Query 032659
Match_columns 136
No_of_seqs 113 out of 350
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 04:18:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032659.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032659hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3198 Signal recognition par 100.0 2.8E-45 6E-50 279.0 9.9 115 4-118 8-123 (152)
2 PF01922 SRP19: SRP19 protein; 100.0 4.1E-41 8.8E-46 240.2 8.9 94 12-108 1-95 (95)
3 PRK00754 signal recognition pa 100.0 2.4E-38 5.1E-43 226.5 8.5 91 8-109 3-94 (95)
4 PRK03745 signal recognition pa 100.0 1.3E-34 2.8E-39 208.9 7.9 90 10-110 2-98 (100)
5 COG1400 SEC65 Signal recogniti 100.0 1.6E-31 3.6E-36 190.5 7.9 88 10-108 2-90 (93)
6 PF12387 Peptidase_C74: Pestiv 70.4 0.17 3.6E-06 40.5 -5.2 68 9-76 53-120 (200)
7 cd07245 Glo_EDI_BRP_like_9 Thi 53.0 30 0.00066 22.1 4.0 44 35-85 68-111 (114)
8 COG3636 Predicted transcriptio 49.2 17 0.00037 26.5 2.5 24 38-61 74-97 (100)
9 PF14830 Haemocyan_bet_s: Haem 46.2 27 0.00058 25.5 3.2 37 41-89 56-92 (103)
10 COG1334 FlaG Uncharacterized f 45.8 1E+02 0.0023 23.0 6.3 35 70-104 76-112 (120)
11 PF00721 TMV_coat: Virus coat 45.4 62 0.0013 24.4 5.2 39 42-80 42-80 (152)
12 COG0602 NrdG Organic radical a 42.8 29 0.00062 27.7 3.2 29 40-68 86-114 (212)
13 PF03484 B5: tRNA synthetase B 39.5 1.1E+02 0.0023 19.9 6.5 50 39-103 18-67 (70)
14 TIGR01565 homeo_ZF_HD homeobox 39.3 34 0.00074 22.3 2.6 19 37-55 27-45 (58)
15 cd08349 BLMA_like Bleomycin bi 36.8 89 0.0019 20.2 4.4 47 35-86 62-108 (112)
16 COG2524 Predicted transcriptio 35.9 39 0.00084 28.9 3.0 58 40-102 218-292 (294)
17 PF00061 Lipocalin: Lipocalin 35.7 17 0.00038 25.2 0.8 51 5-56 83-134 (144)
18 PF02037 SAP: SAP domain; Int 35.0 27 0.00058 20.1 1.4 16 41-56 5-20 (35)
19 PF07487 SopE_GEF: SopE GEF do 34.9 17 0.00038 28.5 0.7 24 39-62 63-86 (165)
20 cd08356 Glo_EDI_BRP_like_17 Th 34.8 1E+02 0.0023 20.9 4.7 52 34-86 58-109 (113)
21 smart00513 SAP Putative DNA-bi 34.6 42 0.00091 19.1 2.2 17 40-56 4-20 (35)
22 PF00046 Homeobox: Homeobox do 34.3 27 0.00059 21.2 1.4 21 37-57 22-42 (57)
23 PF01120 Alpha_L_fucos: Alpha- 33.0 38 0.00083 28.7 2.6 28 41-71 139-166 (346)
24 cd00086 homeodomain Homeodomai 32.7 47 0.001 19.8 2.4 21 37-57 22-42 (59)
25 cd08357 Glo_EDI_BRP_like_18 Th 32.5 71 0.0015 21.3 3.4 49 36-86 72-120 (125)
26 KOG4549 Magnesium-dependent ph 31.7 58 0.0013 25.1 3.1 53 12-65 14-72 (144)
27 cd08351 ChaP_like ChaP, an enz 31.5 1.1E+02 0.0023 20.9 4.3 51 36-86 65-116 (123)
28 PF07524 Bromo_TP: Bromodomain 30.8 49 0.0011 21.8 2.3 19 38-56 57-75 (77)
29 smart00874 B5 tRNA synthetase 30.7 1.4E+02 0.0031 18.8 5.7 50 40-103 19-68 (71)
30 PF04273 DUF442: Putative phos 29.7 33 0.00071 24.7 1.4 24 37-60 41-64 (110)
31 COG0027 PurT Formate-dependent 29.6 44 0.00096 29.5 2.4 20 41-60 137-156 (394)
32 PF13443 HTH_26: Cro/C1-type H 29.1 37 0.0008 20.9 1.4 20 37-56 35-54 (63)
33 cd08794 Death_IRAK1 Death doma 29.0 35 0.00076 24.2 1.4 20 35-54 57-76 (84)
34 PRK09726 antitoxin HipB; Provi 27.7 95 0.0021 20.9 3.4 24 35-58 47-70 (88)
35 TIGR03070 couple_hipB transcri 27.6 82 0.0018 18.4 2.8 18 38-55 40-57 (58)
36 PHA01976 helix-turn-helix prot 27.3 65 0.0014 20.0 2.4 23 34-56 36-58 (67)
37 TIGR02684 dnstrm_HI1420 probab 27.3 72 0.0016 22.2 2.8 21 38-58 68-88 (89)
38 KOG3802 Transcription factor O 27.2 54 0.0012 29.3 2.5 23 37-59 316-338 (398)
39 PRK10477 outer membrane lipopr 26.9 63 0.0014 24.6 2.7 45 5-56 122-166 (177)
40 cd07233 Glyoxalase_I Glyoxalas 25.4 1.6E+02 0.0035 19.3 4.2 43 36-85 75-117 (121)
41 smart00576 BTP Bromodomain tra 25.3 68 0.0015 21.4 2.3 17 39-55 58-74 (77)
42 TIGR03365 Bsubt_queE 7-cyano-7 24.9 84 0.0018 25.2 3.1 41 40-80 87-128 (238)
43 smart00389 HOX Homeodomain. DN 24.8 75 0.0016 18.9 2.2 20 38-57 23-42 (56)
44 KOG3416 Predicted nucleic acid 24.6 52 0.0011 25.2 1.7 49 41-89 6-65 (134)
45 COG2313 IndA Uncharacterized e 24.5 74 0.0016 27.3 2.8 35 15-57 192-229 (310)
46 PF14528 LAGLIDADG_3: LAGLIDAD 24.4 1.2E+02 0.0026 19.4 3.3 25 38-62 30-54 (77)
47 cd07240 ED_TypeI_classII_N N-t 24.0 2E+02 0.0043 18.7 4.4 46 34-85 62-108 (117)
48 PRK00002 aroB 3-dehydroquinate 23.7 1.7E+02 0.0038 24.7 5.0 64 38-104 283-356 (358)
49 PF02222 ATP-grasp: ATP-grasp 23.4 1E+02 0.0022 23.8 3.2 19 41-59 16-34 (172)
50 PRK05783 hypothetical protein; 23.0 77 0.0017 22.1 2.3 27 31-57 9-35 (84)
51 KOG4201 Anthranilate synthase 23.0 58 0.0013 27.4 1.9 24 37-60 170-193 (289)
52 COG1828 PurS Phosphoribosylfor 22.9 80 0.0017 22.2 2.3 60 31-107 8-69 (83)
53 cd08309 Death_IRAK Death domai 22.5 78 0.0017 22.0 2.2 19 37-55 70-88 (95)
54 PF04343 DUF488: Protein of un 22.0 1.4E+02 0.0031 21.2 3.6 26 41-67 1-26 (122)
55 PF13299 CPSF100_C: Cleavage a 21.6 3.4E+02 0.0074 20.7 5.8 58 30-92 90-147 (161)
56 COG0677 WecC UDP-N-acetyl-D-ma 21.4 46 0.001 30.0 1.0 26 41-66 228-255 (436)
57 cd07262 Glo_EDI_BRP_like_19 Th 21.3 2.6E+02 0.0056 18.6 4.7 42 42-86 78-119 (123)
58 PF00550 PP-binding: Phosphopa 21.3 83 0.0018 19.2 2.0 23 27-49 45-67 (67)
59 PF04197 Birna_RdRp: Birnaviru 21.1 55 0.0012 31.8 1.5 27 34-60 501-527 (860)
60 COG0134 TrpC Indole-3-glycerol 21.1 88 0.0019 26.2 2.6 63 38-107 141-207 (254)
61 PF03544 TonB_C: Gram-negative 20.9 26 0.00056 22.3 -0.5 27 61-87 2-32 (79)
62 PF07499 RuvA_C: RuvA, C-termi 20.7 90 0.0019 18.9 2.0 15 42-56 3-17 (47)
63 PRK10291 glyoxalase I; Provisi 20.6 2.3E+02 0.005 19.3 4.4 47 35-86 69-115 (129)
64 PF00218 IGPS: Indole-3-glycer 20.4 81 0.0017 26.1 2.2 19 42-60 147-165 (254)
65 COG0072 PheT Phenylalanyl-tRNA 20.4 1E+02 0.0022 28.8 3.1 35 37-74 471-506 (650)
66 PRK13957 indole-3-glycerol-pho 20.3 97 0.0021 25.7 2.7 24 37-60 134-158 (247)
67 cd07241 Glo_EDI_BRP_like_3 Thi 20.2 2.6E+02 0.0057 18.3 4.5 39 42-86 84-122 (125)
68 PF12681 Glyoxalase_2: Glyoxal 20.1 2.2E+02 0.0047 18.3 4.0 44 37-86 62-105 (108)
No 1
>KOG3198 consensus Signal recognition particle, subunit Srp19 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.8e-45 Score=279.04 Aligned_cols=115 Identities=47% Similarity=0.718 Sum_probs=109.3
Q ss_pred ccccccCeEEEecccccCCcCcccccccchhccCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCC
Q 032659 4 QTARIKKWVILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDG 83 (136)
Q Consensus 4 ~~~~~~~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg 83 (136)
|-.+.++|+||||+|||+++|++||||||+++||+||+..||++||+.|||+|.+|++|+|||||.++|||||+|+++||
T Consensus 8 ~~~~~~r~ivlYP~Y~d~krt~~EGRripke~aVeNP~a~eI~Dvl~~lgl~~~~E~~K~hPrD~~n~GRVRvqlk~edG 87 (152)
T KOG3198|consen 8 DLEDQKRWIVLYPAYIDKKRTRKEGRRIPKEKAVENPLAKEIADVLRALGLNCLLEPNKKHPRDFVNPGRVRVQLKNEDG 87 (152)
T ss_pred ChhhccceEEEEEEEeccccchhhccccCHHHhhcCcchhHHHHHHHHhCCcccccccccCchhcCCCceEEEEeeccCC
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccCCCCCCHHHHHHHHHHHhhcCCCc-cCCCCCCC
Q 032659 84 TFVNPAISSRKQLMLHVAELVPRHPNR-TKKQEPAS 118 (136)
Q Consensus 84 ~~~~~~~~~K~~Ll~~Ia~~I~~~~~r-~~~~~~~~ 118 (136)
++++.+++++..||..+|++++++.+| .+.++++.
