Query psy11599
Match_columns 76
No_of_seqs 100 out of 137
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 22:45:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11599.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11599hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01207 Ena-Vasp Enabled-VASP- 100.0 5.5E-35 1.2E-39 191.9 8.7 70 2-71 42-111 (111)
2 KOG4590|consensus 100.0 7.4E-32 1.6E-36 207.0 2.5 73 2-74 31-104 (409)
3 cd00837 EVH1 EVH1 (Enabled, Va 100.0 4.6E-28 1E-32 155.5 8.7 66 2-67 39-104 (104)
4 cd01206 Homer Homer type EVH1 99.9 3.2E-28 7E-33 159.8 7.0 67 1-69 41-109 (111)
5 smart00461 WH1 WASP homology r 99.9 1.1E-27 2.4E-32 154.5 8.4 65 2-67 42-106 (106)
6 PF00568 WH1: WH1 domain; Int 99.9 9.4E-26 2E-30 145.7 9.5 65 2-66 46-110 (111)
7 cd01205 WASP WASP-type EVH1 do 99.7 1.1E-17 2.4E-22 109.0 8.1 64 3-66 41-104 (105)
8 KOG3671|consensus 99.5 6.6E-15 1.4E-19 116.2 5.5 67 4-70 76-142 (569)
9 smart00160 RanBD Ran-binding d 98.5 6.1E-07 1.3E-11 59.5 7.8 64 3-66 57-130 (130)
10 cd00835 RanBD Ran-binding doma 98.4 2.4E-06 5.2E-11 55.6 8.1 65 3-67 47-121 (122)
11 PF00638 Ran_BP1: RanBP1 domai 97.4 0.0028 6.1E-08 40.6 8.8 66 3-68 46-121 (122)
12 PF08471 Ribonuc_red_2_N: Clas 70.1 5.4 0.00012 25.7 2.6 28 39-67 63-90 (93)
13 cd00900 PH-like Pleckstrin hom 65.0 21 0.00045 19.6 4.2 33 34-66 64-99 (99)
14 PF06058 DCP1: Dcp1-like decap 63.4 39 0.00085 22.1 7.3 44 22-66 77-121 (122)
15 PF04800 ETC_C1_NDUFA4: ETC co 60.7 7.7 0.00017 25.1 2.0 19 44-62 48-67 (101)
16 PF07485 DUF1529: Domain of Un 58.8 7.6 0.00016 25.8 1.8 35 35-69 87-122 (123)
17 PF11360 DUF3110: Protein of u 55.8 46 0.00099 20.7 4.9 29 35-63 14-42 (86)
18 KOG3389|consensus 52.5 11 0.00023 26.6 1.8 17 46-62 127-143 (178)
19 cd03580 NTR_Sfrp1_like NTR dom 51.0 26 0.00055 22.9 3.4 21 2-23 85-105 (126)
20 PF14657 Integrase_AP2: AP2-li 43.8 35 0.00075 18.3 2.7 21 48-68 22-42 (46)
21 PF00847 AP2: AP2 domain; Int 37.6 69 0.0015 17.2 4.5 44 24-67 3-53 (56)
22 PF01693 Cauli_VI: Caulimoviru 35.2 32 0.00069 18.4 1.6 13 47-59 32-44 (44)
23 PRK14128 iraD DNA replication/ 35.0 48 0.001 19.7 2.5 23 48-70 1-23 (69)
24 PF11531 CARM1: Coactivator-as 34.1 1.4E+02 0.0031 19.8 7.8 52 14-65 50-101 (114)
25 PF12444 Sox_N: Sox developmen 33.8 19 0.00041 22.6 0.7 25 49-73 48-72 (84)
26 COG4050 Uncharacterized protei 32.5 54 0.0012 22.5 2.7 22 51-72 128-149 (152)
27 PF04278 Tic22: Tic22-like fam 30.5 64 0.0014 23.9 3.1 28 43-70 97-124 (274)
28 PF13018 ESPR: Extended Signal 30.2 36 0.00078 16.6 1.2 13 1-13 1-13 (24)
29 PF12441 DUF3680: Protein of u 29.9 38 0.00083 18.6 1.4 14 49-62 7-20 (42)
30 cd01220 PH_CDEP Chondrocyte-de 29.7 1.3E+02 0.0028 18.7 4.0 33 37-69 65-99 (99)
31 PF02132 RecR: RecR protein; 27.8 84 0.0018 16.6 2.5 18 54-71 1-18 (41)
32 PF05573 NosL: NosL; InterPro 27.8 53 0.0011 21.8 2.1 15 48-62 119-133 (149)
33 PF09564 RE_NgoBV: NgoBV restr 27.5 2.2E+02 0.0049 21.2 5.4 64 2-71 119-203 (240)
34 PF00387 PI-PLC-Y: Phosphatidy 26.4 38 0.00083 22.2 1.2 27 37-63 75-101 (118)
35 PF12373 Msg2_C: Major surface 26.4 76 0.0017 16.4 2.1 12 51-62 14-25 (30)
36 cd05756 Ig1_IL1R_like First im 26.1 73 0.0016 19.2 2.3 30 14-44 14-43 (94)
37 TIGR03642 cas_csx13 CRISPR-ass 25.7 94 0.002 20.6 3.0 23 50-72 64-86 (124)
38 PF05996 Fe_bilin_red: Ferredo 25.5 38 0.00081 24.4 1.1 59 7-71 56-119 (228)
39 KOG1890|consensus 25.4 67 0.0014 27.7 2.6 39 29-67 665-707 (949)
40 PF15465 DUF4634: Domain of un 25.3 1E+02 0.0022 20.9 3.0 62 7-69 14-76 (129)
41 PLN02837 threonine-tRNA ligase 24.7 93 0.002 25.4 3.3 29 39-67 181-215 (614)
42 COG5171 YRB1 Ran GTPase-activa 24.2 1.3E+02 0.0029 21.8 3.6 25 44-68 178-202 (211)
43 PF14259 RRM_6: RNA recognitio 24.2 74 0.0016 17.3 2.0 17 46-62 42-58 (70)
44 PF03791 KNOX2: KNOX2 domain ; 22.8 1.1E+02 0.0023 17.6 2.4 19 54-72 34-52 (52)
45 PF12006 DUF3500: Protein of u 22.3 1.1E+02 0.0023 23.2 3.0 27 9-37 124-150 (313)
46 PRK12444 threonyl-tRNA synthet 22.2 1.5E+02 0.0032 24.1 4.0 30 38-67 208-243 (639)
47 COG3691 Uncharacterized protei 22.2 2E+02 0.0044 18.6 3.9 29 44-72 32-60 (98)
48 PRK08153 histidinol-phosphate 21.4 1.4E+02 0.003 22.0 3.4 28 46-73 342-369 (369)
49 cd05722 Ig1_Neogenin First imm 21.3 1.6E+02 0.0036 17.0 3.2 28 14-47 14-41 (95)
50 PF05036 SPOR: Sporulation rel 21.1 1.6E+02 0.0034 16.0 3.2 18 49-66 11-28 (76)
