3567874 4888888999999996
No 46
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=34.60 E-value=21 Score=21.23 Aligned_cols=32 Identities=19% Similarity=0.347 Sum_probs=19.7
Q ss_pred ccCCCCccEEEEecC--CCeEEEEeeCCHHHHHHHHH
Q 033646 4 VSGLAGVDSISMDMK--EKKLTVIGDIDPVSIVSKLR 38 (114)
Q Consensus 4 l~~l~GV~sV~vD~~--~~kvtV~G~vDp~~lv~~Lr 38 (114)
|....|+. |.++.. ...++|.| ++..+..+++
T Consensus 25 I~~~t~~~-I~i~~~~~~~~v~I~G--~~~~v~~A~~ 58 (60)
T PF00013_consen 25 IEEETGVK-IQIPDDDERDIVTISG--SPEQVEKAKK 58 (60)
T ss_dssp HHHHHTSE-EEEESTTEEEEEEEEE--SHHHHHHHHH
T ss_pred hhhhcCeE-EEEcCCCCcEEEEEEe--CHHHHHHHHh
Confidence 33444664 666544 35889999 6666666654
No 47
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=33.90 E-value=60 Score=25.20 Aligned_cols=32 Identities=22% Similarity=0.442 Sum_probs=23.3
Q ss_pred ccCCCCccEEEEecCCCeEEEEee---CCHHHHHHH
Q 033646 4 VSGLAGVDSISMDMKEKKLTVIGD---IDPVSIVSK 36 (114)
Q Consensus 4 l~~l~GV~sV~vD~~~~kvtV~G~---vDp~~lv~~ 36 (114)
|....|| .+.+|.+++.|+|..+ -||..++.+
T Consensus 33 ie~~~~~-~~~iD~~~~~V~i~~~~~t~Dp~~~~ka 67 (194)
T COG1094 33 IEEKTGV-KLRIDSKTGSVTIRTTRKTEDPLALLKA 67 (194)
T ss_pred HHhhcCe-EEEEECCCCeEEEEecCCCCChHHHHHH
Confidence 3344444 6899999999999755 688776655
No 48
>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=33.82 E-value=48 Score=22.32 Aligned_cols=21 Identities=33% Similarity=0.621 Sum_probs=17.8
Q ss_pred CeEEEEeeCCHHHHHHHHHhc
Q 033646 20 KKLTVIGDIDPVSIVSKLRKL 40 (114)
Q Consensus 20 ~kvtV~G~vDp~~lv~~LrK~ 40 (114)
-.+.|.|++|+..+...|++.
T Consensus 20 ~~l~i~Gd~~~~~~~~~i~~~ 40 (184)
T PF05193_consen 20 MTLVIVGDIDPDELEKLIEKY 40 (184)
T ss_dssp EEEEEEESSGHHHHHHHHHHH
T ss_pred eEEEEEcCccHHHHHHHHHhh
Confidence 367889999999999999863
No 49
>PF13362 Toprim_3: Toprim domain
Probab=33.65 E-value=81 Score=20.36 Aligned_cols=40 Identities=10% Similarity=0.238 Sum_probs=26.0
Q ss_pred CccEEEEecCCCeEEEEeeCCHH--------HHHHHHHhcC-CeEEeec
Q 033646 9 GVDSISMDMKEKKLTVIGDIDPV--------SIVSKLRKLC-HTEILSV 48 (114)
Q Consensus 9 GV~sV~vD~~~~kvtV~G~vDp~--------~lv~~LrK~g-~aeivsv 48 (114)
++..+.+.....+|+|-++-|.. ++.++|+..| .+.++.+
T Consensus 31 nl~~~~~~~~~~~vii~~D~D~~~~G~~~a~~~~~~~~~~g~~~~~~~p 79 (96)
T PF13362_consen 31 NLKNVAIPEPGRRVIIAADNDKANEGQKAAEKAAERLEAAGIAVSIVEP 79 (96)
T ss_pred hhhhhcCCCCCCeEEEEECCCCchhhHHHHHHHHHHHHhCCCeEEEECC
Confidence 33444444455677777776655 6667777777 7888777
No 50
>cd06526 metazoan_ACD Alpha-crystallin domain (ACD) of metazoan alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps.
Probab=31.99 E-value=44 Score=21.33 Aligned_cols=24 Identities=21% Similarity=0.418 Sum_probs=18.0
Q ss_pred cCCCCccE--EEEecCCCeEEEEeeC
Q 033646 5 SGLAGVDS--ISMDMKEKKLTVIGDI 28 (114)
Q Consensus 5 ~~l~GV~s--V~vD~~~~kvtV~G~v 28 (114)
..|+|+.. |+|...++.|+|.|.-
T Consensus 13 ~dlpG~~~edI~v~v~~~~L~I~g~~ 38 (83)
T cd06526 13 LDVKGFKPEELKVKVSDNKLVVEGKH 38 (83)
T ss_pred EECCCCCHHHcEEEEECCEEEEEEEE
Confidence 34667653 7778888999999974
No 51
>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=31.38 E-value=78 Score=22.39 Aligned_cols=31 Identities=19% Similarity=0.401 Sum_probs=24.2
Q ss_pred CeEEEEeeCCHHHHHHHHHh-cC-CeEEeecCC
Q 033646 20 KKLTVIGDIDPVSIVSKLRK-LC-HTEILSVGP 50 (114)
Q Consensus 20 ~kvtV~G~vDp~~lv~~LrK-~g-~aeivsv~p 50 (114)
.++.|.|++.-..|++.|++ .| .+.+++.|.