T Consensus 88 ~l~~~~~~sr~~~~~~~a~~ip~~~~R~~~~~~~a~ 123 (152)
T KOG3198|consen 88 TLYVIAFISRKSLMLPIAEMIPELKTRQPQKTGEAV 123 (152)
T ss_pred cEEeecchhHHHHHHHhhhhCcccccccccccCCcc
Confidence 999999999999999999999999999 45555544
No 2
>PF01922 SRP19: SRP19 protein; InterPro: IPR002778 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 3DLU_A 3DLV_B 2J37_B 1MFQ_B 3KTV_D 1RY1_B 1JID_A 1KVV_A 1KVN_A 3KTW_B ....
Probab=100.00 E-value=4.1e-41 Score=240.17 Aligned_cols=94 Identities=48% Similarity=0.808 Sum_probs=84.9
Q ss_pred EEEecccccCCcCcccccccchhccCCCCCHHHHHHHHHHcCCCeeEeccccCCcC-cCCCceEEEEeecCCCCccCCCC
Q 032659 12 VILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYPRD-FMQRGRVRVMLKREDGTFVNPAI 90 (136)
Q Consensus 12 ~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrd-w~~~GRVrV~l~~~dg~~~~~~~ 90 (136)
+||||+|||+++|+++|||||+++||+||+++||++||++|||++++|++|+|||| |+++|||+|+++++ ++||.+
T Consensus 1 ~vIyP~Y~Ds~~sr~~GRrv~k~~aV~~P~~~EI~~a~~~Lgl~~~~E~~K~yPr~~~~~~GRV~V~~~~~---~~~~~~ 77 (95)
T PF01922_consen 1 IVIYPAYFDSKKSRSEGRRVPKELAVENPTLEEIADACKKLGLPCVVEPDKRYPRDWWENPGRVRVQLKND---PVNPEI 77 (95)
T ss_dssp EEEEGGGGBTTSSTTTT--SSTTTSBSS--HHHHHHHHHHTTSEEEEETTECTTCGSTSCTTEEEEE-CST---BSSTTS
T ss_pred CEEccchhcCCCChhhccccChhhcCCCCCHHHHHHHHHHcCCCEEEccccCcChhhcccCceEEEEeCCC---cccCCC
Confidence 69999999999999999999999999999999999999999999999999999999 55699999998776 999999
Q ss_pred CCHHHHHHHHHHHhhcCC
Q 032659 91 SSRKQLMLHVAELVPRHP 108 (136)
Q Consensus 91 ~~K~~Ll~~Ia~~I~~~~ 108 (136)
++|.+||++||+.|+++|
T Consensus 78 ~~K~~Ll~~Ia~~i~~~r 95 (95)
T PF01922_consen 78 KSKKELLKKIAEKIKKIR 95 (95)
T ss_dssp SSHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHhC
Confidence 999999999999999763
No 3
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=100.00 E-value=2.4e-38 Score=226.50 Aligned_cols=91 Identities=31% Similarity=0.495 Sum_probs=85.3
Q ss_pred ccCeEEEecccccCCcCcccccccchhccCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcC-CCceEEEEeecCCCCcc
Q 032659 8 IKKWVILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFM-QRGRVRVMLKREDGTFV 86 (136)
Q Consensus 8 ~~~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~-~~GRVrV~l~~~dg~~~ 86 (136)
...++||||+|||+++|+++|||||+++||+||+++||++||++|||++++|++|+|||+|| ++|||+|+.
T Consensus 3 ~~~r~vIyP~Y~d~~~tr~eGRrv~k~~aV~~P~~~EI~~a~~~lgl~~~~e~~K~yPr~~~e~~GRv~V~~-------- 74 (95)
T PRK00754 3 DKGRIVIWPAYIDSTRSRSEGRIISRKLAVKEPRLEEIIEAAEKLGLNPEVEPDKAYPRSWWEVSGRVLVDK-------- 74 (95)
T ss_pred CcCcEEEeeccccCCCChhhcCccCHHHhccCCCHHHHHHHHHHcCCCeEEeeCCCCCchHhcCCCEEEECC--------
Confidence 35679999999999999999999999999999999999999999999999999999999999 699999972
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCC
Q 032659 87 NPAISSRKQLMLHVAELVPRHPN 109 (136)
Q Consensus 87 ~~~~~~K~~Ll~~Ia~~I~~~~~ 109 (136)
+.+|.+||+.||+.|++++.
T Consensus 75 ---~~~K~~ll~~Ia~~I~~~R~ 94 (95)
T PRK00754 75 ---VGSKTNTLRMIAKEIKKLRG 94 (95)
T ss_pred ---CCCHHHHHHHHHHHHHHHhc
Confidence 36899999999999998874
No 4
>PRK03745 signal recognition particle protein Srp19; Provisional
Probab=100.00 E-value=1.3e-34 Score=208.93 Aligned_cols=90 Identities=22% Similarity=0.345 Sum_probs=82.8
Q ss_pred CeEEEecccccCCcCcccccccchhccCCCCCHHHHHHHHHHcCCCe-eEeccccCCcC-----cC-CCceEEEEeecCC
Q 032659 10 KWVILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPH-AIEIDKAYPRD-----FM-QRGRVRVMLKRED 82 (136)
Q Consensus 10 ~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~-~vE~~K~yPrd-----w~-~~GRVrV~l~~~d 82 (136)
.++||||+|||+++|++||||||+++||+||+++||++||+.|||++ ++|++|.|||+ || ..|||+|+- +
T Consensus 2 ~~~vIyP~Y~D~~~sr~eGRrv~k~~aV~~P~~~EI~~a~~~lgl~~~~~E~~K~yPr~~g~~~~~~~~Grv~V~~-~-- 78 (100)
T PRK03745 2 GRFVVWPSELDSRLSRKYGRIVPKNLAVERPTLEEIVDAAEALGFKVIEVDREKLNPRLSGIDEELRTRGRIVIES-P-- 78 (100)
T ss_pred CcEEEeeccccCcCChhhcCccCHHHcccCCCHHHHHHHHHHcCCCcEeeccCCCCCCccCCccchhcCCEEEecC-C--
Confidence 48999999999999999999999999999999999999999999999 59999999998 45 499999972 2
Q ss_pred CCccCCCCCCHHHHHHHHHHHhhcCCCc
Q 032659 83 GTFVNPAISSRKQLMLHVAELVPRHPNR 110 (136)
Q Consensus 83 g~~~~~~~~~K~~Ll~~Ia~~I~~~~~r 110 (136)
.+|..||++||+.|.+++.+
T Consensus 79 --------~~K~~ll~~Ia~~ik~~R~~ 98 (100)
T PRK03745 79 --------YGKSKSLKMIAQKIREFRKR 98 (100)
T ss_pred --------CCHHHHHHHHHHHHHHHHhc
Confidence 38999999999999998864
No 5
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=99.97 E-value=1.6e-31 Score=190.53 Aligned_cols=88 Identities=32% Similarity=0.521 Sum_probs=82.3
Q ss_pred CeEEEecccccCCcCcccccccchhccCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCC-CceEEEEeecCCCCccCC
Q 032659 10 KWVILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQ-RGRVRVMLKREDGTFVNP 88 (136)
Q Consensus 10 ~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~-~GRVrV~l~~~dg~~~~~ 88 (136)
..+||||+|||+++||++|||||+++||+||+++||++|+++|||+|.++++|.|||.||+ .|||.|+. +
T Consensus 2 ~~~vlwp~YfDs~~srs~GRrvpk~laV~~P~~~ei~~a~~~LGl~~~v~~dk~yPr~~w~~~g~vive~-~-------- 72 (93)
T COG1400 2 MRIVLWPAYFDSDLSRSEGRRVPKELAVENPSLEEIAEALRELGLKPKVERDKKYPRLWWEISGRVIVES-N-------- 72 (93)
T ss_pred CceEEeehhhcCccChhhccccchhhcccCCCHHHHHHHHHHcCCCeeechhhcCCCchhhhCceEEEec-C--------
Confidence 4689999999999999999999999999999999999999999999999899999999997 89999984 2
Q ss_pred CCCCHHHHHHHHHHHhhcCC
Q 032659 89 AISSRKQLMLHVAELVPRHP 108 (136)
Q Consensus 89 ~~~~K~~Ll~~Ia~~I~~~~ 108 (136)
.+|.++|+.||+.|++++
T Consensus 73 --~~K~~~lk~ia~~lr~~r 90 (93)
T COG1400 73 --GKKSKLLKAIAAKLREKR 90 (93)
T ss_pred --ccHhHHHHHHHHHHHHhh
Confidence 279999999999999885
No 6
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=70.44 E-value=0.17 Score=40.53 Aligned_cols=68 Identities=22% Similarity=0.245 Sum_probs=60.4
Q ss_pred cCeEEEecccccCCcCcccccccchhccCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEE
Q 032659 9 KKWVILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRV 76 (136)
Q Consensus 9 ~~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV 76 (136)
+.|+++|..|+--+.+.-.-|||-.|.|=-.-.+.-+..|+-+|+....-|+.|.+-+-|.-.|||+=
T Consensus 53 S~Wq~~Yl~yL~ie~~Yy~H~kIIeEiaGgtN~iSR~iAaliElNW~~d~eE~kGlKKFflLS~R~r~ 120 (200)
T PF12387_consen 53 SKWQCFYLLYLIIELSYYMHRKIIEEIAGGTNFISRLIAALIELNWAMDEEESKGLKKFFLLSGRVRN 120 (200)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHhhccccchhhcCcceeeeehhHHHH
Confidence 57999999999999999999999999998777788899999999999988888888888777999863
No 7
>cd07245 Glo_EDI_BRP_like_9 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases.
Probab=52.97 E-value=30 Score=22.11 Aligned_cols=44 Identities=11% Similarity=-0.016 Sum_probs=29.1
Q ss_pred ccCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCc
Q 032659 35 KACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTF 85 (136)
Q Consensus 35 ~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~ 85 (136)
.|..-+.+.++.+.++.+|+++.-++.. .| .++ .+.+.|.+|..
T Consensus 68 ~~~~v~d~~~~~~~l~~~g~~~~~~~~~----~~--~~~-~~~~~DP~G~~ 111 (114)
T cd07245 68 IAFRVDDLDAFRARLKAAGVPYTESDVP----GD--GVR-QLFVRDPDGNR 111 (114)
T ss_pred EEEEeCCHHHHHHHHHHcCCCcccccCC----CC--Ccc-EEEEECCCCCE
Confidence 3444456999999999999997765432 11 223 34557888864
No 8
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=49.18 E-value=17 Score=26.50 Aligned_cols=24 Identities=21% Similarity=0.162 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHHHcCCCeeEecc
Q 032659 38 ENPTCIEIADCCQYLKIPHAIEID 61 (136)
Q Consensus 38 ~~Pt~~EI~~A~~~Lgl~~~vE~~ 61 (136)
-||++.-|..+|+.|||...+.+.
T Consensus 74 GNPtf~Til~V~kAlG~rl~~~ps 97 (100)
T COG3636 74 GNPTFDTILAVLKALGLRLSAQPS 97 (100)
T ss_pred CCCcHHHHHHHHHHcCceeecccC
Confidence 499999999999999999877653
No 9
>PF14830 Haemocyan_bet_s: Haemocyanin beta-sandwich; PDB: 1JS8_B 3QJO_A 1LNL_A.