51 PF07042 TrfA: TrfA protein; 20.4 50 0.0011 24.9 0.9 30 35-73 236-265 (282)
52 PF08553 VID27: VID27 cytoplas 20.3 3E+02 0.0066 23.8 5.5 53 18-70 297-356 (794)
No 1
>cd01207 Ena-Vasp Enabled-VASP-type homology (EVH1) domain. Enabled-VASP-type homology (EVH1) domain. The EVH1 domain binds to other proteins at proline rich sequences. It is found in proteins involved in cytoskeletal reorganization such as Enabled and VASP. Ena-VASP type EVH1 domains specifically recognize FPPPP motifs in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=100.00 E-value=5.5e-35 Score=191.90 Aligned_cols=70 Identities=30% Similarity=0.590 Sum_probs=68.5
Q ss_pred ceeEEEEeccccCCeEEEeEeeecCeEEeecCCceeeEeeCCeEEEeecCCHHHHHHHHHHHHHHhhhhh
Q psy11599 2 NIVGAWLGSEISFTGVVLSCTITRDFTYNKVMPTFHHWQTGNKKFGLTFQAAADARAFDQGVRNALQEYL 71 (76)
Q Consensus 2 ~~~~~i~G~~l~D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~~GLnF~s~~eA~~F~~~v~~al~~l~ 71 (76)
+++|||+|++++|++++|||+||++|+||+++|+||||++++|+|||||+||+||++|.++|++||+.|+
T Consensus 42 ~~~yrIvg~~~~~~~~v~e~~l~~~l~y~k~~p~Fh~w~~~~~v~GLnF~Se~eA~~F~~~v~~Al~~L~ 111 (111)
T cd01207 42 NNTFRVVGRKLQDHQVVINCAIVKGLKYNQATPTFHQWRDARQVYGLNFGSKEDATMFASAMLSALEVLN 111 (111)
T ss_pred CCEEEEEEeecCCCcEEEEEEecCCceeeecCCcceeeecCCeEEeeccCCHHHHHHHHHHHHHHHHhhC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999984
No 2
>KOG4590|consensus
Probab=99.97 E-value=7.4e-32 Score=207.04 Aligned_cols=73 Identities=37% Similarity=0.629 Sum_probs=71.1
Q ss_pred ceeEEEEeccccC-CeEEEeEeeecCeEEeecCCceeeEeeCCeEEEeecCCHHHHHHHHHHHHHHhhhhhccC
Q psy11599 2 NIVGAWLGSEISF-TGVVLSCTITRDFTYNKVMPTFHHWQTGNKKFGLTFQAAADARAFDQGVRNALQEYLHDK 74 (76)
Q Consensus 2 ~~~~~i~G~~l~D-~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~~GLnF~s~~eA~~F~~~v~~al~~l~~g~ 74 (76)
||+|||||++++| ++|||||.|+|||+||+|||+|||||++++||||||+|++||++|+++|.+|||.|.+|+
T Consensus 31 ~n~frVvg~k~qdd~~vVlnC~I~kGlkYnkatptFHqWR~arqvyGLnFqs~~DA~~Fa~~~~~A~e~l~~g~ 104 (409)
T KOG4590|consen 31 GNTFRVVGRKSQDDQQVVLNCLILKGLKYNKATPTFHQWRDARQVYGLTFQSEQDARAFARGVPVAIEALSGGT 104 (409)
T ss_pred CCceeEEeeecccCcccccccccccCcceeecccchhhhhhhhhhhcccccChhhhhhhhhhhhhhhhhhccCC
Confidence 7999999999998 999999999999999999999999999999999999999999999999999999999884
No 3
>cd00837 EVH1 EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. The EVH1 domain binds to other proteins at proline rich sequences in either FPPPP or PPXXF motifs. It is found in the cytoskeletal reorganization proteins Enabled VASP, and WASP, and in the synaptic scaffolding protein Homer. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=99.95 E-value=4.6e-28 Score=155.47 Aligned_cols=66 Identities=26% Similarity=0.476 Sum_probs=63.7
Q ss_pred ceeEEEEeccccCCeEEEeEeeecCeEEeecCCceeeEeeCCeEEEeecCCHHHHHHHHHHHHHHh
Q psy11599 2 NIVGAWLGSEISFTGVVLSCTITRDFTYNKVMPTFHHWQTGNKKFGLTFQAAADARAFDQGVRNAL 67 (76)
Q Consensus 2 ~~~~~i~G~~l~D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~~GLnF~s~~eA~~F~~~v~~al 67 (76)
.++|||+++++++++|+|||+||++++|++++|+||||++++|++||||+|++||+.|.++|.+++
T Consensus 39 ~~~y~i~~~~~~~~~vv~~~~l~~~~~y~~~~~~Fh~w~~~~~~~GL~F~se~eA~~F~~~v~~~~ 104 (104)
T cd00837 39 RNTYRIRGVDIQDQKVIWNQEIYKGLKYTQATPFFHQWEDDNCVYGLNFASEEEAAQFRKKVLEAI 104 (104)
T ss_pred CCEEEEEEEecCCCeEEEEEEecCCcEEeecCCeEEEEEcCCcEEEEeeCCHHHHHHHHHHHHhcC
Confidence 578999999999999999999999999999999999999999999999999999999999998764
No 4
>cd01206 Homer Homer type EVH1 domain. Homer type EVH1 domain. Homer is a synaptic scaffolding protein, involved in neuronal signaling. It contains an EVH1 domain, which binds to both neurotransmitter receptors, such as the metabotropic glutamate receptor (mGluR) and to other scaffolding proteins via PPXXF motifs, in order to target them to the synaptic junction. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=99.95 E-value=3.2e-28 Score=159.78 Aligned_cols=67 Identities=19% Similarity=0.363 Sum_probs=63.5
Q ss_pred CceeEEEEeccccCCeEEEeEeeecCeEEeecCCceeeEeeCC--eEEEeecCCHHHHHHHHHHHHHHhhh
Q psy11599 1 MNIVGAWLGSEISFTGVVLSCTITRDFTYNKVMPTFHHWQTGN--KKFGLTFQAAADARAFDQGVRNALQE 69 (76)
Q Consensus 1 ~~~~~~i~G~~l~D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~--~~~GLnF~s~~eA~~F~~~v~~al~~ 69 (76)
.+++|||||. .|.+++|||.|.++|+|++++|+||||||.+ ++|||||+||+||..|..++.++++.