T Consensus 35 Dr~~v~~~~Tl~~li~~~~~~~~lev~ml~~g~ 67 (125)
T PF09358_consen 35 DRIEVNGDMTLQELIDYFKEKYGLEVTMLSQGV 67 (125)
T ss_dssp -EEEEES--BHHHHHHHHHHTTS-EEEEEEETT
T ss_pred eEEEEcCCCCHHHHHHHHHHHhCceEEEEEeCC
Confidence 47888899999999999985 57 999999874
No 52
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=31.24 E-value=87 Score=19.38 Aligned_cols=26 Identities=23% Similarity=0.346 Sum_probs=19.8
Q ss_pred EEEEecCCCeEEEEeeCCHHHHHHHH
Q 033646 12 SISMDMKEKKLTVIGDIDPVSIVSKL 37 (114)
Q Consensus 12 sV~vD~~~~kvtV~G~vDp~~lv~~L 37 (114)
+|.+|...+.|.|.|+-+-...+..|
T Consensus 47 ~i~~d~~tNsliv~g~~~~~~~i~~l 72 (82)
T PF03958_consen 47 RIVADERTNSLIVRGTPEDLEQIREL 72 (82)
T ss_dssp EEEEECTTTEEEEEEEHHHHHHHHHH
T ss_pred EEEEECCCCEEEEEeCHHHHHHHHHH
Confidence 89999999999999985444444433
No 53
>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways. They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.
Probab=30.81 E-value=65 Score=21.44 Aligned_cols=23 Identities=30% Similarity=0.561 Sum_probs=17.5
Q ss_pred CCeEEEEeeCCHHHHHHHHHhcC
Q 033646 19 EKKLTVIGDIDPVSIVSKLRKLC 41 (114)
Q Consensus 19 ~~kvtV~G~vDp~~lv~~LrK~g 41 (114)
..+++|.|.+|+..+.+.|++..
T Consensus 38 p~~i~i~gRl~~~~~~~yl~~i~ 60 (119)
T PF07744_consen 38 PKKIDIRGRLDPEKVWDYLRQIR 60 (119)
T ss_dssp -EEE-EEEE-SHHHHHHHHHHTS
T ss_pred CcEEEEEeecCHHHHHHHHHhcc
Confidence 46889999999999999998754
No 54
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=30.33 E-value=96 Score=20.09 Aligned_cols=23 Identities=13% Similarity=0.242 Sum_probs=19.0
Q ss_pred CCCeEEEEeeCCHHHHHHHHHhc
Q 033646 18 KEKKLTVIGDIDPVSIVSKLRKL 40 (114)
Q Consensus 18 ~~~kvtV~G~vDp~~lv~~LrK~ 40 (114)
.+|+++|+|.-++.++..++++.
T Consensus 56 ~sGki~itGaks~~~~~~a~~~i 78 (86)
T PF00352_consen 56 SSGKIVITGAKSEEEAKKAIEKI 78 (86)
T ss_dssp TTSEEEEEEESSHHHHHHHHHHH
T ss_pred cCCEEEEEecCCHHHHHHHHHHH
Confidence 67999999998888888777653
No 55
>cd06472 ACD_ScHsp26_like Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large 24-mers storage forms which upon heat shock disassociate into dimers. These dimers initiate the interaction with non-native substrate proteins and re-assemble into large globular assemblies having one monomer of substrate bound per dimer. This group also contains Arabidopsis thaliana (Ath) Hsp15.7, a peroxisomal matrix protein which can complement the morphological phenotype of S. cerevisiae mutants deficient in Hsps26. AthHsp15.7 is minimally expressed under normal conditions and is strongly induced by heat and oxidative st
Probab=30.11 E-value=60 Score=21.03 Aligned_cols=25 Identities=16% Similarity=0.516 Sum_probs=18.6
Q ss_pred ccCCCCcc--EEEEecCC-CeEEEEeeC
Q 033646 4 VSGLAGVD--SISMDMKE-KKLTVIGDI 28 (114)
Q Consensus 4 l~~l~GV~--sV~vD~~~-~kvtV~G~v 28 (114)
...|+||. +|+|+..+ +.|+|.|.-
T Consensus 14 ~~~lPGv~~edi~i~v~~~~~L~I~g~~ 41 (92)
T cd06472 14 KADVPGVKKEDVKVEVEDGRVLRISGER 41 (92)
T ss_pred EEECCCCChHhEEEEEeCCCEEEEEEEe
Confidence 35688886 47777766 489999975
No 56
>PTZ00423 glideosome-associated protein 45; Provisional
Probab=29.09 E-value=20 Score=27.29 Aligned_cols=11 Identities=55% Similarity=1.105 Sum_probs=9.2
Q ss_pred cccCCCCeeeC
Q 033646 104 AEEDPNACVIC 114 (114)
Q Consensus 104 ~eE~pn~C~Ic 114 (114)
-+-|||+|.||
T Consensus 171 ~~Hden~CkIC 181 (193)
T PTZ00423 171 ERHDENACKIC 181 (193)
T ss_pred cccCcccCchh
Confidence 35689999999
No 57
>COG2072 TrkA Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]
Probab=28.27 E-value=87 Score=26.43 Aligned_cols=35 Identities=23% Similarity=0.387 Sum_probs=29.7
Q ss_pred EecCCCeEEEEee-CCHHHHHHHHHhcC-CeEEeecC
Q 033646 15 MDMKEKKLTVIGD-IDPVSIVSKLRKLC-HTEILSVG 49 (114)
Q Consensus 15 vD~~~~kvtV~G~-vDp~~lv~~LrK~g-~aeivsv~ 49 (114)
.|+..++|.|+|. ....+|+..|.+.| ++.+.-=.