Probab=46.19 E-value=27 Score=25.50 Aligned_cols=37 Identities=16% Similarity=0.144 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCccCCC
Q 032659 41 TCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFVNPA 89 (136)
Q Consensus 41 t~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~~~~ 89 (136)
---||.+++++|||++ ...=.|+|++.+-||+.+.+.
T Consensus 56 ykydIT~~l~~l~l~~------------~~~f~i~~~i~~~nGt~l~~~ 92 (103)
T PF14830_consen 56 YKYDITDALKKLGLHY------------DDPFHIKVEITAVNGTELPSD 92 (103)
T ss_dssp EEEE-HHHHHHCT--T------------TSSEEEEEEEEESSSSBE-CC
T ss_pred chhhHHHHHHHcCCCC------------CCCEEEEEEEEecCCCCCccc
Confidence 3358999999999981 112378999989999988765
No 10
>COG1334 FlaG Uncharacterized flagellar protein FlaG [Cell motility and secretion]
Probab=45.82 E-value=1e+02 Score=23.03 Aligned_cols=35 Identities=17% Similarity=0.245 Sum_probs=25.7
Q ss_pred CCceEEEEeecCCCCccCCCCCCHHH--HHHHHHHHh
Q 032659 70 QRGRVRVMLKREDGTFVNPAISSRKQ--LMLHVAELV 104 (136)
Q Consensus 70 ~~GRVrV~l~~~dg~~~~~~~~~K~~--Ll~~Ia~~I 104 (136)
..|.+.|.+.+.+..=+..+||++.. |+.+|++.|
T Consensus 76 ~lg~~vVkI~d~~TgeVIRqIPpee~L~l~~r~~d~~ 112 (120)
T COG1334 76 ELGELVVKIIDKDTGEVIRQIPPEEALELAARMRDVI 112 (120)
T ss_pred ccCcEEEEEEECCCCcchhhCChHHHHHHHHHHHHhh
Confidence 47899999988887778889998864 345555444
No 11
>PF00721 TMV_coat: Virus coat protein (TMV like); InterPro: IPR001337 This family contains coat proteins from tobamoviruses, which are ssRNA positive-strand viruses with no DNA stage. Examples include Tobacco mosaic virus (TMV), Cucumber green mottle mosaic virus and Ribgrass mosaic virus (RMV). In order to establish infections, viruses must be delivered to the cells of potential hosts and must then engage in activities that enable their genomes to be expressed and replicated. With most viruses, the events that precede the onset of production of progeny virus particles are referred to as the early events and, in the case of positive-strand RNA viruses, they include the initial interaction with and entry of host cells and the release (uncoating) of the genome from the virus particles. The uncoating process in TMV may involve the bidirectional release of coat protein subunits from the viral RNA which may be mediated by cotranslational and coreplicational disassembly mechanisms []. The TMV particle is assembled from its constituent coat protein and RNA by a complex process. The protein forms an obligatory intermediate (a cylindrical disk composed of two layers of protein units), which recognises a specific RNA hairpin sequence. This mechanism simultaneously fulfils the physical requirement for nucleating the growth of the helical particle and the biological requirement for specific recognition of the viral DNA [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 3KML_I 1EI7_A 2TMV_P 3J06_A 1VTM_P 3PDM_P 1CGM_E 1RMV_A 2OM3_A 2XEA_A.
Probab=45.44 E-value=62 Score=24.37 Aligned_cols=39 Identities=18% Similarity=0.129 Sum_probs=24.0
Q ss_pred HHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeec
Q 032659 42 CIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKR 80 (136)
Q Consensus 42 ~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~ 80 (136)
..+|.+++..||..+.+-+.+++|-.-...|-+.|.+-+
T Consensus 42 r~~v~~~ls~lg~~~~~s~~~RFP~~~~~~g~~~~~~~~ 80 (152)
T PF00721_consen 42 RDTVRDQLSDLGKDNPVSRTKRFPGSRGDGGSFYVNLSD 80 (152)
T ss_dssp HHHHHHHHHHC--BSSSCSSS---SS------EEEESSS
T ss_pred HHHHHHHHHHccccCCCCcceeCCCCCCcceeEEEEecC
Confidence 578999999999999999999999997777888887633
No 12
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=42.84 E-value=29 Score=27.69 Aligned_cols=29 Identities=21% Similarity=0.257 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHcCCCeeEeccccCCcCc
Q 032659 40 PTCIEIADCCQYLKIPHAIEIDKAYPRDF 68 (136)
Q Consensus 40 Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw 68 (136)
|.+.++.+.++.+|+++.+|-+..+|..|
T Consensus 86 ~~l~~Ll~~l~~~g~~~~lETngti~~~~ 114 (212)
T COG0602 86 PNLLELLELLKRLGFRIALETNGTIPVWT 114 (212)
T ss_pred ccHHHHHHHHHhCCceEEecCCCCccccc
Confidence 47899999999999999999989999987
No 13
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=39.54 E-value=1.1e+02 Score=19.92 Aligned_cols=50 Identities=14% Similarity=0.090 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCccCCCCCCHHHHHHHHHHH
Q 032659 39 NPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFVNPAISSRKQLMLHVAEL 103 (136)
Q Consensus 39 ~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~~~~~~~K~~Ll~~Ia~~ 103 (136)
+-+.++|.++|+.||+.+....+. .+.|.... ...++...-.|+..||..
T Consensus 18 ~i~~~~i~~~L~~lg~~~~~~~~~----------~~~v~vP~-----~R~Di~~~~DliEEiaR~ 67 (70)
T PF03484_consen 18 DISPEEIIKILKRLGFKVEKIDGD----------TLEVTVPS-----YRFDIEHEEDLIEEIARI 67 (70)
T ss_dssp ---HHHHHHHHHHTT-EEEE-CTT----------EEEEEEET-----TSTT-SSHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHCCCEEEECCCC----------EEEEEcCC-----CcCCcCcccHHHHHHHHH
Confidence 557899999999999998875222 34444322 345677888998888864
No 14
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=39.26 E-value=34 Score=22.27 Aligned_cols=19 Identities=11% Similarity=0.345 Sum_probs=16.9
Q ss_pred CCCCCHHHHHHHHHHcCCC
Q 032659 37 CENPTCIEIADCCQYLKIP 55 (136)
Q Consensus 37 V~~Pt~~EI~~A~~~Lgl~ 55 (136)
+..|+..++.+.|..|||+
T Consensus 27 ~~~~~~~~r~~la~~lgl~ 45 (58)
T TIGR01565 27 LKDKRREEVREFCEEIGVT 45 (58)
T ss_pred CCCCCHHHHHHHHHHhCCC
Confidence 4459999999999999997
No 15
>cd08349 BLMA_like Bleomycin binding protein (BLMA) and similar proteins; BLMA confers bleomycin (Bm) resistance by directly binding to Bm. BLMA also called Bleomycin resistance protein, confers Bm resistance by directly binding to Bm. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMA is produced by actinomycetes to protect themselves against their own lethal compound. BLMA has two identically-folded subdomains, with the same alpha/beta fold; these two halves have no sequence similarity. BLMAs are dimers and each dimer binds to two Bm molecules at the Bm-binding pockets formed at the dimer interface; two Bm molecules are bound per dimer. BLMA belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. As for the large
Probab=36.78 E-value=89 Score=20.24 Aligned_cols=47 Identities=9% Similarity=0.010 Sum_probs=29.2
Q ss_pred ccCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCcc
Q 032659 35 KACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFV 86 (136)
Q Consensus 35 ~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~ 86 (136)
.|+.-+.++++.+.+.++|..+.+.+-... .| |.-.+.+.|.+|..+
T Consensus 62 ~~~~~~~~~~~~~~l~~~G~~~~~~~~~~~--~~---g~~~~~~~DP~G~~i 108 (112)
T cd08349 62 VYIEVEDVDALYAELKAKGADLIVYPPEDQ--PW---GMREFAVRDPDGNLL 108 (112)
T ss_pred EEEEeCCHHHHHHHHHHcCCcceecCccCC--Cc---ccEEEEEECCCCCEE
Confidence 445556699999999999998433221211 12 433455678888643
No 16
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=35.88 E-value=39 Score=28.92 Aligned_cols=58 Identities=19% Similarity=0.191 Sum_probs=41.2
Q ss_pred CCHHHHHHHHHHcCCCeeEeccccCCc-----------------CcCCCceEEEEeecCCCCccCCCCCCHHHHHHHHHH
Q 032659 40 PTCIEIADCCQYLKIPHAIEIDKAYPR-----------------DFMQRGRVRVMLKREDGTFVNPAISSRKQLMLHVAE 102 (136)
Q Consensus 40 Pt~~EI~~A~~~Lgl~~~vE~~K~yPr-----------------dw~~~GRVrV~l~~~dg~~~~~~~~~K~~Ll~~Ia~ 102 (136)
-|+.+|++|+.+-.+...|+. =.-+- +.++-||+.|. |.+|.|+ .+.+|..+|..||-
T Consensus 218 it~~dI~~aia~g~~~~kV~~-~M~k~vitI~eDe~i~dAir~M~~~nVGRLlV~--ds~gkpv--GiITrTDIL~~ia~ 292 (294)
T COG2524 218 ITLSDIAKAIANGNLDAKVSD-YMRKNVITINEDEDIYDAIRLMNKNNVGRLLVT--DSNGKPV--GIITRTDILTRIAG 292 (294)
T ss_pred EEHHHHHHHHHcCCccccHHH-HhccCCceEcCchhHHHHHHHHHhcCcceEEEE--ccCCcEE--EEEehHHHHHHhhc
Confidence 377888888888777776652 11111 13467999997 6788776 46799999999985
No 17
>PF00061 Lipocalin: Lipocalin / cytosolic fatty-acid binding protein family fatty acid-binding protein signature lipocalin signature; InterPro: IPR000566 Proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids share limited regions of sequence homology and a common tertiary structure architecture [, , , , ]. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing a internal ligand binding site [, ]. The name 'lipocalin' has been proposed [] for this protein family, but cytosolic fatty-acid binding proteins are also included. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these [, ]. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); alpha-1-acid glycoprotein (orosomucoid) []; aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain []; crustacyanin []; epididymal-retinoic acid binding protein (E-RABP) []; insectacyanin; odorant-binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin; probasin (PB), a rat prostatic protein; prostaglandin D synthase (5.3.99.2 from EC) []; purpurin; Von Ebner's gland protein (VEGP) []; and lizard epididymal secretory protein IV (LESP IV) [].; GO: 0005488 binding; PDB: 1I05_A 1MUP_A 2LB6_A 1I04_A 1I06_A 1DC9_A 1URE_A 1AEL_A 1T8V_A 1ICM_A ....