T Consensus 41 ~~ntfRIi~~--~~~~~iINc~i~~~~~y~kas~~FhQWrD~R~~tVyGLnF~Sk~ea~~F~~~f~~~~~~ 109 (111)
T cd01206 41 TRNVYRIISV--GGTKAIINSTITPNMTFTKTSQKFGQWADSRANTVYGLGFSSEQQLTKFAEKFQEVKEA 109 (111)
T ss_pred CCcEEEEEEe--cCcEEEEeccccCCcceeecccccccccccccceeeecccCCHHHHHHHHHHHHHHHHh
Confidence 3799999995 6789999999999999999999999999999 89999999999999999999999975
No 5
>smart00461 WH1 WASP homology region 1. Region of the Wiskott-Aldrich syndrome protein (WASp) that contains point mutations in the majority of patients with WAS. Unknown function. Ena-like WH1 domains bind polyproline-containing peptides, and that Homer contains a WH1 domain.
Probab=99.95 E-value=1.1e-27 Score=154.46 Aligned_cols=65 Identities=28% Similarity=0.524 Sum_probs=61.7
Q ss_pred ceeEEEEeccccCCeEEEeEeeecCeEEeecCCceeeEeeCCeEEEeecCCHHHHHHHHHHHHHHh
Q psy11599 2 NIVGAWLGSEISFTGVVLSCTITRDFTYNKVMPTFHHWQTGNKKFGLTFQAAADARAFDQGVRNAL 67 (76)
Q Consensus 2 ~~~~~i~G~~l~D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~~GLnF~s~~eA~~F~~~v~~al 67 (76)
...|||+|.+.+| +|+|||+||++++||+++|+||||++++|+|||||+|++||++|.++|.+++
T Consensus 42 ~~~~ri~~~~~~~-~vv~e~ely~~~~y~~~~~~Fh~f~~~~~~~GLnF~se~EA~~F~~~v~~~~ 106 (106)
T smart00461 42 SYFFRIVGIKGQD-KVIWNQELYKNFKYNQATPTFHQWADDKCVYGLNFASEEEAKKFRKKVLKAL 106 (106)
T ss_pred eEEEEEEEecCCC-eEEEEEeccCCCEEeecCCceEEEEeCCeEEEeecCCHHHHHHHHHHHHhcC
Confidence 3579999999988 8999999999999999999999999999999999999999999999998764
No 6
>PF00568 WH1: WH1 domain; InterPro: IPR000697 The EVH1 (WH1, RanBP1-WASP) domain is found in multi-domain proteins implicated in a diverse range of signalling, nuclear transport and cytoskeletal events. This domain of around 115 amino acids is present in species ranging from yeast to mammals. Many EVH1-containing proteins associate with actin-based structures and play a role in cytoskeletal organisation. EVH1 domains recognise and bind the proline-rich motif FPPPP with low-affinity, further interactions then form between flanking residues [][]. WASP family proteins contain a EVH1 (WH1) in their N-terminals which bind proline-rich sequences in the WASP interacting protein. Proteins of the RanBP1 family contain a WH1 domain in their N-terminal region, which seems to bind a different sequence motif present in the C-terminal part of RanGTP protein [,]. Tertiary structure of the WH1 domain of the Mena protein revealed structure similarities with the pleckstrin homology (PH) domain. The overall fold consists of a compact parallel beta-sandwich, closed along one edge by a long alpha-helix. A highly conserved cluster of three surface-exposed aromatic side-chains forms the recognition site for the molecules target ligands. [].; GO: 0005515 protein binding; PDB: 1I2H_A 1DDV_A 1DDW_A 1EGX_A 3SYX_A 1TJ6_B 1XOD_B 1EVH_A 1I7A_B 2JP2_A ....
Probab=99.93 E-value=9.4e-26 Score=145.66 Aligned_cols=65 Identities=23% Similarity=0.331 Sum_probs=61.9
Q ss_pred ceeEEEEeccccCCeEEEeEeeecCeEEeecCCceeeEeeCCeEEEeecCCHHHHHHHHHHHHHH
Q psy11599 2 NIVGAWLGSEISFTGVVLSCTITRDFTYNKVMPTFHHWQTGNKKFGLTFQAAADARAFDQGVRNA 66 (76)
Q Consensus 2 ~~~~~i~G~~l~D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~~GLnF~s~~eA~~F~~~v~~a 66 (76)
.++|+|++.+++|++++|||+||++++|++++|+||||++++|+|||||+|++||+.|...|.++
T Consensus 46 ~~~y~I~~~~~~~~~~v~e~~l~~~~~Y~~~~~~Fh~f~~~~~~~GLnF~se~eA~~F~~~v~~~ 110 (111)
T PF00568_consen 46 RRSYFIRLYDLQDGKVVWEQELYPGFVYTKARPFFHQFEDDDCVYGLNFASEEEADQFYKKVQEA 110 (111)
T ss_dssp TTEEEEEEEETTTTEEEEEEEESTT-EEEEESSSEEEEEETTCEEEEEESSHHHHHHHHHHHHHH
T ss_pred CCEEEEEEEEccccEEEEEeEecCCCEEEeCCCcEEEEEeCCeEEEEecCCHHHHHHHHHHHhcc
Confidence 46899999999999999999999999999999999999999999999999999999999999876
No 7
>cd01205 WASP WASP-type EVH1 domain. WASP-type EVH1 domain. Wiskott-Aldrich syndrome (WAS) is an X-linked recessive disease, characterized by eczema, immunodeficiency, and thrombocytopenia. The majority of patients with WAS, or a milder version of the disorder, X-linked thrombocytopenia (XLT), have point mutations in the EVH1 domain of WASP (Wiskott-Aldrich syndrome protein). WASP is an actin regulatory protein consisting of an N-terminal EVH1 domain, a basic region, a GTP binding domain, a proline rich region and a WH2 acidic region. Yeast members lack the GTP binding domain. WASP binds a 25 residue proline rich motif from the WASP Interacting Protein (WIP) via its N-terminal EVH1 domain.