T Consensus 171 ~~~~GKrV~VIG~GaSA~di~~~l~~~ga~vt~~qRs 207 (443)
T COG2072 171 EDLRGKRVLVIGAGASAVDIAPELAEVGASVTLSQRS 207 (443)
T ss_pred cccCCCeEEEECCCccHHHHHHHHHhcCCeeEEEecC
Confidence 4788999999998 89999999999998 77766433
No 58
>PF05309 TraE: TraE protein; InterPro: IPR007973 This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilisation of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression []. The exact function of the TraE protein is unknown.; GO: 0000746 conjugation
Probab=28.08 E-value=63 Score=23.98 Aligned_cols=19 Identities=26% Similarity=0.350 Sum_probs=16.2
Q ss_pred ccEEEEecCCCeEEEEeeC
Q 033646 10 VDSISMDMKEKKLTVIGDI 28 (114)
Q Consensus 10 V~sV~vD~~~~kvtV~G~v 28 (114)
+.++.+|..++++.|+|++
T Consensus 130 ~~~i~~d~~~~~V~V~G~l 148 (187)
T PF05309_consen 130 PKSIEVDPETLTVFVTGTL 148 (187)
T ss_pred EeEEEEecCCCEEEEEEEE
Confidence 3578999999999999973
No 59
>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=28.05 E-value=84 Score=19.20 Aligned_cols=20 Identities=25% Similarity=0.312 Sum_probs=17.0
Q ss_pred CeEEEEee-CCHHHHHHHHHh
Q 033646 20 KKLTVIGD-IDPVSIVSKLRK 39 (114)
Q Consensus 20 ~kvtV~G~-vDp~~lv~~LrK 39 (114)
+.|+|+|. -+|.++.++|.+
T Consensus 6 G~Isvs~~~~s~~d~~~~la~ 26 (56)
T PF07338_consen 6 GTISVSGNFGSPDDAEEALAK 26 (56)
T ss_dssp EEEEEEEECSSHHHHHHHHHH
T ss_pred EEEEEccccCCHHHHHHHHHH
Confidence 47899998 899999999973
No 60
>PRK06719 precorrin-2 dehydrogenase; Validated
Probab=27.83 E-value=1.2e+02 Score=21.99 Aligned_cols=38 Identities=16% Similarity=0.242 Sum_probs=28.0
Q ss_pred EEEEecCCCeEEEEee-CCHHHHHHHHHhcC-CeEEeecC
Q 033646 12 SISMDMKEKKLTVIGD-IDPVSIVSKLRKLC-HTEILSVG 49 (114)
Q Consensus 12 sV~vD~~~~kvtV~G~-vDp~~lv~~LrK~g-~aeivsv~ 49 (114)
-+-+|+++.++.|.|- -=....+..|.+.| .+.+|++.
T Consensus 6 P~~l~l~~~~vlVvGGG~va~rka~~Ll~~ga~V~VIsp~ 45 (157)
T PRK06719 6 PLMFNLHNKVVVIIGGGKIAYRKASGLKDTGAFVTVVSPE 45 (157)
T ss_pred ceEEEcCCCEEEEECCCHHHHHHHHHHHhCCCEEEEEcCc
Confidence 3678999999999975 33345666777778 88888643
No 61
>PRK12342 hypothetical protein; Provisional
Probab=27.75 E-value=95 Score=24.67 Aligned_cols=46 Identities=20% Similarity=0.169 Sum_probs=32.0
Q ss_pred CCCCccEEEEecCCCeEE------EEeeCCHHHHHHHHH-h-cC-CeEEeecCCCC
Q 033646 6 GLAGVDSISMDMKEKKLT------VIGDIDPVSIVSKLR-K-LC-HTEILSVGPAK 52 (114)
Q Consensus 6 ~l~GV~sV~vD~~~~kvt------V~G~vDp~~lv~~Lr-K-~g-~aeivsv~p~k 52 (114)
..+....+.+|. ++.+. +.+.+|...|=.+|| | .| .+..+|+||+.