Probab=35.68 E-value=17 Score=25.23 Aligned_cols=51 Identities=12% Similarity=0.117 Sum_probs=39.5
Q ss_pred cccccCeEEEecccccCCcCccccccc-chhccCCCCCHHHHHHHHHHcCCCe
Q 032659 5 TARIKKWVILYPVYINSKKTIAEGRRI-SASKACENPTCIEIADCCQYLKIPH 56 (136)
Q Consensus 5 ~~~~~~~~vIYP~Y~Ds~~sr~eGRRV-~k~~aV~~Pt~~EI~~A~~~Lgl~~ 56 (136)
++|++.+.++|=+-.+... ...-+.+ +++.-+....+++..+.|+.+||.-
T Consensus 83 ~tdy~~yai~~~~~~~~g~-~~~~~~l~~R~~~l~~~~~~~f~~~~~~~gi~~ 134 (144)
T PF00061_consen 83 DTDYDNYAIVYSCKKDNGK-HTIVAWLLSRTPELSPEALEKFKKFAKSLGIDE 134 (144)
T ss_dssp EEESSTEEEEEEEEEETTE-EEEEEEEEESSSEEEHHHHHHHHHHHHHTTETG
T ss_pred ccCCCCEEEEEEEccCCCc-eEEEEEEEcCCCcCCHHHHHHHHHHHHhCCCCH
Confidence 5788999999999886654 5555555 7766666667899999999999864
No 18
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=35.01 E-value=27 Score=20.12 Aligned_cols=16 Identities=13% Similarity=0.092 Sum_probs=12.2
Q ss_pred CHHHHHHHHHHcCCCe
Q 032659 41 TCIEIADCCQYLKIPH 56 (136)
Q Consensus 41 t~~EI~~A~~~Lgl~~ 56 (136)
++.|+.+.|+++||+.
T Consensus 5 ~v~eLk~~l~~~gL~~ 20 (35)
T PF02037_consen 5 TVAELKEELKERGLST 20 (35)
T ss_dssp HHHHHHHHHHHTTS-S
T ss_pred cHHHHHHHHHHCCCCC
Confidence 5788888899888863
No 19
>PF07487 SopE_GEF: SopE GEF domain; InterPro: IPR016019 The type III secretion system of Gram-negative bacteria is used to transport virulence factors from the pathogen directly into the host cell [] and is only triggered when the bacterium comes into close contact with the host. Effector proteins secreted by the type III system do not possess a secretion signal, and are considered unique because of this. Salmonella spp. secrete an effector protein called SopE that is responsible for stimulating the reorganisation of the host cell actin cytoskeleton, and ruffling of the cellular membrane []. It acts as a guanyl-nucleotide-exchange factor on Rho-GTPase proteins such as Cdc42 and Rac. As it is imperative for the bacterium to revert the cell back to its "normal" state as quickly as possible, another tyrosine phosphatase effector called SptP reverses the actions brought about by SopE []. Recently, it has been found that SopE and its protein homologue SopE2 can activate different sets of Rho-GTPases in the host cell []. Far from being a redundant set of two similar type III effectors, they both act in unison to specifically activate different Rho-GTPase signalling cascades in the host cell during infection. This entry represents the guanine nucleotide exchange factor domain of SopE. This domain has an alpha-helical structure consisting of two three-helix bundles arranged in a lamdba shape [, ].; GO: 0005085 guanyl-nucleotide exchange factor activity, 0009405 pathogenesis, 0031532 actin cytoskeleton reorganization, 0032862 activation of Rho GTPase activity, 0005576 extracellular region; PDB: 1GZS_B 1R9K_A 1R6E_A 2JOL_A 2JOK_A.
Probab=34.88 E-value=17 Score=28.51 Aligned_cols=24 Identities=17% Similarity=0.254 Sum_probs=19.5
Q ss_pred CCCHHHHHHHHHHcCCCeeEeccc
Q 032659 39 NPTCIEIADCCQYLKIPHAIEIDK 62 (136)
Q Consensus 39 ~Pt~~EI~~A~~~Lgl~~~vE~~K 62 (136)
+|-+.||.+||+..||++++-..-
T Consensus 63 ~pFL~eiGeaak~aGLPge~KNgV 86 (165)
T PF07487_consen 63 QPFLFEIGEAAKNAGLPGENKNGV 86 (165)
T ss_dssp HHHHHHHHHHHHHTT-SEEEETTE
T ss_pred cHHHHHHHHHHHHCCCCccccCCe
Confidence 578999999999999999976543
No 20
>cd08356 Glo_EDI_BRP_like_17 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=34.76 E-value=1e+02 Score=20.88 Aligned_cols=52 Identities=12% Similarity=0.020 Sum_probs=31.7
Q ss_pred hccCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCcc
Q 032659 34 SKACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFV 86 (136)
Q Consensus 34 ~~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~ 86 (136)
..+..-+.+++..+.|+..|++...+ ....+-.+...|--.+.+.|.||..+
T Consensus 58 ~~~~~v~did~~~~~l~~~G~~~~~~-~~~~~~~~~~~g~r~f~~~DPdGn~~ 109 (113)
T cd08356 58 MLHLEVDDLEAYYEHIKALGLPKKFP-GVKLPPITQPWWGREFFLHDPSGVLW 109 (113)
T ss_pred EEEEEECCHHHHHHHHHHcCCccccc-ceecCccccCCCcEEEEEECCCccEE
Confidence 45566678999999999999874322 11112112223444555579999765
No 21
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=34.58 E-value=42 Score=19.07 Aligned_cols=17 Identities=12% Similarity=0.026 Sum_probs=13.9
Q ss_pred CCHHHHHHHHHHcCCCe
Q 032659 40 PTCIEIADCCQYLKIPH 56 (136)
Q Consensus 40 Pt~~EI~~A~~~Lgl~~ 56 (136)
=++.|+.+.|+.+||+.
T Consensus 4 l~~~~Lk~~l~~~gl~~ 20 (35)
T smart00513 4 LKVSELKDELKKRGLST 20 (35)
T ss_pred CcHHHHHHHHHHcCCCC
Confidence 36788999999999874
No 22
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=34.29 E-value=27 Score=21.22 Aligned_cols=21 Identities=14% Similarity=0.116 Sum_probs=18.4
Q ss_pred CCCCCHHHHHHHHHHcCCCee
Q 032659 37 CENPTCIEIADCCQYLKIPHA 57 (136)
Q Consensus 37 V~~Pt~~EI~~A~~~Lgl~~~ 57 (136)
-..|+..++..++..|||+..
T Consensus 22 ~~~p~~~~~~~la~~l~l~~~ 42 (57)
T PF00046_consen 22 NPYPSKEEREELAKELGLTER 42 (57)
T ss_dssp SSSCHHHHHHHHHHHHTSSHH
T ss_pred hcccccccccccccccccccc
Confidence 468999999999999999864
No 23
>PF01120 Alpha_L_fucos: Alpha-L-fucosidase; InterPro: IPR000933 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Family 29 (GH29 from CAZY) encompasses alpha-L-fucosidases (3.2.1.51 from EC) [], which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Alpha-L-fucosidase is responsible for hydrolysing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Fucosylated glycoconjugates are involved in numerous biological events, making alpha-l-fucosidases, the enzymes responsible for their processing, critically important. Deficiency in alpha-l-fucosidase activity is associated with fucosidosis, a lysosomal storage disorder characterised by rapid neurodegeneration, resulting in severe mental and motor deterioration []. The enzyme is a hexamer and displays a two-domain fold, composed of a catalytic (beta/alpha)(8)-like domain and a C-terminal beta-sandwich domain []. Drosophila melanogaster spermatozoa contains an alpha-l-fucosidase that might be involved in fertilisation by interacting with alpha-l-fucose residues on the micropyle of the eggshell []. In human sperm, membrane-associated alpha-l-fucosidase is stable for extended periods of time, which is made possible by membrane domains and compartmentalisation. These help preserve protein integrity []. ; GO: 0004560 alpha-L-fucosidase activity, 0005975 carbohydrate metabolic process; PDB: 3EYP_B 2ZX6_A 2ZWY_B 2ZX8_B 2WSP_A 2ZXA_A 2ZWZ_B 1ODU_B 1HL9_A 2ZX5_B ....
Probab=32.97 E-value=38 Score=28.69 Aligned_cols=28 Identities=21% Similarity=0.366 Sum_probs=21.0
Q ss_pred CHHHHHHHHHHcCCCeeEeccccCCcCcCCC
Q 032659 41 TCIEIADCCQYLKIPHAIEIDKAYPRDFMQR 71 (136)
Q Consensus 41 t~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~ 71 (136)
-+.|+++||++.||.+-+- -+|.||+.+
T Consensus 139 iv~El~~A~rk~Glk~G~Y---~S~~dw~~~ 166 (346)
T PF01120_consen 139 IVGELADACRKYGLKFGLY---YSPWDWHHP 166 (346)
T ss_dssp HHHHHHHHHHHTT-EEEEE---EESSSCCCT
T ss_pred HHHHHHHHHHHcCCeEEEE---ecchHhcCc
Confidence 4799999999999999885 234487653
No 24
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=32.73 E-value=47 Score=19.83 Aligned_cols=21 Identities=14% Similarity=0.126 Sum_probs=18.3
Q ss_pred CCCCCHHHHHHHHHHcCCCee
Q 032659 37 CENPTCIEIADCCQYLKIPHA 57 (136)
Q Consensus 37 V~~Pt~~EI~~A~~~Lgl~~~ 57 (136)
...|+..|+.+.+..+||+..
T Consensus 22 ~~~P~~~~~~~la~~~~l~~~ 42 (59)
T cd00086 22 NPYPSREEREELAKELGLTER 42 (59)
T ss_pred CCCCCHHHHHHHHHHHCcCHH
Confidence 468999999999999998764
No 25
>cd08357 Glo_EDI_BRP_like_18 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=32.55 E-value=71 Score=21.27 Aligned_cols=49 Identities=12% Similarity=0.080 Sum_probs=30.2
Q ss_pred cCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCcc
Q 032659 36 ACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFV 86 (136)
Q Consensus 36 aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~ 86 (136)
++....++++.+-|++.|+++..++...++... .|.-.+.+.|.||..+
T Consensus 72 ~~~~~dv~~~~~~l~~~g~~~~~~p~~~~~~~~--~~~~~~~~~DPdG~~i 120 (125)
T cd08357 72 ILSEEEFDALAERLEAAGVEFLIEPYTRFEGQP--GEQETFFLKDPSGNAL 120 (125)
T ss_pred EEeHHHHHHHHHHHHHCCCcEecCcceeccCCc--CceeEEEEECCCCCEE
Confidence 455678899999999999987766433222211 1122244568888654
No 26
>KOG4549 consensus Magnesium-dependent phosphatase [General function prediction only]
Probab=31.68 E-value=58 Score=25.13 Aligned_cols=53 Identities=9% Similarity=0.015 Sum_probs=36.2
Q ss_pred EEEecccccCCcCc------ccccccchhccCCCCCHHHHHHHHHHcCCCeeEeccccCC
Q 032659 12 VILYPVYINSKKTI------AEGRRISASKACENPTCIEIADCCQYLKIPHAIEIDKAYP 65 (136)
Q Consensus 12 ~vIYP~Y~Ds~~sr------~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yP 65 (136)
..|||+|+|-.+.. .+-|+-.-+.+ --|.+.-|..+|+.+|+.+.+-..-.-|
T Consensus 14 ytiwP~~vdthl~~pfkP~k~~~g~~g~e~~-fY~Di~rIL~dLk~~GVtl~~ASRt~ap 72 (144)
T KOG4549|consen 14 YTIWPRLVDTHLDYPFKPFKCECGSKGEEMI-FYDDIRRILVDLKKLGVTLIHASRTMAP 72 (144)
T ss_pred ceeeeEEEEecccccccccccCcccCcceee-eccchhHHHHHHHhcCcEEEEecCCCCH
Confidence 57999999876543 23334344444 3778889999999999999876433333
No 27
>cd08351 ChaP_like ChaP, an enzyme involved in the biosynthesis of the antitumor agent chartreusin (cha); and similar proteins. ChaP is an enzyme involved in the biosynthesis of the potent antitumor agent chartreusin (cha). Cha is an aromatic polyketide glycoside produced by Streptomyces chartreusis. ChaP may play a role as a meta-cleavage dioxygenase in the oxidative rearrangement of the anthracyclic polyketide. ChaP belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.