Probab=99.74 E-value=1.1e-17 Score=109.03 Aligned_cols=64 Identities=19% Similarity=0.292 Sum_probs=58.9
Q ss_pred eeEEEEeccccCCeEEEeEeeecCeEEeecCCceeeEeeCCeEEEeecCCHHHHHHHHHHHHHH
Q psy11599 3 IVGAWLGSEISFTGVVLSCTITRDFTYNKVMPTFHHWQTGNKKFGLTFQAAADARAFDQGVRNA 66 (76)
Q Consensus 3 ~~~~i~G~~l~D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~~GLnF~s~~eA~~F~~~v~~a 66 (76)
.+|.|.=-+++.+.++|+++||.++.|++.+|+||+|..++|++||||+|++||..|...|...
T Consensus 41 ~sy~lrl~D~~~~~v~weqElY~~f~y~~~r~fFhtFe~d~c~~GL~Fade~EA~~F~k~v~~~ 104 (105)
T cd01205 41 KSYFIRLFDIKANRIIWEQELYDNFEYQQPRPFFHTFEGDDCVVGLNFADETEAAEFRKKVLDK 104 (105)
T ss_pred CEEEEEEEEccCCcEEEEEEcccCcEEccCCCcEEEEeccCcEEEEEECCHHHHHHHHHHHHhc
Confidence 4666666788889999999999999999999999999999999999999999999999998764
No 8
>KOG3671|consensus
Probab=99.54 E-value=6.6e-15 Score=116.20 Aligned_cols=67 Identities=16% Similarity=0.288 Sum_probs=60.8
Q ss_pred eEEEEeccccCCeEEEeEeeecCeEEeecCCceeeEeeCCeEEEeecCCHHHHHHHHHHHHHHhhhh
Q psy11599 4 VGAWLGSEISFTGVVLSCTITRDFTYNKVMPTFHHWQTGNKKFGLTFQAAADARAFDQGVRNALQEY 70 (76)
Q Consensus 4 ~~~i~G~~l~D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~~GLnF~s~~eA~~F~~~v~~al~~l 70 (76)
+|.+.=-+|.++.++|+++||.+|.|++.+++||+|..++|+.||||.||+||+.|.+.|+..+.+=
T Consensus 76 syFlrl~di~~~rliWdqELY~nf~y~q~r~ffhtFegddc~aGLnF~~E~EA~~F~k~V~~r~~~~ 142 (569)
T KOG3671|consen 76 SYFLRLVDIVNNRLIWDQELYQNFEYRQPRTFFHTFEGDDCQAGLNFASEEEAQKFRKKVQDRICHR 142 (569)
T ss_pred eeeeEEeeecCceeeehHHhhhhceeccCccceeeeccccceeeecccCHHHHHHHHHHHHHHhhhh
Confidence 4555556788899999999999999999999999999999999999999999999999999888654
No 9
>smart00160 RanBD Ran-binding domain. Domain of apporximately 150 residues that stabilises the GTP-bound form of Ran (the Ras-like nuclear small GTPase).
Probab=98.54 E-value=6.1e-07 Score=59.54 Aligned_cols=64 Identities=13% Similarity=0.140 Sum_probs=53.2
Q ss_pred eeEEEEeccccCCeEEEeEeeecCeEEeecCCc--eeeEee----C----CeEEEeecCCHHHHHHHHHHHHHH
Q psy11599 3 IVGAWLGSEISFTGVVLSCTITRDFTYNKVMPT--FHHWQT----G----NKKFGLTFQAAADARAFDQGVRNA 66 (76)
Q Consensus 3 ~~~~i~G~~l~D~~vvlnc~l~~~l~Yn~atp~--FHqWr~----~----~~~~GLnF~s~~eA~~F~~~v~~a 66 (76)
..+||+.|+-+...|++|+.|+++++|..+.+. ...|-. + ...|.+.|.++++|..|..+|++|
T Consensus 57 ~~~RivmR~~~~~kv~lN~~i~~~~~~~~~~~~~~~~~~~~~d~~d~~~~~~~~~irfk~~e~a~~f~~~~~ea 130 (130)
T smart00160 57 GKVRIVMRRDGVLKVCANHPIFKSMTLKPLAGSNRALKWTPEDFADDIPKLVLYAVRFKTKEEADSFKNIFEEA 130 (130)
T ss_pred CeEEEEEEECCCceEEeccEecCCcEEeecCCCcceEEEeeeecCCCCCceEEEEEEeCCHHHHHHHHHHHHhC
Confidence 579999998888899999999999999887664 455521 1 256999999999999999998864
No 10
>cd00835 RanBD Ran-binding domain. Ran-binding domain; This domain of approximately 150 residues shares structural similarity to the PH domain, but lacks detectable sequence similarity. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran . The Ran-binding domain is found in multiple copies in Nuclear pore complex proteins.
Probab=98.42 E-value=2.4e-06 Score=55.61 Aligned_cols=65 Identities=12% Similarity=0.150 Sum_probs=56.6
Q ss_pred eeEEEEeccccCCeEEEeEeeecCeEEeecC--CceeeEee--------CCeEEEeecCCHHHHHHHHHHHHHHh
Q psy11599 3 IVGAWLGSEISFTGVVLSCTITRDFTYNKVM--PTFHHWQT--------GNKKFGLTFQAAADARAFDQGVRNAL 67 (76)
Q Consensus 3 ~~~~i~G~~l~D~~vvlnc~l~~~l~Yn~at--p~FHqWr~--------~~~~~GLnF~s~~eA~~F~~~v~~al 67 (76)
..+||+-|+-+...|++|+.|+++++|..+. ..++.|-. .-+.|.+.|.++++|..|..++..+.
T Consensus 47 ~~~RivmR~d~~~kv~lN~~i~~~~~~~~~~~~~k~~~~~~~d~~~~~~~~~~~~lrfk~~~~a~~f~~~~~~~~ 121 (122)
T cd00835 47 GKYRLLMRRDQVLKLCLNHKLVPGMKLQPMGNSDKSIVWAAMDFSDDEPKPETFAIRFKTEEIADEFKEAIEEAK 121 (122)
T ss_pred CcEEEEEEeCCccEEEEeeEecCCcEEeecCCCCcEEEEEeeecCCCCCcEEEEEEEECCHHHHHHHHHHHHHhh
Confidence 5789999988889999999999999999998 79999942 12359999999999999999988764
No 11
>PF00638 Ran_BP1: RanBP1 domain; InterPro: IPR000156 Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran Binding Protein 1 (RanBP1) has guanine nucleotide dissociation inhibitory activity, specific for the GTP form of Ran and also functions to stimulate Ran GTPase activating protein(GAP)-mediated GTP hydrolysis by Ran. RanBP1 contributes to maintaining the gradient of RanGTP across the nuclear envelope high (GDI activity) or the cytoplasmic levels of RanGTP low (GAP cofactor) []. All RanBP1 proteins contain an approx 150 amino acid residue Ran binding domain. Ran BP1 binds directly to RanGTP with high affinity. There are four sites of contact between Ran and the Ran binding domain. One of these involves binding of the C-terminal segment of Ran to a groove on the Ran binding domain that is analogous to the surface utilised in the EVH1-peptide interaction []. Nup358 contains four Ran binding domains. The structure of the first of these is known [].; GO: 0046907 intracellular transport; PDB: 2Y8F_A 2Y8G_B 2CRF_A 1XKE_A 1RRP_D 2EC1_A 3M1I_B 1K5D_E 3OAN_A 3N7C_A ....