T Consensus 9 qVPD~~~v~~~~-~~~l~r~~~~~~iNp~D~~AlE~AlrLk~~g~~Vtvls~Gp~~ 63 (254)
T PRK12342 9 LVPEEQDIVVTP-ERTLNFDNAEAKISQFDLNAIEAASQLATDGDEIAALTVGGSL 63 (254)
T ss_pred ECcCCCceEECC-CCCEEcCCCCccCChhhHHHHHHHHHHhhcCCEEEEEEeCCCh
Confidence 345566788885 45544 334567777878887 4 46 99999999975
No 62
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=27.66 E-value=2.5e+02 Score=20.66 Aligned_cols=41 Identities=10% Similarity=0.255 Sum_probs=31.6
Q ss_pred CCccE--EEEecCCCeEEEEee--CCHHHHHHHHHhcCCeEEeec
Q 033646 8 AGVDS--ISMDMKEKKLTVIGD--IDPVSIVSKLRKLCHTEILSV 48 (114)
Q Consensus 8 ~GV~s--V~vD~~~~kvtV~G~--vDp~~lv~~LrK~g~aeivsv 48 (114)
+|.+. .-+|+.++-|.+... +|..+|++.|...|+.-||.-
T Consensus 39 PG~ttgiAildL~G~~l~l~S~R~~~~~evi~~I~~~G~PviVAt 83 (138)
T PF04312_consen 39 PGTTTGIAILDLDGELLDLKSSRNMSRSEVIEWISEYGKPVIVAT 83 (138)
T ss_pred CCceeEEEEEecCCcEEEEEeecCCCHHHHHHHHHHcCCEEEEEe
Confidence 45544 356888888888763 999999999999996666654
No 63
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=27.22 E-value=1.2e+02 Score=22.85 Aligned_cols=39 Identities=10% Similarity=0.139 Sum_probs=27.9
Q ss_pred EEEecCCCeEEEEee-CCHHHHHHHHHhcC-CeEEeecCCC
Q 033646 13 ISMDMKEKKLTVIGD-IDPVSIVSKLRKLC-HTEILSVGPA 51 (114)
Q Consensus 13 V~vD~~~~kvtV~G~-vDp~~lv~~LrK~g-~aeivsv~p~ 51 (114)
+-+|+.++++.|.|- --...-+..|.+.| ++.++++.+.
T Consensus 3 ~~l~l~gk~vlVvGgG~va~rk~~~Ll~~ga~VtVvsp~~~ 43 (205)
T TIGR01470 3 VFANLEGRAVLVVGGGDVALRKARLLLKAGAQLRVIAEELE 43 (205)
T ss_pred eEEEcCCCeEEEECcCHHHHHHHHHHHHCCCEEEEEcCCCC
Confidence 457899999999875 33344456666788 9999987544
No 64
>PRK11023 outer membrane lipoprotein; Provisional
Probab=27.10 E-value=95 Score=23.28 Aligned_cols=28 Identities=11% Similarity=0.253 Sum_probs=23.1
Q ss_pred EEEEecCCCeEEEEeeCCHHHHHHHHHh
Q 033646 12 SISMDMKEKKLTVIGDIDPVSIVSKLRK 39 (114)
Q Consensus 12 sV~vD~~~~kvtV~G~vDp~~lv~~LrK 39 (114)
+|.+...++.|+++|.++-.....+..+
T Consensus 69 ~I~V~v~~G~V~L~G~V~~~~~k~~A~~ 96 (191)
T PRK11023 69 RINVTAYQGKVLLTGQSPNAELSERAKQ 96 (191)
T ss_pred eEEEEEECCEEEEEEEeCCHHHHHHHHH
Confidence 6889999999999999988776666553
No 65
>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=26.50 E-value=62 Score=21.28 Aligned_cols=45 Identities=24% Similarity=0.459 Sum_probs=25.7
Q ss_pred ccCCCCccEEEEec-CCCeEEEEeeCCHHHHHHHH----HhcCCeEEeecC
Q 033646 4 VSGLAGVDSISMDM-KEKKLTVIGDIDPVSIVSKL----RKLCHTEILSVG 49 (114)
Q Consensus 4 l~~l~GV~sV~vD~-~~~kvtV~G~vDp~~lv~~L----rK~g~aeivsv~ 49 (114)
+....|-+.+++.. .+++++|.|+ +++.|...| +-.|++.|..-|
T Consensus 25 ~~~~~~~d~F~l~~~~~gki~I~G~-s~vala~Gl~~YLk~~c~~~isW~g 74 (86)
T PF12971_consen 25 IPSSNGKDVFELSSADNGKIVIRGN-SGVALASGLNWYLKYYCHVHISWNG 74 (86)
T ss_dssp ---BTTBEEEEEEE-SSS-EEEEES-SHHHHHHHHHHHHHHHS--B--TT-
T ss_pred ecCCCCCCEEEEEeCCCCeEEEEeC-CHHHHHHHHHHHHHHHhCceEeecC
Confidence 33445888999998 9999999997 344555554 445677665543
No 66
>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=26.44 E-value=1.8e+02 Score=18.85 Aligned_cols=37 Identities=16% Similarity=0.248 Sum_probs=24.9
Q ss_pred ccccCCCCccEEEEecCCCeEEEEee-CCHHHHHHHHHh
Q 033646 2 KTVSGLAGVDSISMDMKEKKLTVIGD-IDPVSIVSKLRK 39 (114)
Q Consensus 2 Kal~~l~GV~sV~vD~~~~kvtV~G~-vDp~~lv~~LrK 39 (114)
++|..++||+=-..|-. +|++|+=. -+...+.+.|..