Probab=31.54 E-value=1.1e+02 Score=20.87 Aligned_cols=51 Identities=14% Similarity=0.085 Sum_probs=30.1
Q ss_pred cCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCC-CceEEEEeecCCCCcc
Q 032659 36 ACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQ-RGRVRVMLKREDGTFV 86 (136)
Q Consensus 36 aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~-~GRVrV~l~~~dg~~~ 86 (136)
.|..-.+.++.+.|...|+++..++.-.-+..+.. .|--.+.+.|.||..+
T Consensus 65 ~v~~~dl~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~g~~~~~f~DPdG~~i 116 (123)
T cd08351 65 LVSEEEFDRIFARIRERGIDYWADPQRTEPGQINTNDGGRGVYFLDPDGHLL 116 (123)
T ss_pred EeCHHHHHHHHHHHHHcCCceecCCcccccccccCCCCeeEEEEECCCCCEE
Confidence 45544689999999999999866543221211111 1223344468888654
No 28
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=30.75 E-value=49 Score=21.80 Aligned_cols=19 Identities=11% Similarity=0.253 Sum_probs=16.6
Q ss_pred CCCCHHHHHHHHHHcCCCe
Q 032659 38 ENPTCIEIADCCQYLKIPH 56 (136)
Q Consensus 38 ~~Pt~~EI~~A~~~Lgl~~ 56 (136)
..|++.+|..||..+|+..
T Consensus 57 t~~~~~Dv~~al~~~gi~v 75 (77)
T PF07524_consen 57 TEPNLQDVEQALEEMGISV 75 (77)
T ss_pred CCCCHHHHHHHHHHhCCCC
Confidence 3689999999999999864
No 29
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=30.69 E-value=1.4e+02 Score=18.83 Aligned_cols=50 Identities=18% Similarity=0.145 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCccCCCCCCHHHHHHHHHHH
Q 032659 40 PTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFVNPAISSRKQLMLHVAEL 103 (136)
Q Consensus 40 Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~~~~~~~K~~Ll~~Ia~~ 103 (136)
-+.+||.+.|.+||+.+....+ .+.+.|... +..+++...-.|+..||..
T Consensus 19 i~~~ei~~~L~~lg~~~~~~~~---------~~~~~v~~P-----~~R~Di~~~~DliEei~r~ 68 (71)
T smart00874 19 LSAEEIEEILKRLGFEVEVSGD---------DDTLEVTVP-----SYRFDILIEADLIEEVARI 68 (71)
T ss_pred CCHHHHHHHHHHCCCeEEecCC---------CCeEEEECC-----CCccccCcccHHHHHHHHH
Confidence 4678999999999998754211 223444432 1234566777888877753
No 30
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=29.74 E-value=33 Score=24.74 Aligned_cols=24 Identities=17% Similarity=0.066 Sum_probs=16.7
Q ss_pred CCCCCHHHHHHHHHHcCCCeeEec
Q 032659 37 CENPTCIEIADCCQYLKIPHAIEI 60 (136)
Q Consensus 37 V~~Pt~~EI~~A~~~Lgl~~~vE~ 60 (136)
-..|...++.++++.+||.|+--|
T Consensus 41 ~~qp~~~~~~~~a~~~Gl~y~~iP 64 (110)
T PF04273_consen 41 PGQPSSAEEAAAAEALGLQYVHIP 64 (110)
T ss_dssp TT-T-HHCHHHHHHHCT-EEEE--
T ss_pred CCCCCHHHHHHHHHHcCCeEEEee
Confidence 346899999999999999998554
No 31
>COG0027 PurT Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]
Probab=29.61 E-value=44 Score=29.53 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=18.9
Q ss_pred CHHHHHHHHHHcCCCeeEec
Q 032659 41 TCIEIADCCQYLKIPHAIEI 60 (136)
Q Consensus 41 t~~EI~~A~~~Lgl~~~vE~ 60 (136)
++.|+.+||..+||+|++-|
T Consensus 137 s~~e~~~a~~~iGfPcvvKP 156 (394)
T COG0027 137 SLEELRAAVEKIGFPCVVKP 156 (394)
T ss_pred cHHHHHHHHHHcCCCeeccc
Confidence 78999999999999999987
No 32
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=29.11 E-value=37 Score=20.93 Aligned_cols=20 Identities=15% Similarity=0.162 Sum_probs=12.4
Q ss_pred CCCCCHHHHHHHHHHcCCCe
Q 032659 37 CENPTCIEIADCCQYLKIPH 56 (136)
Q Consensus 37 V~~Pt~~EI~~A~~~Lgl~~ 56 (136)
+.+|++.+|..+|..||+++
T Consensus 35 ~~~~~~~~l~~ia~~l~~~~ 54 (63)
T PF13443_consen 35 PSNPSLDTLEKIAKALNCSP 54 (63)
T ss_dssp -----HHHHHHHHHHHT--H
T ss_pred cccccHHHHHHHHHHcCCCH
Confidence 45899999999999999875
No 33
>cd08794 Death_IRAK1 Death domain of Interleukin 1 Receptor Associated Kinase-1. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 1 (IRAK1). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK1 is an active kinase and also plays adaptor functions. It binds to the MyD88-IRAK4 complex via its DD, which facilitates its phosphorylation by IRAK4, activating it for further auto-phosphorylation. Hyper-phosphorylated IRAK1 forms a cytosolic complex with TRAF6, leading to the activation of NF-kB and MAPK pathways. IRAK1 is involved in autoimmunity and may be associated with lupus pathogenesis. DDs are protein-protein interaction domains found in a variety of domain architectures.
Probab=28.96 E-value=35 Score=24.16 Aligned_cols=20 Identities=20% Similarity=0.137 Sum_probs=17.9
Q ss_pred ccCCCCCHHHHHHHHHHcCC
Q 032659 35 KACENPTCIEIADCCQYLKI 54 (136)
Q Consensus 35 ~aV~~Pt~~EI~~A~~~Lgl 54 (136)
=+..|+++.|+.++++.|++
T Consensus 57 W~~Rn~tV~~Ll~iL~~L~l 76 (84)
T cd08794 57 WENRNGRVGELLDILERLQL 76 (84)
T ss_pred HHhcccHHHHHHHHHHHhhh
Confidence 36789999999999999986
No 34
>PRK09726 antitoxin HipB; Provisional
Probab=27.65 E-value=95 Score=20.89 Aligned_cols=24 Identities=17% Similarity=0.171 Sum_probs=19.7
Q ss_pred ccCCCCCHHHHHHHHHHcCCCeeE
Q 032659 35 KACENPTCIEIADCCQYLKIPHAI 58 (136)
Q Consensus 35 ~aV~~Pt~~EI~~A~~~Lgl~~~v 58 (136)
.....|++..|..+|..||++..+
T Consensus 47 ~g~~~ps~~~l~~ia~~lgv~~~~ 70 (88)
T PRK09726 47 NNPDNTTLTTFFKILQSLELSMTL 70 (88)
T ss_pred CCCCCCCHHHHHHHHHHcCCCcch
Confidence 344579999999999999998654
No 35
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=27.60 E-value=82 Score=18.42 Aligned_cols=18 Identities=6% Similarity=-0.036 Sum_probs=16.0
Q ss_pred CCCCHHHHHHHHHHcCCC
Q 032659 38 ENPTCIEIADCCQYLKIP 55 (136)
Q Consensus 38 ~~Pt~~EI~~A~~~Lgl~ 55 (136)
.+|++.++..+|..||++
T Consensus 40 ~~~~~~~~~~i~~~lgv~ 57 (58)
T TIGR03070 40 PTVRLDKVLRVLDALGLE 57 (58)
T ss_pred CCCCHHHHHHHHHHcCCC
Confidence 478999999999999986
No 36
>PHA01976 helix-turn-helix protein
Probab=27.26 E-value=65 Score=20.03 Aligned_cols=23 Identities=9% Similarity=0.027 Sum_probs=19.1
Q ss_pred hccCCCCCHHHHHHHHHHcCCCe
Q 032659 34 SKACENPTCIEIADCCQYLKIPH 56 (136)
Q Consensus 34 ~~aV~~Pt~~EI~~A~~~Lgl~~ 56 (136)
+.....|+...+..+|..||++.
T Consensus 36 e~g~~~p~~~~l~~ia~~l~v~~ 58 (67)
T PHA01976 36 EADKRLPNLKTLLRLADALGVTL 58 (67)
T ss_pred HcCCCCCCHHHHHHHHHHHCcCH
Confidence 44556899999999999999875
No 37
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=27.26 E-value=72 Score=22.19 Aligned_cols=21 Identities=24% Similarity=0.216 Sum_probs=18.7
Q ss_pred CCCCHHHHHHHHHHcCCCeeE
Q 032659 38 ENPTCIEIADCCQYLKIPHAI 58 (136)
Q Consensus 38 ~~Pt~~EI~~A~~~Lgl~~~v 58 (136)
.+|++.-|..+|..||++..|
T Consensus 68 ~~Ps~~tL~kI~~aLgi~l~v 88 (89)
T TIGR02684 68 GNPTFDTILKVTKALGLKLTA 88 (89)
T ss_pred CCCCHHHHHHHHHHcCCceee
Confidence 489999999999999998755
No 38
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=27.16 E-value=54 Score=29.27 Aligned_cols=23 Identities=22% Similarity=0.352 Sum_probs=20.0
Q ss_pred CCCCCHHHHHHHHHHcCCCeeEe
Q 032659 37 CENPTCIEIADCCQYLKIPHAIE 59 (136)
Q Consensus 37 V~~Pt~~EI~~A~~~Lgl~~~vE 59 (136)
+..|+.+||.+++.+|+|+=+|-
T Consensus 316 npKPt~qEIt~iA~~L~leKEVV 338 (398)
T KOG3802|consen 316 NPKPTSQEITHIAESLQLEKEVV 338 (398)
T ss_pred CCCCCHHHHHHHHHHhccccceE
Confidence 56899999999999999986654
No 39
>PRK10477 outer membrane lipoprotein Blc; Provisional
Probab=26.94 E-value=63 Score=24.63 Aligned_cols=45 Identities=2% Similarity=-0.090 Sum_probs=34.4
Q ss_pred cccccCeEEEecccccCCcCcccccccchhccCCCCCHHHHHHHHHHcCCCe
Q 032659 5 TARIKKWVILYPVYINSKKTIAEGRRISASKACENPTCIEIADCCQYLKIPH 56 (136)
Q Consensus 5 ~~~~~~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~ 56 (136)
+.|++ |.+|+ ...+...--++++.-++....+++.+.++.+|++.