Probab=97.39 E-value=0.0028 Score=40.65 Aligned_cols=66 Identities=15% Similarity=0.184 Sum_probs=49.0
Q ss_pred eeEEEEeccccCCeEEEeEeeecCeEEeec--CCceeeE--ee---C---CeEEEeecCCHHHHHHHHHHHHHHhh
Q psy11599 3 IVGAWLGSEISFTGVVLSCTITRDFTYNKV--MPTFHHW--QT---G---NKKFGLTFQAAADARAFDQGVRNALQ 68 (76)
Q Consensus 3 ~~~~i~G~~l~D~~vvlnc~l~~~l~Yn~a--tp~FHqW--r~---~---~~~~GLnF~s~~eA~~F~~~v~~al~ 68 (76)
..+||+=|+-+-+.|++|..|.++++|... ++...-| .+ + -..|-+.|.++++|..|...+.++-+
T Consensus 46 ~~~RlvmR~d~~~kv~lN~~i~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~irf~~~e~a~~f~~~i~e~~~ 121 (122)
T PF00638_consen 46 GKYRLVMRRDGTGKVLLNHPIFKGMKLKPMKGSEKSLVWTAIDYADEEGKPETYLIRFKSAEDADEFKKKIEEAKE 121 (122)
T ss_dssp CEEEEEEEETTTTEEEEEEE--TTC-EEESTTTTTEEEEEEEECTTSSSEEEEEEEE-SSHHHHHHHHHHHHHHHH
T ss_pred cceEEEEEEcccCceeEEEEecCCceecccccCCcEEEEEeccccCCCCceEEEEEEECCHHHHHHHHHHHHHHhc
Confidence 468899898888899999999999999643 3456666 22 1 13599999999999999999998754
No 12
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=70.07 E-value=5.4 Score=25.69 Aligned_cols=28 Identities=32% Similarity=0.417 Sum_probs=20.5
Q ss_pred EeeCCeEEEeecCCHHHHHHHHHHHHHHh
Q psy11599 39 WQTGNKKFGLTFQAAADARAFDQGVRNAL 67 (76)
Q Consensus 39 Wr~~~~~~GLnF~s~~eA~~F~~~v~~al 67 (76)
|++-..+.|. |.|++||+.|...|.-.|
T Consensus 63 w~~wG~~~GY-F~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 63 WTYWGWKGGY-FATEEDAEAFYDELTYML 90 (93)
T ss_pred HHHHHHhCCC-cCCHHHHHHHHHHHHHHH
Confidence 4444444444 999999999998887665
No 13
>cd00900 PH-like Pleckstrin homology-like domain. Pleckstrin homology-like domain. This family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. The PH domain is commonly found in eukaryotic signaling proteins. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins.
Probab=65.05 E-value=21 Score=19.63 Aligned_cols=33 Identities=15% Similarity=0.275 Sum_probs=27.5
Q ss_pred CceeeEeeC---CeEEEeecCCHHHHHHHHHHHHHH
Q psy11599 34 PTFHHWQTG---NKKFGLTFQAAADARAFDQGVRNA 66 (76)
Q Consensus 34 p~FHqWr~~---~~~~GLnF~s~~eA~~F~~~v~~a 66 (76)
++..++... ...+-|...+++|+.....++.+|
T Consensus 64 ~~~F~i~~~~~~~~~~~~~~~~~~~~~~W~~al~~~ 99 (99)
T cd00900 64 PNCFAIVTKDRGRRVFVFQADSEEEAQEWVEALQQA 99 (99)
T ss_pred CceEEEECCCCCcEEEEEEcCCHHHHHHHHHHHhcC
Confidence 577778777 677999999999999998887653
No 14
>PF06058 DCP1: Dcp1-like decapping family; InterPro: IPR010334 An essential step in mRNA turnover is decapping. In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2 (IPR007722 from INTERPRO). The precise role of these proteins in the decapping reaction has not been established. Evidence suggests that the Dcp1 may enhance the function of Dcp2 [].; PDB: 1Q67_A 2QKM_C 2QKL_A.
Probab=63.42 E-value=39 Score=22.10 Aligned_cols=44 Identities=14% Similarity=0.278 Sum_probs=32.9
Q ss_pred eeecCeEEeecCCceeeEeeC-CeEEEeecCCHHHHHHHHHHHHHH
Q psy11599 22 TITRDFTYNKVMPTFHHWQTG-NKKFGLTFQAAADARAFDQGVRNA 66 (76)
Q Consensus 22 ~l~~~l~Yn~atp~FHqWr~~-~~~~GLnF~s~~eA~~F~~~v~~a 66 (76)
.|.+++.+.... .|.-+|.+ .+.||+=|-+++|..+....+.+.
T Consensus 77 ~i~~~~~~e~~~-~~l~~r~~~~~I~GiWf~~~~d~~ri~~~l~~l 121 (122)
T PF06058_consen 77 PITPDLDFELQD-PYLIYRNDNQEIYGIWFYDDEDRQRIYNLLQRL 121 (122)
T ss_dssp EE-SGGGEEEET-TEEEEEETTTEEEEEEESSHHHHHHHHHHHHHH
T ss_pred ecCCCcEEEEeC-CEEEEEcCCceEEEEEEEeHHHHHHHHHHHHhc
Confidence 467777775444 46778875 577999999999999988877654
No 15
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=60.68 E-value=7.7 Score=25.05 Aligned_cols=19 Identities=26% Similarity=0.457 Sum_probs=16.4
Q ss_pred eE-EEeecCCHHHHHHHHHH
Q psy11599 44 KK-FGLTFQAAADARAFDQG 62 (76)
Q Consensus 44 ~~-~GLnF~s~~eA~~F~~~ 62 (76)
.+ .-|.|.|+|||-+|...