T Consensus 22 ~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~ 59 (79)
T PF03927_consen 22 EALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDA 59 (79)
T ss_dssp HHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHH
T ss_pred HHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHH
Confidence 46889999965566665 78777633 555666666654
No 67
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=25.79 E-value=1.2e+02 Score=22.00 Aligned_cols=24 Identities=21% Similarity=0.403 Sum_probs=21.0
Q ss_pred CCCeEEEEeeCCHHHHHHHHHhcC
Q 033646 18 KEKKLTVIGDIDPVSIVSKLRKLC 41 (114)
Q Consensus 18 ~~~kvtV~G~vDp~~lv~~LrK~g 41 (114)
+++++++.|.+++..|-+.|++.-
T Consensus 76 ~~~~lii~G~~~~~~i~~~L~~yI 99 (138)
T PRK03988 76 EGGRLILQGKFSPRVINEKIDRYV 99 (138)
T ss_pred cCCEEEEEEeeCHHHHHHHHHHHH
Confidence 469999999999999999998744
No 68
>TIGR02761 TraE_TIGR type IV conjugative transfer system protein TraE. TraE is a component of type IV secretion systems involved in conjugative transfer of plasmid DNA. The function of the TraE protein is unknown.
Probab=25.79 E-value=69 Score=23.89 Aligned_cols=19 Identities=21% Similarity=0.349 Sum_probs=16.1
Q ss_pred ccEEEEecCCCeEEEEeeC
Q 033646 10 VDSISMDMKEKKLTVIGDI 28 (114)
Q Consensus 10 V~sV~vD~~~~kvtV~G~v 28 (114)
+.++.+|.++++|.|.|++
T Consensus 130 ~~~i~v~~~~~~V~V~G~l 148 (181)
T TIGR02761 130 PKSVEWNPQEGTVKVRGHL 148 (181)
T ss_pred eeeEEEccCCCEEEEEEEE
Confidence 3578999999999999973
No 69
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=25.42 E-value=1.2e+02 Score=22.00 Aligned_cols=23 Identities=9% Similarity=0.238 Sum_probs=20.4
Q ss_pred CCeEEEEeeCCHHHHHHHHHhcC
Q 033646 19 EKKLTVIGDIDPVSIVSKLRKLC 41 (114)
Q Consensus 19 ~~kvtV~G~vDp~~lv~~LrK~g 41 (114)
++++++.|.+++..|-..|++.-
T Consensus 72 ~~rlii~G~~~~~~i~~~L~~yI 94 (133)
T TIGR00311 72 GGRLILQGKFTHFLLNERIEDYV 94 (133)
T ss_pred CCEEEEEeecCHHHHHHHHHHHH
Confidence 58999999999999999998754
No 70
>PF01565 FAD_binding_4: FAD binding domain This is only a subset of the Pfam family; InterPro: IPR006094 Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. One of the enzymes Vanillyl-alcohol oxidase (VAO, 1.1.3.38 from EC) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 []. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging from aromatic amines to 4-alkylphenols. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZR6_A 3HSU_A 2AXR_A 3D2J_A 3D2H_A 3FW9_A 3FW8_A 3FW7_A 3GSY_A 3FWA_A ....
Probab=24.39 E-value=1.5e+02 Score=19.96 Aligned_cols=29 Identities=17% Similarity=0.109 Sum_probs=25.7
Q ss_pred EEEecCCCeEEEEeeCCHHHHHHHHHhcC
Q 033646 13 ISMDMKEKKLTVIGDIDPVSIVSKLRKLC 41 (114)
Q Consensus 13 V~vD~~~~kvtV~G~vDp~~lv~~LrK~g 41 (114)
+++|.+.+.++|.+-+.-.+|.+.|...+
T Consensus 57 ~~id~~~~~v~v~aG~~~~~l~~~l~~~g 85 (139)
T PF01565_consen 57 IEIDPENGTVTVGAGVTWGDLYEALAPRG 85 (139)
T ss_dssp EEEETTTTEEEEETTSBHHHHHHHHHHHT
T ss_pred ccccccceeEEEeccccchhccccccccc
Confidence 67788899999999999999999997766
No 71
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=24.00 E-value=1.7e+02 Score=17.47 Aligned_cols=31 Identities=19% Similarity=0.344 Sum_probs=20.3
Q ss_pred CCCccEEEEecCCCeEEEEeeCCHHHHHHHHHhc
Q 033646 7 LAGVDSISMDMKEKKLTVIGDIDPVSIVSKLRKL 40 (114)
Q Consensus 7 l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~ 40 (114)
+.||=++-+ +++....|..++..|.+.|+++
T Consensus 51 v~~vPt~~~---~g~~~~~G~~~~~~l~~~l~~~ 81 (82)
T TIGR00411 51 IMAVPAIVI---NGDVEFIGAPTKEELVEAIKKR 81 (82)
T ss_pred CccCCEEEE---CCEEEEecCCCHHHHHHHHHhh
Confidence 345555555 3446777888888888887753
No 72
>cd02991 UAS_ETEA UAS family, ETEA subfamily; composed of proteins similar to human ETEA protein, the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. ETEA shows homology to Fas-associated factor 1 (FAF1); both containing UAS and UBX (ubiquitin-associated) domains. Compared to FAF1, however, ETEA lacks the ubiquitin-associated UBA domain and a nuclear targeting domain. The function of ETEA is still unknown. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that ETEA could be involved in modulating Fas-mediated apoptosis of T-cells and eosinophils of atopic dermatitis patients, making them more resistant to apoptosis.