T Consensus 122 d~dY~-~aiv~------~~~~~~~wIlsR~p~l~~~~~~~~~~~~~~~G~d~ 166 (177)
T PRK10477 122 DREYR-HALVC------GPDRDYLWILSRTPTISDEVKQQMLAVATREGFDV 166 (177)
T ss_pred cCCCC-EEEEE------cCCCCEEEEEeCCCCCCHHHHHHHHHHHHHcCCCH
Confidence 35665 77774 22466666788888888888899999999999985
No 40
>cd07233 Glyoxalase_I Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione. Glyoxalase I (also known as lactoylglutathione lyase; EC 4.4.1.5) is part of the glyoxalase system, a two-step system for detoxifying methylglyoxal, a side product of glycolysis. This system is responsible for the conversion of reactive, acyclic alpha-oxoaldehydes into the corresponding alpha-hydroxyacids and involves 2 enzymes, glyoxalase I and II. Glyoxalase I catalyses an intramolecular redox reaction of the hemithioacetal (formed from methylglyoxal and glutathione) to form the thioester, S-D-lactoylglutathione. This reaction involves the transfer of two hydrogen atoms from C1 to C2 of the methylglyoxal, and proceeds via an ene-diol intermediate. Glyoxalase I has a requirement for bound metal ions for catalysis. Eukaryotic glyoxalase I prefers the divalent cation zinc as cofactor, whereas Escherichia coil and other prokaryotic gly
Probab=25.41 E-value=1.6e+02 Score=19.30 Aligned_cols=43 Identities=9% Similarity=0.066 Sum_probs=29.4
Q ss_pred cCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCc
Q 032659 36 ACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTF 85 (136)
Q Consensus 36 aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~ 85 (136)
|..-+.++++.+.+...|+++.-+++- + ..|++ ..+.|.||..
T Consensus 75 ~~~v~did~~~~~l~~~G~~~~~~~~~-~-----~~~~~-~~~~DpdG~~ 117 (121)
T cd07233 75 AFAVDDVYAACERLEEMGVEVTKPPGD-G-----GMKGI-AFIKDPDGYW 117 (121)
T ss_pred EEEeCCHHHHHHHHHHCCCEEeeCCcc-C-----CCceE-EEEECCCCCE
Confidence 444456999999999999998876542 1 23444 4557888864
No 41
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=25.30 E-value=68 Score=21.37 Aligned_cols=17 Identities=18% Similarity=0.227 Sum_probs=15.7
Q ss_pred CCCHHHHHHHHHHcCCC
Q 032659 39 NPTCIEIADCCQYLKIP 55 (136)
Q Consensus 39 ~Pt~~EI~~A~~~Lgl~ 55 (136)
.|++.||..|+..+|+.
T Consensus 58 ~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 58 EPNLGDVVLALENLGIS 74 (77)
T ss_pred CCCHHHHHHHHHHhCcc
Confidence 68999999999999985
No 42
>TIGR03365 Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE. This uncharacterized enzyme, designated QueE, participates in the biosynthesis, from GTP, of 7-cyano-7-deazaguanosine, also called preQ0 because in many species it is a precursor of queuosine. In most Archaea, it is instead the precursor of a different tRNA modified base, archaeosine.
Probab=24.86 E-value=84 Score=25.15 Aligned_cols=41 Identities=15% Similarity=0.085 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHcCCCeeEeccccCCcCcCC-CceEEEEeec
Q 032659 40 PTCIEIADCCQYLKIPHAIEIDKAYPRDFMQ-RGRVRVMLKR 80 (136)
Q Consensus 40 Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~-~GRVrV~l~~ 80 (136)
|.+.+|.++++.+|+.+.+|-+-..|-++.. -+.|-|.++-
T Consensus 87 ~~l~~li~~l~~~g~~v~leTNGtl~~~~l~~~d~v~vs~K~ 128 (238)
T TIGR03365 87 KPLGELIDLGKAKGYRFALETQGSVWQDWFRDLDDLTLSPKP 128 (238)
T ss_pred HhHHHHHHHHHHCCCCEEEECCCCCcHHHHhhCCEEEEeCCC
Confidence 4567888899999999999999988877432 3477788753
No 43
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=24.84 E-value=75 Score=18.87 Aligned_cols=20 Identities=15% Similarity=0.149 Sum_probs=17.6
Q ss_pred CCCCHHHHHHHHHHcCCCee
Q 032659 38 ENPTCIEIADCCQYLKIPHA 57 (136)
Q Consensus 38 ~~Pt~~EI~~A~~~Lgl~~~ 57 (136)
..|+..++.+.+..|||+..
T Consensus 23 ~~P~~~~~~~la~~~~l~~~ 42 (56)
T smart00389 23 PYPSREEREELAAKLGLSER 42 (56)
T ss_pred CCCCHHHHHHHHHHHCcCHH
Confidence 48999999999999999843
No 44
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=24.57 E-value=52 Score=25.16 Aligned_cols=49 Identities=10% Similarity=0.216 Sum_probs=39.6
Q ss_pred CHHHHHHHHHHcCCCeeEeccccCCcC--------cC---CCceEEEEeecCCCCccCCC
Q 032659 41 TCIEIADCCQYLKIPHAIEIDKAYPRD--------FM---QRGRVRVMLKREDGTFVNPA 89 (136)
Q Consensus 41 t~~EI~~A~~~Lgl~~~vE~~K~yPrd--------w~---~~GRVrV~l~~~dg~~~~~~ 89 (136)
.+.||...++.+.+.++|-....+-+. |. ..|-|-+.++|+.|.+++|.
T Consensus 6 ~ikdi~P~~kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~TgsI~isvW~e~~~~~~PG 65 (134)
T KOG3416|consen 6 FIKDIKPGLKNINVTFIVLEYGRATKTKDGHEVRSCKVADETGSINISVWDEEGCLIQPG 65 (134)
T ss_pred hHhhcChhhhcceEEEEEEeeceeeeccCCCEEEEEEEecccceEEEEEecCcCcccCCc
Confidence 578999999999999886656777662 43 37999999999999888875
No 45
>COG2313 IndA Uncharacterized enzyme involved in pigment biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.47 E-value=74 Score=27.27 Aligned_cols=35 Identities=20% Similarity=0.301 Sum_probs=26.9
Q ss_pred ecccccCCcCcccccccchhccCCCCCHHHHHHHHH---HcCCCee
Q 032659 15 YPVYINSKKTIAEGRRISASKACENPTCIEIADCCQ---YLKIPHA 57 (136)
Q Consensus 15 YP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~---~Lgl~~~ 57 (136)
+|+|| ||.-|+++|...- +.+||++++. +|||+.-
T Consensus 192 fPaF~----sR~Sg~~~pl~l~----~pe~ia~~~~t~~~lglegg 229 (310)
T COG2313 192 FPAFF----SRESGFRVPLRLE----SPEEIARILATKWQLGLEGG 229 (310)
T ss_pred ccchh----cccCCCcCccccC----CHHHHHHHHHHHHHhCCCCc
Confidence 57776 7889999997766 6788888875 7888763
No 46
>PF14528 LAGLIDADG_3: LAGLIDADG-like domain; PDB: 2CW7_A 2CW8_A 2VS8_F 2VS7_G 1B24_A 1DQ3_A 2DCH_X.
Probab=24.37 E-value=1.2e+02 Score=19.36 Aligned_cols=25 Identities=16% Similarity=0.050 Sum_probs=17.5
Q ss_pred CCCCHHHHHHHHHHcCCCeeEeccc
Q 032659 38 ENPTCIEIADCCQYLKIPHAIEIDK 62 (136)
Q Consensus 38 ~~Pt~~EI~~A~~~Lgl~~~vE~~K 62 (136)
....+++|...|..||+.+.+...+
T Consensus 30 s~~ll~~v~~lL~~lGi~~~i~~~~ 54 (77)
T PF14528_consen 30 SKELLEDVQKLLLRLGIKASIYEKK 54 (77)
T ss_dssp -HHHHHHHHHHHHHTT--EEEEEEE
T ss_pred CHHHHHHHHHHHHHCCCeeEEEEEc
Confidence 3457889999999999999876433
No 47
>cd07240 ED_TypeI_classII_N N-terminal domain of type I, class II extradiol dioxygenases; non-catalytic domain. This family contains the N-terminal, non-catalytic, domain of type I, class II extradiol dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site; extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon, whereas intradiol enzymes cleave the aromatic ring between two hydroxyl groups. Extradiol dioxygenases are classified into type I and type II enzymes. Type I extradiol dioxygenases include class I and class II enzymes. These two classes of enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. The extradiol dioxygenases represented in this fa
Probab=23.95 E-value=2e+02 Score=18.74 Aligned_cols=46 Identities=13% Similarity=0.102 Sum_probs=28.1
Q ss_pred hccCCCC-CHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCc
Q 032659 34 SKACENP-TCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTF 85 (136)
Q Consensus 34 ~~aV~~P-t~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~ 85 (136)
...|.++ .++++.+.+.++|+++..++. .+++ .|+ .+.+.|.+|..
T Consensus 62 ~~~v~~~~~v~~~~~~l~~~g~~~~~~~~----~~~~-~~~-~~~~~DP~G~~ 108 (117)
T cd07240 62 GFEVASEEDLEALAAHLEAAGVAPEEASD----PEPG-VGR-GLRFQDPDGHL 108 (117)
T ss_pred EEEcCCHHHHHHHHHHHHHcCCceEEcCc----cCCC-Cce-EEEEECCCCCE
Confidence 3446666 688888889999998766543 1121 222 23456777754
No 48
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=23.73 E-value=1.7e+02 Score=24.65 Aligned_cols=64 Identities=14% Similarity=0.201 Sum_probs=45.0
Q ss_pred CCCCHHHHHHHHHHcCCCeeEeccccCCcC-c--------CC-CceEEEEeecCCCCccCCCCCCHHHHHHHHHHHh
Q 032659 38 ENPTCIEIADCCQYLKIPHAIEIDKAYPRD-F--------MQ-RGRVRVMLKREDGTFVNPAISSRKQLMLHVAELV 104 (136)
Q Consensus 38 ~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrd-w--------~~-~GRVrV~l~~~dg~~~~~~~~~K~~Ll~~Ia~~I 104 (136)
+.+..++|.++++.+|++..+. ....+ + .. .||+++-|..+-|.+.-..-.+...|...+.+.+
T Consensus 283 ~~~~~~~~~~~l~~~g~p~~~~---~~~~~~~~~~l~~dkk~~~~~~~~vl~~~ig~~~~~~~v~~~~l~~~~~~~~ 356 (358)
T PRK00002 283 SEADAERIRALLERAGLPTSLP---DLDAEALLEAMKRDKKVRGGKLRFVLLKGIGKAVIAEDVDDELLLAALEECL 356 (358)
T ss_pred CHHHHHHHHHHHHHcCCCCCCC---CCCHHHHHHHHHHhhhccCCCEEEEEecCCccEEEeCCCCHHHHHHHHHHHh
Confidence 4467899999999999987655 12222 1 23 6999999988888865544456777777776554
No 49
>PF02222 ATP-grasp: ATP-grasp domain; InterPro: IPR003135 The ATP-grasp domain has an unusual nucleotide-binding fold, also referred to as palmate, and is found in a superfamily of enzymes including D-alanine-D-alanine ligase, glutathione synthetase, biotin carboxylase, and carbamoyl phosphate synthetase, the ribosomal protein S6 modification enzyme (RimK), urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis. This family does not contain all known ATP-grasp domain members. All the enzymes of this family possess ATP-dependent carboxylate-amine ligase activity, and their catalytic mechanisms are likely to include acylphosphate intermediates.; PDB: 3K5H_C 3K5I_C 3AX6_A 3Q2O_B 3QFF_B 3R5H_A 3ORQ_B 3ORR_B 4E4T_B 2Z04_A ....