T Consensus 48 ~q~v~l~F~skE~Ai~yaer 67 (101)
T PF04800_consen 48 SQSVRLKFDSKEDAIAYAER 67 (101)
T ss_dssp EE-CEEEESSHHHHHHHHHH
T ss_pred hCeeEeeeCCHHHHHHHHHH
Confidence 44 89999999999999864
No 16
>PF07485 DUF1529: Domain of Unknown Function (DUF1259); InterPro: IPR011094 This family is the lppY/lpqO homologue family. They are related to 'probable conserved lipoproteins' LppY and LpqO from Mycobacterium bovis.
Probab=58.77 E-value=7.6 Score=25.80 Aligned_cols=35 Identities=23% Similarity=0.405 Sum_probs=26.7
Q ss_pred ceeeEeeCCeE-EEeecCCHHHHHHHHHHHHHHhhh
Q psy11599 35 TFHHWQTGNKK-FGLTFQAAADARAFDQGVRNALQE 69 (76)
Q Consensus 35 ~FHqWr~~~~~-~GLnF~s~~eA~~F~~~v~~al~~ 69 (76)
.=-||=.++.+ |=+.|.+.+|+..|+++++.||+.
T Consensus 87 lHNH~l~e~Prl~ymH~~~~gdp~~lA~~vr~Ald~ 122 (123)
T PF07485_consen 87 LHNHWLFEQPRLFYMHIWGVGDPAKLARKVRAALDV 122 (123)
T ss_pred EecccccCCCCEEEEEEEecCCHHHHHHHHHHHHhc
Confidence 34456555443 778888899999999999999963
No 17
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=55.77 E-value=46 Score=20.72 Aligned_cols=29 Identities=17% Similarity=0.231 Sum_probs=24.8
Q ss_pred ceeeEeeCCeEEEeecCCHHHHHHHHHHH
Q psy11599 35 TFHHWQTGNKKFGLTFQAAADARAFDQGV 63 (76)
Q Consensus 35 ~FHqWr~~~~~~GLnF~s~~eA~~F~~~v 63 (76)
=-|+....+...=|-|.+++||.+|..-+
T Consensus 14 GI~si~~~~~~~Vl~FE~edDA~RYa~lL 42 (86)
T PF11360_consen 14 GIYSIQNKDRNVVLMFEDEDDAERYAGLL 42 (86)
T ss_pred cEEEEEeCCCCEEEEEccHHHHHHHHHHH
Confidence 46888888877889999999999998764
No 18
>KOG3389|consensus
Probab=52.46 E-value=11 Score=26.62 Aligned_cols=17 Identities=29% Similarity=0.647 Sum_probs=14.8
Q ss_pred EEeecCCHHHHHHHHHH
Q psy11599 46 FGLTFQAAADARAFDQG 62 (76)
Q Consensus 46 ~GLnF~s~~eA~~F~~~ 62 (76)
..|.|+++|||.+|...
T Consensus 127 m~L~F~tkEdA~sFaEk 143 (178)
T KOG3389|consen 127 MALAFDTKEDAKSFAEK 143 (178)
T ss_pred eeeeeccHHHHHHHHHH
Confidence 56999999999999753
No 19
>cd03580 NTR_Sfrp1_like NTR domain, Secreted frizzled-related protein (Sfrp) 1-like subfamily; composed of proteins similar to human Sfrp1, Sfrp2 and Sfrp5. Sfrps are soluble proteins containing an NTR domain C-terminal to a cysteine-rich Frizzled domain. They show diverse functions and are thought to work in Wnt signaling indirectly, as modulators or antagonists by binding Wnt ligands, and directly, via the Wnt receptor, Frizzled. They participate in regulating the patterning along the anteroposterior axis in vertebrates. Human Sfrp1 has been found frequently to be downregulated in breast cancer and is associated with disease progression and poor prognosis.
Probab=51.01 E-value=26 Score=22.92 Aligned_cols=21 Identities=19% Similarity=0.089 Sum_probs=17.0
Q ss_pred ceeEEEEeccccCCeEEEeEee
Q psy11599 2 NIVGAWLGSEISFTGVVLSCTI 23 (76)
Q Consensus 2 ~~~~~i~G~~l~D~~vvlnc~l 23 (76)
+..|.|.|+. .|+.++++...
T Consensus 85 ~~~YLImG~~-~~g~~~v~~i~ 105 (126)
T cd03580 85 NGVYLVMGRK-VDGKLLLTSIY 105 (126)
T ss_pred CceEEEEEEE-eCCEEEEEEEe
Confidence 5689999988 89998886543
No 20
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=43.83 E-value=35 Score=18.28 Aligned_cols=21 Identities=14% Similarity=0.183 Sum_probs=16.9
Q ss_pred eecCCHHHHHHHHHHHHHHhh
Q psy11599 48 LTFQAAADARAFDQGVRNALQ 68 (76)
Q Consensus 48 LnF~s~~eA~~F~~~v~~al~ 68 (76)
-.|.++.||......+...++
T Consensus 22 ~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 22 RGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CCCCcHHHHHHHHHHHHHHHH
Confidence 459999999999888776654
No 21
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=37.60 E-value=69 Score=17.23 Aligned_cols=44 Identities=18% Similarity=0.435 Sum_probs=23.6
Q ss_pred ecCeEEeecCCcee-e---EeeC--CeEEEe-ecCCHHHHHHHHHHHHHHh
Q psy11599 24 TRDFTYNKVMPTFH-H---WQTG--NKKFGL-TFQAAADARAFDQGVRNAL 67 (76)
Q Consensus 24 ~~~l~Yn~atp~FH-q---Wr~~--~~~~GL-nF~s~~eA~~F~~~v~~al 67 (76)
++|+.|.+.+.-.. + |..+ .+.|.+ .|.+++||..-.......+
T Consensus 3 ~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~ 53 (56)
T PF00847_consen 3 YKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKEL 53 (56)
T ss_dssp STTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHC
T ss_pred cEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHh
Confidence 56777766554311 2 2111 244544 4888888877665554443
No 22
>PF01693 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR011320 This entry represents the N-terminal domain of RNase HI, which has a 3-layer alpha/beta/alpha structure []. This domain is lacking in retroviral and prokaryotic enzymes, but shows a striking structural similarity to the ribosomal protein L9 N-terminal domain, and may function as a regulatory RNA-binding module. However, the topology of this domain differs from structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP motif. Eukaryotic RNases HI possess either one or two copies of this small N-terminal domain, in addition to the well-conserved catalytic RNase H domain. RNase HI belongs to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. ; PDB: 1QHK_A 3BSU_C.