Probab=23.79 E-value=1.3e+02 Score=20.66 Aligned_cols=28 Identities=21% Similarity=0.481 Sum_probs=21.1
Q ss_pred EEecCCCeEE----EEeeCCHHHHHHHHHhcC
Q 033646 14 SMDMKEKKLT----VIGDIDPVSIVSKLRKLC 41 (114)
Q Consensus 14 ~vD~~~~kvt----V~G~vDp~~lv~~LrK~g 41 (114)
-+++.+++++ +.|.++|.+|+..|+...
T Consensus 82 ~l~~~~~~~~vv~~i~G~~~~~~ll~~L~~~~ 113 (116)
T cd02991 82 MIMLKDNRMTIVGRLEGLIQPEDLINRLTFIM 113 (116)
T ss_pred EEEecCCceEEEEEEeCCCCHHHHHHHHHHHH
Confidence 3456666665 468899999999998754
No 73
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=23.73 E-value=27 Score=17.94 Aligned_cols=12 Identities=33% Similarity=0.833 Sum_probs=9.6
Q ss_pred ccccCCCCeeeC
Q 033646 103 SAEEDPNACVIC 114 (114)
Q Consensus 103 ~~eE~pn~C~Ic 114 (114)
...|.|+.|.+|
T Consensus 9 H~~~k~~~C~~C 20 (26)
T PF13465_consen 9 HTGEKPYKCPYC 20 (26)
T ss_dssp HSSSSSEEESSS
T ss_pred cCCCCCCCCCCC
Confidence 357889999888
No 74
>PRK06718 precorrin-2 dehydrogenase; Reviewed
Probab=23.44 E-value=1.6e+02 Score=22.18 Aligned_cols=37 Identities=19% Similarity=0.287 Sum_probs=27.6
Q ss_pred EEEecCCCeEEEEeeCCH-HHHHHHHHhcC-CeEEeecC
Q 033646 13 ISMDMKEKKLTVIGDIDP-VSIVSKLRKLC-HTEILSVG 49 (114)
Q Consensus 13 V~vD~~~~kvtV~G~vDp-~~lv~~LrK~g-~aeivsv~ 49 (114)
+-+|+++.++.|.|-=+. ...+..|.+.| ++.+++..
T Consensus 4 l~l~l~~k~vLVIGgG~va~~ka~~Ll~~ga~V~VIs~~ 42 (202)
T PRK06718 4 LMIDLSNKRVVIVGGGKVAGRRAITLLKYGAHIVVISPE 42 (202)
T ss_pred eEEEcCCCEEEEECCCHHHHHHHHHHHHCCCeEEEEcCC
Confidence 467999999999986333 44566777888 88888754
No 75
>PRK12698 flgH flagellar basal body L-ring protein; Reviewed
Probab=22.99 E-value=48 Score=26.02 Aligned_cols=28 Identities=18% Similarity=0.300 Sum_probs=24.5
Q ss_pred CCCccEEEEecCCCeEEEEeeCCHHHHH
Q 033646 7 LAGVDSISMDMKEKKLTVIGDIDPVSIV 34 (114)
Q Consensus 7 l~GV~sV~vD~~~~kvtV~G~vDp~~lv 34 (114)
+.|-..|.++-..+.+++.|.|.|.+|-
T Consensus 154 I~GeK~i~vN~~~e~I~lsGvVRP~DI~ 181 (224)
T PRK12698 154 IRGEKWISINNGDEFIRLTGIVRSQDIT 181 (224)
T ss_pred EEEEEEEEECCCEEEEEEEEEECHHHCC
Confidence 4677889999999999999999999864
No 76
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=22.98 E-value=2.3e+02 Score=18.64 Aligned_cols=35 Identities=20% Similarity=0.264 Sum_probs=26.3
Q ss_pred cEEEEecCCCeEEE----EeeCCHHHHHHHHHhcC--CeEE
Q 033646 11 DSISMDMKEKKLTV----IGDIDPVSIVSKLRKLC--HTEI 45 (114)
Q Consensus 11 ~sV~vD~~~~kvtV----~G~vDp~~lv~~LrK~g--~aei 45 (114)
-+++.-...+++|+ .+.+|=-.|+..|.+.. ++++
T Consensus 45 vd~e~~~D~~k~~fyy~a~~rvDFR~Lvr~L~~~f~~RIem 85 (88)
T PF04468_consen 45 VDVEYQFDGSKLTFYYTAESRVDFRELVRDLAREFKTRIEM 85 (88)
T ss_pred EEEEEEcCCCEEEEEEEeCCcCcHHHHHHHHHHHhCceEEE
Confidence 35566778889999 35699999999998755 4444
No 77
>TIGR00735 hisF imidazoleglycerol phosphate synthase, cyclase subunit.
Probab=22.42 E-value=2.1e+02 Score=22.02 Aligned_cols=37 Identities=19% Similarity=0.350 Sum_probs=27.1
Q ss_pred EEEecCCCeEEEEee--------CCHHHHHHHHHhcC--CeEEeecCC
Q 033646 13 ISMDMKEKKLTVIGD--------IDPVSIVSKLRKLC--HTEILSVGP 50 (114)
Q Consensus 13 V~vD~~~~kvtV~G~--------vDp~~lv~~LrK~g--~aeivsv~p 50 (114)
..+|+.++++ |.|. .||..++++++..| ..-++-...