Probab=23.41 E-value=1e+02 Score=23.82 Aligned_cols=19 Identities=5% Similarity=0.350 Sum_probs=17.3
Q ss_pred CHHHHHHHHHHcCCCeeEe
Q 032659 41 TCIEIADCCQYLKIPHAIE 59 (136)
Q Consensus 41 t~~EI~~A~~~Lgl~~~vE 59 (136)
+.+|+.+|+..+|+++++-
T Consensus 16 ~~~~l~~a~~~iG~P~vlK 34 (172)
T PF02222_consen 16 SLEDLEEAAESIGFPAVLK 34 (172)
T ss_dssp SHHHHHHHHHHHTSSEEEE
T ss_pred CHHHHHHHHHHcCCCEEEE
Confidence 5679999999999999987
No 50
>PRK05783 hypothetical protein; Provisional
Probab=23.04 E-value=77 Score=22.14 Aligned_cols=27 Identities=11% Similarity=0.017 Sum_probs=23.0
Q ss_pred cchhccCCCCCHHHHHHHHHHcCCCee
Q 032659 31 ISASKACENPTCIEIADCCQYLKIPHA 57 (136)
Q Consensus 31 V~k~~aV~~Pt~~EI~~A~~~Lgl~~~ 57 (136)
|.....|-+|.-+-|..||..||+..+
T Consensus 9 V~lK~gVlDPqG~aI~~aL~~lg~~~V 35 (84)
T PRK05783 9 IINKDSVRDPEGETIQRYVIERYTGNI 35 (84)
T ss_pred EEECCCCcCchHHHHHHHHHHcCCCCc
Confidence 345567999999999999999999874
No 51
>KOG4201 consensus Anthranilate synthase component II [Amino acid transport and metabolism]
Probab=22.96 E-value=58 Score=27.44 Aligned_cols=24 Identities=13% Similarity=0.120 Sum_probs=21.7
Q ss_pred CCCCCHHHHHHHHHHcCCCeeEec
Q 032659 37 CENPTCIEIADCCQYLKIPHAIEI 60 (136)
Q Consensus 37 V~~Pt~~EI~~A~~~Lgl~~~vE~ 60 (136)
..++.++++...|+.||+.+.||-
T Consensus 170 Ls~~~lk~l~k~~K~L~me~LVEV 193 (289)
T KOG4201|consen 170 LSDLLLKELYKISKDLGMEPLVEV 193 (289)
T ss_pred cChHHHHHHHHHHHHcCCcceeee
Confidence 468899999999999999999984
No 52
>COG1828 PurS Phosphoribosylformylglycinamidine (FGAM) synthase, PurS component [Nucleotide transport and metabolism]
Probab=22.88 E-value=80 Score=22.18 Aligned_cols=60 Identities=12% Similarity=0.165 Sum_probs=39.9
Q ss_pred cchhccCCCCCHHHHHHHHHHcCCCeeEe--ccccCCcCcCCCceEEEEeecCCCCccCCCCCCHHHHHHHHHHHhhcC
Q 032659 31 ISASKACENPTCIEIADCCQYLKIPHAIE--IDKAYPRDFMQRGRVRVMLKREDGTFVNPAISSRKQLMLHVAELVPRH 107 (136)
Q Consensus 31 V~k~~aV~~Pt~~EI~~A~~~Lgl~~~vE--~~K~yPrdw~~~GRVrV~l~~~dg~~~~~~~~~K~~Ll~~Ia~~I~~~ 107 (136)
|.....|-+|.-+-|..||..||+.-+-+ -.| ++.+.+-.+|- ..=.+.++.||+.|-..
T Consensus 8 V~lK~~VlDPqG~ti~~aL~~lg~~~V~~vR~gK----------~~el~ld~~~~-------e~a~~~v~~mcekLLaN 69 (83)
T COG1828 8 VTLKPGVLDPEGETIEKALHRLGYNEVSDVRVGK----------VIELELDAESE-------EKAEEEVKEMCEKLLAN 69 (83)
T ss_pred EEeCCcccCchhHHHHHHHHHcCCcccceeeeee----------EEEEEecCcch-------hHHHHHHHHHHHHHhCC
Confidence 44566799999999999999999984433 223 45666533211 12357888888876543
No 53
>cd08309 Death_IRAK Death domain of Interleukin-1 Receptor-Associated Kinases. Death Domains (DDs) found in Interleukin-1 (IL-1) Receptor-Associated Kinases (IRAK1-4) and similar proteins. IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. All four types are involved in signal transduction involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinase pathways. IRAK1 and IRAK4 are active kinases while IRAK2 and IRAK-M (also called IRAK3) are inactive. In general, IRAKs are expressed ubiquitously, except for IRAK-M which is detected only in macrophages. The insect homologs, Pelle and Tube, are important components of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in the innate immune response. Most members have an N-terminal DD followed by a kinase domain. In general, DDs are protein-protein interaction domains found in a variety of domain a
Probab=22.47 E-value=78 Score=22.04 Aligned_cols=19 Identities=16% Similarity=0.223 Sum_probs=16.6
Q ss_pred CCCCCHHHHHHHHHHcCCC
Q 032659 37 CENPTCIEIADCCQYLKIP 55 (136)
Q Consensus 37 V~~Pt~~EI~~A~~~Lgl~ 55 (136)
-.|||+.++.+++.++++-
T Consensus 70 ~~~~Tv~~L~~~L~~~~l~ 88 (95)
T cd08309 70 TQNATVQDLVQVLVQLELY 88 (95)
T ss_pred hcCCCHHHHHHHHHHcccH
Confidence 4599999999999999873
No 54
>PF04343 DUF488: Protein of unknown function, DUF488; InterPro: IPR007438 This family includes several proteins of uncharacterised function.
Probab=21.99 E-value=1.4e+02 Score=21.15 Aligned_cols=26 Identities=15% Similarity=0.195 Sum_probs=21.2
Q ss_pred CHHHHHHHHHHcCCCeeEeccccCCcC
Q 032659 41 TCIEIADCCQYLKIPHAIEIDKAYPRD 67 (136)
Q Consensus 41 t~~EI~~A~~~Lgl~~~vE~~K~yPrd 67 (136)
+++++.+.++..|+.++|. =..+|++
T Consensus 1 ~~e~f~~~l~~~~i~~lVD-VR~~P~S 26 (122)
T PF04343_consen 1 SIERFYDLLKKNGIRVLVD-VRLWPRS 26 (122)
T ss_pred CHHHHHHHHHHCCCeEEEE-ECCCCCC
Confidence 3688999999999999987 2568884
No 55
>PF13299 CPSF100_C: Cleavage and polyadenylation factor 2 C-terminal
Probab=21.56 E-value=3.4e+02 Score=20.65 Aligned_cols=58 Identities=21% Similarity=0.126 Sum_probs=40.8
Q ss_pred ccchhccCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCccCCCCCC
Q 032659 30 RISASKACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFVNPAISS 92 (136)
Q Consensus 30 RV~k~~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~~~~~~~ 92 (136)
-.+....|-++.+.++.+++...|+..++--.-. -...|.|.|. +.++|..+.....+
T Consensus 90 ~~~~~~~iGd~rL~~lk~~L~~~g~~aEF~g~G~----Lv~~~~V~Vr-K~~~G~i~ieG~~~ 147 (161)
T PF13299_consen 90 PGHQSLFIGDLRLSDLKQALQSAGIQAEFRGEGV----LVCNGGVAVR-KSEDGRIVIEGCLS 147 (161)
T ss_pred CCCCceecCcccHHHHHHHHHHCCCceEEeeCCe----EEECCEEEEE-EcCCCCEEEEecCc
Confidence 3466778999999999999999999888752121 2246678888 67777655444333
No 56
>COG0677 WecC UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]
Probab=21.36 E-value=46 Score=29.99 Aligned_cols=26 Identities=31% Similarity=0.355 Sum_probs=22.7
Q ss_pred CHHHHHHHHHHcCCCee--EeccccCCc
Q 032659 41 TCIEIADCCQYLKIPHA--IEIDKAYPR 66 (136)
Q Consensus 41 t~~EI~~A~~~Lgl~~~--vE~~K~yPr 66 (136)
.+.|++-+|.++|+++. +|--++|||
T Consensus 228 LaNElali~~~~GIdvwevIeaAnt~P~ 255 (436)
T COG0677 228 LANELALICNAMGIDVWEVIEAANTKPR 255 (436)
T ss_pred HHHHHHHHHHHhCCcHHHHHHHhccCCc
Confidence 35799999999999984 888889999
No 57
>cd07262 Glo_EDI_BRP_like_19 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=21.34 E-value=2.6e+02 Score=18.58 Aligned_cols=42 Identities=10% Similarity=-0.015 Sum_probs=24.8
Q ss_pred HHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCcc
Q 032659 42 CIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFV 86 (136)
Q Consensus 42 ~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~ 86 (136)
++++.+.+...|+....++. .+.|+..+...+.+.|.||..+
T Consensus 78 v~~~~~~~~~~g~~~~~~~~---~~~~~~~~~~~~~~~DPdG~~i 119 (123)
T cd07262 78 VDAFHAAALAAGGTDEGAPG---LRPHYGPGYYAAYVRDPDGNKI 119 (123)
T ss_pred HHHHHHHHHHcCCccCCCCC---CCCCCCCCeEEEEEECCCCCEE
Confidence 56667777788887654431 2334444443455678888643
No 58
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=21.26 E-value=83 Score=19.23 Aligned_cols=23 Identities=30% Similarity=0.419 Sum_probs=19.6
Q ss_pred cccccchhccCCCCCHHHHHHHH
Q 032659 27 EGRRISASKACENPTCIEIADCC 49 (136)
Q Consensus 27 eGRRV~k~~aV~~Pt~~EI~~A~ 49 (136)
-|..|+.+.-.+.||+.+|++.+
T Consensus 45 ~g~~i~~~~~~~~~ti~~l~~~i 67 (67)
T PF00550_consen 45 FGIKIPPSDLFEHPTIRDLAEYI 67 (67)
T ss_dssp HTSSTTHHHHCTSSSHHHHHHHH
T ss_pred HcCCCCHHHHHcCCCHHHHHhHC
Confidence 37888988889999999998764
No 59
>PF04197 Birna_RdRp: Birnavirus RNA dependent RNA polymerase (VP1); InterPro: IPR007100 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This family consists of the Birnaviridae enzymes. These proteins lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RNA-directed RNA polymerases [].; GO: 0003968 RNA-directed RNA polymerase activity, 0019079 viral genome replication; PDB: 2QJ1_A 2R72_A 2R70_A 2PUS_A 2PGG_A 2YI8_C 2YIA_H 2YIB_A 2YI9_E.