Probab=35.24 E-value=32 Score=18.39 Aligned_cols=13 Identities=23% Similarity=0.422 Sum_probs=10.9
Q ss_pred EeecCCHHHHHHH
Q psy11599 47 GLTFQAAADARAF 59 (76)
Q Consensus 47 GLnF~s~~eA~~F 59 (76)
=..|.+.+||..|
T Consensus 32 ~k~F~t~~eA~~~ 44 (44)
T PF01693_consen 32 YKSFKTREEAEEF 44 (44)
T ss_dssp EEEESSHHHHHHH
T ss_pred ECCcCCHHHHhhC
Confidence 4678999999886
No 23
>PRK14128 iraD DNA replication/recombination/repair protein; Provisional
Probab=35.00 E-value=48 Score=19.73 Aligned_cols=23 Identities=13% Similarity=-0.025 Sum_probs=20.4
Q ss_pred eecCCHHHHHHHHHHHHHHhhhh
Q psy11599 48 LTFQAAADARAFDQGVRNALQEY 70 (76)
Q Consensus 48 LnF~s~~eA~~F~~~v~~al~~l 70 (76)
||.+++++-..+.+.+++||..-
T Consensus 1 ~~~~~~~~r~~i~~~I~~aI~~f 23 (69)
T PRK14128 1 HNVSDKRLQSWYCRQLRSALLFH 23 (69)
T ss_pred CCcccHHHHHHHHHHHHHHHHHc
Confidence 58899999999999999999754
No 24
>PF11531 CARM1: Coactivator-associated arginine methyltransferase 1 N terminal; InterPro: IPR020989 Histone-arginine methyltransferase CARM1 (also known as coactivator-associated arginine methyltransferase 1) methylates arginine residues in several proteins involved in DNA packaging, transcription regulation, and mRNA stability []. CARM1 is recruited by several transcription factors and plays a critical role in gene expression as a positive regulator. This entry represents the N-terminal domain of CARM1. Structurally this domain adopts a PH domain-like fold, a common structural scaffold found in a broad range proteins with diverse activities, which is frequently found to regulate protein-protein interactions []. ; GO: 0009405 pathogenesis; PDB: 2OQB_B 2Y1W_C 2Y1X_D.
Probab=34.09 E-value=1.4e+02 Score=19.82 Aligned_cols=52 Identities=21% Similarity=0.277 Sum_probs=33.8
Q ss_pred CCeEEEeEeeecCeEEeecCCceeeEeeCCeEEEeecCCHHHHHHHHHHHHH
Q psy11599 14 FTGVVLSCTITRDFTYNKVMPTFHHWQTGNKKFGLTFQAAADARAFDQGVRN 65 (76)
Q Consensus 14 D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~~GLnF~s~~eA~~F~~~v~~ 65 (76)
++-+++.|.+.++-..-++-.----.-.+.--.=|+|+|++|-..|...+..
T Consensus 50 ~~~cvfkc~VsreTEccRVG~~SfliTlg~nSlLl~F~s~~df~~F~n~lk~ 101 (114)
T PF11531_consen 50 ECVCVFKCTVSRETECCRVGKQSFLITLGCNSLLLQFASPADFSSFHNILKR 101 (114)
T ss_dssp T--EEEEEEEETTSEEEEETTTEEEEEETTEEEEEE-SSHHHHHHHHHHHCC
T ss_pred CCEEEEEEEEcCCcceeEecceEEEEEecCCeEEEEecCHHHHHHHHHHHHH
Confidence 3447899999888777666553323333333456889999999999976543
No 25
>PF12444 Sox_N: Sox developmental protein N terminal ; InterPro: IPR022151 This domain family is found in eukaryotes, and is typically between 69 and 88 amino acids in length. The family is found in association with PF00505 from PFAM. There are two conserved sequence motifs: YDW and PVR. This family contains Sox8, Sox9 and Sox10 proteins which have structural similarity. Sox proteins are involved in developmental processes.
Probab=33.83 E-value=19 Score=22.62 Aligned_cols=25 Identities=16% Similarity=0.323 Sum_probs=22.9
Q ss_pred ecCCHHHHHHHHHHHHHHhhhhhcc
Q psy11599 49 TFQAAADARAFDQGVRNALQEYLHD 73 (76)
Q Consensus 49 nF~s~~eA~~F~~~v~~al~~l~~g 73 (76)
...++++...|...|+.|+.++.+|
T Consensus 48 ~~~~~~~d~~fp~~IrdAVsqVLkG 72 (84)
T PF12444_consen 48 KAKSEDEDDRFPVCIRDAVSQVLKG 72 (84)
T ss_pred ccccccccccccHHHHHHHHHHhcc
Confidence 6788889999999999999999887
No 26
>COG4050 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.52 E-value=54 Score=22.52 Aligned_cols=22 Identities=18% Similarity=0.226 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHHHHHHhhhhhc
Q psy11599 51 QAAADARAFDQGVRNALQEYLH 72 (76)
Q Consensus 51 ~s~~eA~~F~~~v~~al~~l~~ 72 (76)
.|+|||..|...+..-|+.|..
T Consensus 128 ~s~Eea~~~VnkI~~FL~sLe~ 149 (152)
T COG4050 128 RSEEEAIDFVNKIANFLKSLEA 149 (152)
T ss_pred CcHHHHHHHHHHHHHHHHhhhh
Confidence 5899999999999999998864
No 27
>PF04278 Tic22: Tic22-like family; InterPro: IPR007378 Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accompished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex loacted at the inner membrane []. The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane. This entry represents Tic22, a core member of the Tic complex. It is believed to act as a link between both protein complexes, contacting the translocated protein in the intermembrane space after transport through the Toc complex, and directing it to the Tic complex [].; PDB: 4EV1_A.