T Consensus 8 p~iD~~~G~~-V~~~~~~~~~~~~dp~~~a~~~~~~G~~~l~v~Dl~~ 54 (254)
T TIGR00735 8 PCLDVRDGRV-VKGVQFLNLRDAGDPVELAQRYDEEGADELVFLDITA 54 (254)
T ss_pred EEEEeECCEE-EEeEeecCceECCCHHHHHHHHHHcCCCEEEEEcCCc
Confidence 4789999988 7763 59999999999877 344444433
No 78
>PRK14114 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=21.39 E-value=2.1e+02 Score=22.25 Aligned_cols=35 Identities=29% Similarity=0.542 Sum_probs=26.9
Q ss_pred EEEEecCCCeEEEEe-----eCCHHHHHHHHHhcC-CeEEe
Q 033646 12 SISMDMKEKKLTVIG-----DIDPVSIVSKLRKLC-HTEIL 46 (114)
Q Consensus 12 sV~vD~~~~kvtV~G-----~vDp~~lv~~LrK~g-~aeiv 46 (114)
-+++|.+++++.+.| .+++.+++..+.+.| ..-|+
T Consensus 123 vvslD~k~g~v~~~gw~~~~~~~~~e~~~~~~~~g~~~ii~ 163 (241)
T PRK14114 123 VFSLDTRGGKVAFKGWLAEEEIDPVSLLKRLKEYGLEEIVH 163 (241)
T ss_pred EEEEEccCCEEeeCCCeecCCCCHHHHHHHHHhcCCCEEEE
Confidence 478898888888766 378999999999888 43333
No 79
>PRK13726 conjugal transfer pilus assembly protein TraE; Provisional
Probab=21.28 E-value=94 Score=23.66 Aligned_cols=18 Identities=11% Similarity=0.159 Sum_probs=15.6
Q ss_pred cEEEEecCCCeEEEEeeC
Q 033646 11 DSISMDMKEKKLTVIGDI 28 (114)
Q Consensus 11 ~sV~vD~~~~kvtV~G~v 28 (114)
.++.+|..++++.|.|++
T Consensus 131 ~~i~v~~~~~~V~V~Gtl 148 (188)
T PRK13726 131 TSVRVWPQYGRVDIRGVL 148 (188)
T ss_pred eeEEEccCCCEEEEEEEE
Confidence 578999999999999874
No 80
>PF00988 CPSase_sm_chain: Carbamoyl-phosphate synthase small chain, CPSase domain; InterPro: IPR002474 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the N-terminal domain of the small subunit of carbamoyl phosphate synthase. The small subunit has a 3-layer beta/beta/alpha structure, and is thought to be mobile in most proteins that carry it. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity.; GO: 0006807 nitrogen compound metabolic process; PDB: 1CE8_B 1KEE_B 1CS0_D 1T36_D 1M6V_H 1A9X_F 1JDB_I 1BXR_F 1C3O_B 1C30_F ....
Probab=21.25 E-value=62 Score=23.55 Aligned_cols=28 Identities=29% Similarity=0.366 Sum_probs=19.3
Q ss_pred CCCeEEEEeeCCHHHHHHHHHhcC--CeEE
Q 033646 18 KEKKLTVIGDIDPVSIVSKLRKLC--HTEI 45 (114)
Q Consensus 18 ~~~kvtV~G~vDp~~lv~~LrK~g--~aei 45 (114)
+.+.+-..-.+|.-.|+.+||+.| .+.|
T Consensus 101 ~~~~ipgi~gvDTRaLt~~lR~~G~m~g~I 130 (131)
T PF00988_consen 101 KEHGIPGISGVDTRALTRKLREKGSMKGVI 130 (131)
T ss_dssp HHTT-EEEESS-HHHHHHHHHHH--EEEEE
T ss_pred HHCCCeeeeCCcHHHHHHHHHhcCCceEEE
Confidence 345566666799999999999988 6655
No 81
>PF13738 Pyr_redox_3: Pyridine nucleotide-disulphide oxidoreductase; PDB: 3D1C_A 4A9W_B 2YLX_A 2YM2_A 2YLW_A 2YLR_A 2YM1_A 2YLS_A 1W4X_A 2YLT_A ....