Probab=21.14 E-value=55 Score=31.75 Aligned_cols=27 Identities=22% Similarity=0.251 Sum_probs=19.7
Q ss_pred hccCCCCCHHHHHHHHHHcCCCeeEec
Q 032659 34 SKACENPTCIEIADCCQYLKIPHAIEI 60 (136)
Q Consensus 34 ~~aV~~Pt~~EI~~A~~~Lgl~~~vE~ 60 (136)
+..|++|+..++.+.|.++|+++.||.
T Consensus 501 ~~g~p~p~s~~~~~~~~~tGI~~KiE~ 527 (860)
T PF04197_consen 501 EAGCPRPDSKEFMKLEAKTGINFKIER 527 (860)
T ss_dssp HTT---TTSHHHHTHHHHHT--EEEEE
T ss_pred HcCCCCCCcHHHHHHHHhhCCceEEEE
Confidence 456889999999999999999999985
No 60
>COG0134 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]
Probab=21.10 E-value=88 Score=26.16 Aligned_cols=63 Identities=16% Similarity=0.244 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHcCCCeeEeccccCCcCc----CCCceEEEEeecCCCCccCCCCCCHHHHHHHHHHHhhcC
Q 032659 38 ENPTCIEIADCCQYLKIPHAIEIDKAYPRDF----MQRGRVRVMLKREDGTFVNPAISSRKQLMLHVAELVPRH 107 (136)
Q Consensus 38 ~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw----~~~GRVrV~l~~~dg~~~~~~~~~K~~Ll~~Ia~~I~~~ 107 (136)
++-.++|+++.+..||++++||- |-.+= ..-|-..|=+.|-|=. .+..-.+.-..++..||.-
T Consensus 141 ~~~~l~el~~~A~~LGm~~LVEV---h~~eEl~rAl~~ga~iIGINnRdL~----tf~vdl~~t~~la~~~p~~ 207 (254)
T COG0134 141 DDEQLEELVDRAHELGMEVLVEV---HNEEELERALKLGAKIIGINNRDLT----TLEVDLETTEKLAPLIPKD 207 (254)
T ss_pred CHHHHHHHHHHHHHcCCeeEEEE---CCHHHHHHHHhCCCCEEEEeCCCcc----hheecHHHHHHHHhhCCCC
Confidence 34458999999999999999993 44431 1245545544332211 1222333456666666654
No 61
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=20.85 E-value=26 Score=22.30 Aligned_cols=27 Identities=26% Similarity=0.465 Sum_probs=16.5
Q ss_pred cccCCcCcC---CCceEEEEee-cCCCCccC
Q 032659 61 DKAYPRDFM---QRGRVRVMLK-REDGTFVN 87 (136)
Q Consensus 61 ~K~yPrdw~---~~GRVrV~l~-~~dg~~~~ 87 (136)
+..||.+-. ..|.|.|.+. +.||.+.+
T Consensus 2 ~~~YP~~a~~~~~~G~v~v~~~I~~~G~v~~ 32 (79)
T PF03544_consen 2 NPVYPEEARRRGIEGTVVVEFTIDPDGRVSD 32 (79)
T ss_dssp S----CHHHHHTEEEEEEEEEEEETTTEEEE
T ss_pred CCCCCHHHHHCCCeEEEEEEEEEeCCCCEEE
Confidence 467998753 4799999874 67887654
No 62
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=20.74 E-value=90 Score=18.90 Aligned_cols=15 Identities=7% Similarity=-0.051 Sum_probs=11.5
Q ss_pred HHHHHHHHHHcCCCe
Q 032659 42 CIEIADCCQYLKIPH 56 (136)
Q Consensus 42 ~~EI~~A~~~Lgl~~ 56 (136)
..|..+||..|||..
T Consensus 3 ~~d~~~AL~~LGy~~ 17 (47)
T PF07499_consen 3 LEDALEALISLGYSK 17 (47)
T ss_dssp HHHHHHHHHHTTS-H
T ss_pred HHHHHHHHHHcCCCH
Confidence 468889999999864
No 63
>PRK10291 glyoxalase I; Provisional
Probab=20.61 E-value=2.3e+02 Score=19.33 Aligned_cols=47 Identities=15% Similarity=0.006 Sum_probs=29.2
Q ss_pred ccCCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCcc
Q 032659 35 KACENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFV 86 (136)
Q Consensus 35 ~aV~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~ 86 (136)
.|..-+.+++..+.|+..|+.+..++. |..| .++...-+.|.||..+
T Consensus 69 laf~V~d~~~~~~~l~~~G~~~~~~~~---~~~~--~~~~~~~i~DPdG~~i 115 (129)
T PRK10291 69 IALSVDNAAEACEKIRQNGGNVTREAG---PVKG--GTTVIAFVEDPDGYKI 115 (129)
T ss_pred EEEEeCCHHHHHHHHHHcCCccccCCc---ccCC--CceEEEEEECCCCCEE
Confidence 455555688999999999998876542 2222 2232233468888643
No 64
>PF00218 IGPS: Indole-3-glycerol phosphate synthase; InterPro: IPR013798 Indole-3-glycerol phosphate synthase (4.1.1.48 from EC) (IGPS) catalyses the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyses N-(5'-phosphoribosyl)anthranilate isomerase (5.3.1.24 from EC) (PRAI) activity (see IPR001240 from INTERPRO), the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (2.4.2 from EC) (GATase) N-terminal domain (see IPR000991 from INTERPRO). A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium E. coli (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand []. ; GO: 0004425 indole-3-glycerol-phosphate synthase activity; PDB: 1VC4_A 1PII_A 1JCM_P 1I4N_B 1J5T_A 3TSM_B 4FB7_A 3QJA_A 1JUL_A 2C3Z_A ....
Probab=20.44 E-value=81 Score=26.12 Aligned_cols=19 Identities=16% Similarity=0.265 Sum_probs=16.6
Q ss_pred HHHHHHHHHHcCCCeeEec
Q 032659 42 CIEIADCCQYLKIPHAIEI 60 (136)
Q Consensus 42 ~~EI~~A~~~Lgl~~~vE~ 60 (136)
+.++.+.|..|||+++||-
T Consensus 147 l~~l~~~a~~lGle~lVEV 165 (254)
T PF00218_consen 147 LEELLELAHSLGLEALVEV 165 (254)
T ss_dssp HHHHHHHHHHTT-EEEEEE
T ss_pred HHHHHHHHHHcCCCeEEEE
Confidence 5899999999999999994
No 65
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=20.43 E-value=1e+02 Score=28.77 Aligned_cols=35 Identities=14% Similarity=0.103 Sum_probs=24.0
Q ss_pred CCCCCHHHHHHH-HHHcCCCeeEeccccCCcCcCCCceE
Q 032659 37 CENPTCIEIADC-CQYLKIPHAIEIDKAYPRDFMQRGRV 74 (136)
Q Consensus 37 V~~Pt~~EI~~A-~~~Lgl~~~vE~~K~yPrdw~~~GRV 74 (136)
|..-.++.+.++ +..||+.+.+++. .|| ||++||-
T Consensus 471 v~f~d~Kg~ve~ll~~lg~~~~~~~~-~~~--~~hpgrs 506 (650)
T COG0072 471 VDFYDAKGDLEALLEALGVEYEFEPA-EHP--AFHPGRS 506 (650)
T ss_pred cCHHHHHHHHHHHHHHhCCceEEEEc-cCC--CccCCce
Confidence 333455555554 4689999999965 477 8888773
No 66
>PRK13957 indole-3-glycerol-phosphate synthase; Provisional
Probab=20.32 E-value=97 Score=25.65 Aligned_cols=24 Identities=13% Similarity=0.145 Sum_probs=20.4
Q ss_pred CCCC-CHHHHHHHHHHcCCCeeEec
Q 032659 37 CENP-TCIEIADCCQYLKIPHAIEI 60 (136)
Q Consensus 37 V~~P-t~~EI~~A~~~Lgl~~~vE~ 60 (136)
+-.| .+.++.+.|..|||+++||-
T Consensus 134 ~L~~~~l~~l~~~a~~lGle~LVEV 158 (247)
T PRK13957 134 ILTPSQIKSFLKHASSLGMDVLVEV 158 (247)
T ss_pred hCCHHHHHHHHHHHHHcCCceEEEE
Confidence 3444 68999999999999999994
No 67
>cd07241 Glo_EDI_BRP_like_3 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=20.19 E-value=2.6e+02 Score=18.26 Aligned_cols=39 Identities=10% Similarity=-0.025 Sum_probs=22.5
Q ss_pred HHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCcc
Q 032659 42 CIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFV 86 (136)
Q Consensus 42 ~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~ 86 (136)
++++.+-|++.|+++.-++. |...|...+.+.|.||..+
T Consensus 84 v~~~~~~l~~~g~~~~~~~~------~~~~g~~~~~~~DPdG~~i 122 (125)
T cd07241 84 VDELTERLRADGYLIIGEPR------TTGDGYYESVILDPEGNRI 122 (125)
T ss_pred HHHHHHHHHHCCCEEEeCce------ecCCCeEEEEEECCCCCEE
Confidence 56667777777987654331 2223433333568888654
No 68
>PF12681 Glyoxalase_2: Glyoxalase-like domain; PDB: 3G12_B 1JIF_B 1JIE_B 1QTO_A 3OXH_A 2PJS_A 2RBB_A 3SK1_B 3SK2_B 3RRI_A ....
Probab=20.11 E-value=2.2e+02 Score=18.28 Aligned_cols=44 Identities=14% Similarity=0.108 Sum_probs=27.9
Q ss_pred CCCCCHHHHHHHHHHcCCCeeEeccccCCcCcCCCceEEEEeecCCCCcc
Q 032659 37 CENPTCIEIADCCQYLKIPHAIEIDKAYPRDFMQRGRVRVMLKREDGTFV 86 (136)
Q Consensus 37 V~~Pt~~EI~~A~~~Lgl~~~vE~~K~yPrdw~~~GRVrV~l~~~dg~~~ 86 (136)
+.-..++++.+.+.++|++.+.++... .| |--.+.+.|.||..+
T Consensus 62 ~~v~dv~~~~~~l~~~G~~~~~~~~~~---~~---g~~~~~~~DPdG~~i 105 (108)
T PF12681_consen 62 FEVEDVDALYERLKELGAEIVTEPRDD---PW---GQRSFYFIDPDGNRI 105 (108)
T ss_dssp EEESHHHHHHHHHHHTTSEEEEEEEEE---TT---SEEEEEEE-TTS-EE
T ss_pred EEEcCHHHHHHHHHHCCCeEeeCCEEc---CC---CeEEEEEECCCCCEE
Confidence 333789999999999999887665441 12 433444568787643
Done!