Probab=21.11 E-value=1.1e+02 Score=21.74 Aligned_cols=35 Identities=29% Similarity=0.463 Sum_probs=25.7
Q ss_pred ecCCCeEEEEee-CCHHHHHHHHHhcC-CeEEeecCC
Q 033646 16 DMKEKKLTVIGD-IDPVSIVSKLRKLC-HTEILSVGP 50 (114)
Q Consensus 16 D~~~~kvtV~G~-vDp~~lv~~LrK~g-~aeivsv~p 50 (114)
+..+++|.|.|. ....+++..|.+.+ ++.++.=.|
T Consensus 164 ~~~~k~V~VVG~G~SA~d~a~~l~~~g~~V~~~~R~~ 200 (203)
T PF13738_consen 164 DFKGKRVVVVGGGNSAVDIAYALAKAGKSVTLVTRSP 200 (203)
T ss_dssp GCTTSEEEEE--SHHHHHHHHHHTTTCSEEEEEESS-
T ss_pred hcCCCcEEEEcChHHHHHHHHHHHhhCCEEEEEecCC
Confidence 456789999987 78889999998888 787775433
No 82
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=20.74 E-value=1.1e+02 Score=24.97 Aligned_cols=36 Identities=17% Similarity=0.141 Sum_probs=28.8
Q ss_pred ccCCCCccEEEEecCCCeEEEEeeCCHHHHHHHHHhcC
Q 033646 4 VSGLAGVDSISMDMKEKKLTVIGDIDPVSIVSKLRKLC 41 (114)
Q Consensus 4 l~~l~GV~sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g 41 (114)
+++|.+|. ++|..++.+||..-+--.+|.+.|+..|
T Consensus 81 l~~mn~i~--~id~~~~~~~v~aGv~l~~l~~~l~~~G 116 (459)
T COG0277 81 LSRLNRIL--EIDPEDGTATVQAGVTLEDLEKALAPHG 116 (459)
T ss_pred chhhcchh--ccCcCCCEEEEcCCccHHHHHHHHHHcC
Confidence 34555555 6788999999998888899999998765
No 83
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=20.59 E-value=1.1e+02 Score=24.47 Aligned_cols=29 Identities=24% Similarity=0.369 Sum_probs=24.1
Q ss_pred EEEEecCCCeEEEEeeCCHHHHHHHHHhcC
Q 033646 12 SISMDMKEKKLTVIGDIDPVSIVSKLRKLC 41 (114)
Q Consensus 12 sV~vD~~~~kvtV~G~vDp~~lv~~LrK~g 41 (114)
+.++| .+++++|.|.+.+.++-..||+--
T Consensus 150 sGSid-g~~rLviKGrfq~kq~e~VLRrYI 178 (231)
T KOG2768|consen 150 SGSID-GQQRLVIKGRFQQKQFENVLRRYI 178 (231)
T ss_pred ccccC-CCceEEEeccccHHHHHHHHHHHH
Confidence 45677 468999999999999999999744
No 84
>PRK12788 flgH flagellar basal body L-ring protein; Reviewed
Probab=20.42 E-value=57 Score=25.89 Aligned_cols=28 Identities=21% Similarity=0.480 Sum_probs=24.6
Q ss_pred CCCccEEEEecCCCeEEEEeeCCHHHHH
Q 033646 7 LAGVDSISMDMKEKKLTVIGDIDPVSIV 34 (114)
Q Consensus 7 l~GV~sV~vD~~~~kvtV~G~vDp~~lv 34 (114)
+.|=..|.++.+.+.++|.|-|.|.+|-
T Consensus 165 I~G~kev~vN~e~~~i~vsGvVRP~DI~ 192 (234)
T PRK12788 165 ISGSQEVRVNYEMRVLNVGGIVRPLDIT 192 (234)
T ss_pred EEEEEEEEECCCEEEEEEEEEECHHHCC
Confidence 4677889999999999999999999864
No 85
>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=20.33 E-value=1.2e+02 Score=20.11 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=27.2
Q ss_pred cccCCCCccEEEEecCCCeEEEE--eeCCHHHHHHHHHhc
Q 033646 3 TVSGLAGVDSISMDMKEKKLTVI--GDIDPVSIVSKLRKL 40 (114)
Q Consensus 3 al~~l~GV~sV~vD~~~~kvtV~--G~vDp~~lv~~LrK~ 40 (114)
+|-.++||.+|-+.. +=|||+ +++|=..|...|+..
T Consensus 42 ~Lf~i~gV~~Vf~~~--dfItVtK~~~~~W~~l~~~I~~~ 79 (87)
T PF08712_consen 42 ALFAIPGVKSVFIGD--DFITVTKNPDADWEDLKPEIREV 79 (87)
T ss_dssp HHHTSTTEEEEEEET--TEEEEEE-TTS-HHHHHHHHHHH
T ss_pred HhcCCCCEeEEEEEC--CEEEEeeCCCCCHHHHHHHHHHH
Confidence 466899999998864 578886 458888888888754
No 86
>PF05188 MutS_II: MutS domain II; InterPro: IPR007860 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the connector domain (domain 2) found in proteins of the MutS family. The structure of the MutS connector domain consists of a parallel beta-sheet surrounded by four alpha helices, which is similar to the structure of the Holliday junction resolvase ruvC.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 2WTU_A ....
Probab=20.30 E-value=2.7e+02 Score=18.35 Aligned_cols=37 Identities=22% Similarity=0.205 Sum_probs=29.6
Q ss_pred EEEecCCCeEEEEeeCCHHHHHHHHHhcCCeEEeecC
Q 033646 13 ISMDMKEKKLTVIGDIDPVSIVSKLRKLCHTEILSVG 49 (114)
Q Consensus 13 V~vD~~~~kvtV~G~vDp~~lv~~LrK~g~aeivsv~ 49 (114)
+-+|...|.+.+.---|..+|...|.+....||+-..
T Consensus 18 a~~D~sTGe~~~~~~~d~~~L~~~L~~~~P~EIi~~~ 54 (137)
T PF05188_consen 18 AYIDLSTGEFYVTEFEDYSELKSELARLSPREIIIPE 54 (137)
T ss_dssp EEEETTTTEEEEEEEECHHHHHHHHHHH-ESEEEEET
T ss_pred EEEECCCCEEEEEEeCCHHHHHHHHHhcCCeEEEEcC
Confidence 4679999999998766799999999998877777654
Done!