Probab=30.53 E-value=64 Score=23.87 Aligned_cols=28 Identities=32% Similarity=0.427 Sum_probs=21.2
Q ss_pred CeEEEeecCCHHHHHHHHHHHHHHhhhh
Q psy11599 43 NKKFGLTFQAAADARAFDQGVRNALQEY 70 (76)
Q Consensus 43 ~~~~GLnF~s~~eA~~F~~~v~~al~~l 70 (76)
...+|+-|-|++||.+|...+...-.++
T Consensus 97 ~~~v~~~F~s~~dA~~~L~~lk~~~p~~ 124 (274)
T PF04278_consen 97 GKSVGLFFFSQQDAEAFLAQLKKSNPEL 124 (274)
T ss_dssp -SEEEEEES-HHHHHHHHHHHHH-SSHH
T ss_pred CceEEEEEecHHHHHHHHHHHhhhCccc
Confidence 4679999999999999998887765444
No 28
>PF13018 ESPR: Extended Signal Peptide of Type V secretion system
Probab=30.15 E-value=36 Score=16.60 Aligned_cols=13 Identities=15% Similarity=0.097 Sum_probs=8.0
Q ss_pred CceeEEEEecccc
Q psy11599 1 MNIVGAWLGSEIS 13 (76)
Q Consensus 1 ~~~~~~i~G~~l~ 13 (76)
||-.||++=.+-+
T Consensus 1 MNkiyr~iwn~~~ 13 (24)
T PF13018_consen 1 MNKIYRLIWNKAR 13 (24)
T ss_pred CCccEEEEEECCC
Confidence 6777777654443
No 29
>PF12441 DUF3680: Protein of unknown function (DUF3680) ; InterPro: IPR022148 This domain family is found in bacteria and archaea, and is approximately 40 amino acids in length.
Probab=29.89 E-value=38 Score=18.55 Aligned_cols=14 Identities=21% Similarity=0.442 Sum_probs=11.7
Q ss_pred ecCCHHHHHHHHHH
Q psy11599 49 TFQAAADARAFDQG 62 (76)
Q Consensus 49 nF~s~~eA~~F~~~ 62 (76)
.|.|++|++.|-..
T Consensus 7 ~f~se~Ee~eFW~~ 20 (42)
T PF12441_consen 7 EFKSEEEEREFWDT 20 (42)
T ss_pred CCCCHHHHHHHHHh
Confidence 58999999999654
No 30
>cd01220 PH_CDEP Chondrocyte-derived ezrin-like domain containing protein (CDEP) Pleckstrin homology (PH) domain. Chondrocyte-derived ezrin-like domain containing protein (CDEP) Pleckstrin homology (PH) domain. CDEP consists of a Ferm domain, a rhoGEF (DH) domain followed by two PH domains. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=29.73 E-value=1.3e+02 Score=18.72 Aligned_cols=33 Identities=9% Similarity=0.149 Sum_probs=27.9
Q ss_pred eeEeeC--CeEEEeecCCHHHHHHHHHHHHHHhhh
Q psy11599 37 HHWQTG--NKKFGLTFQAAADARAFDQGVRNALQE 69 (76)
Q Consensus 37 HqWr~~--~~~~GLnF~s~~eA~~F~~~v~~al~~ 69 (76)
|.|..- .+-|=|..+|++|-.....++.+|+++
T Consensus 65 ~~F~I~~~~ks~~l~A~s~~Ek~~Wi~~i~~aI~~ 99 (99)
T cd01220 65 HCFTIFGGQCAITVAASTRAEKEKWLADLSKAIAD 99 (99)
T ss_pred eeEEEEcCCeEEEEECCCHHHHHHHHHHHHHHhhC
Confidence 788874 445999999999999999999999863
No 31
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=27.80 E-value=84 Score=16.58 Aligned_cols=18 Identities=11% Similarity=0.259 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHhhhhh
Q psy11599 54 ADARAFDQGVRNALQEYL 71 (76)
Q Consensus 54 ~eA~~F~~~v~~al~~l~ 71 (76)
|++..|..++..+.+.+.
T Consensus 1 e~~~~La~al~~~~~~i~ 18 (41)
T PF02132_consen 1 EEAEQLADALKEAKENIK 18 (41)
T ss_dssp HHHHHHHHHHHHHHHH-E
T ss_pred CcHHHHHHHHHHHHHcCC
Confidence 678899999998888764
No 32
>PF05573 NosL: NosL; InterPro: IPR008719 NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallocentre assembly []. This entry also contains HTH-type transcriptional repressors, including YcnK. YcnK may act as a negative transcriptional regulator of YcnJ in the presence of copper and may use copper as a corepressor. The gene, ycnK, is significantly induced under copper-limiting conditions.; PDB: 2HQ3_A 2HPU_A.
Probab=27.77 E-value=53 Score=21.81 Aligned_cols=15 Identities=33% Similarity=0.627 Sum_probs=11.8
Q ss_pred eecCCHHHHHHHHHH
Q psy11599 48 LTFQAAADARAFDQG 62 (76)
Q Consensus 48 LnF~s~~eA~~F~~~ 62 (76)
+-|+++++|.+|...
T Consensus 119 ~aF~~~~~A~~F~~~ 133 (149)
T PF05573_consen 119 IAFASKEDAEAFAKE 133 (149)
T ss_dssp EEES-HHHHHHHHHH
T ss_pred cccCCHHHHHHHHHH
Confidence 349999999999875
No 33
>PF09564 RE_NgoBV: NgoBV restriction endonuclease; InterPro: IPR019064 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the restriction endonuclease NgoBV, which recognises the sequence GGNNCC, but whose cleavage site is unknown.
Probab=27.52 E-value=2.2e+02 Score=21.16 Aligned_cols=64 Identities=19% Similarity=0.320 Sum_probs=42.7
Q ss_pred ceeEEEEeccccCCe-EE--------------------EeEeeecCeEEeecCCceeeEeeCCeEEEeecCCHHHHHHHH
Q psy11599 2 NIVGAWLGSEISFTG-VV--------------------LSCTITRDFTYNKVMPTFHHWQTGNKKFGLTFQAAADARAFD 60 (76)
Q Consensus 2 ~~~~~i~G~~l~D~~-vv--------------------lnc~l~~~l~Yn~atp~FHqWr~~~~~~GLnF~s~~eA~~F~ 60 (76)
|.-|.|-|-++.|+. |+ |+|-+.+++.|+- +|.- |-..++.=---|.|.+| |-
T Consensus 119 d~~YlIfgY~M~d~g~i~IKdiwLKKIWEIt~~s~~ypi~~QvKr~~iyni-RP~~--~f~~~k~~~~~Fes~ed---fI 192 (240)
T PF09564_consen 119 DADYLIFGYDMDDNGGITIKDIWLKKIWEITGRSTKYPIKLQVKRGVIYNI-RPGS--WFKTNKTNASVFESLED---FI 192 (240)
T ss_pred cceEEEEEEEecCCCCEEEehHHHhhHHHhhccCCCCceEEEEecceeEEe-cCCc--eeeecCCCchhhhhHHH---HH
Confidence 456889999999883 22 6888999999954 4433 43322211245777776 88
Q ss_pred HHHHHHhhhhh
Q psy11599 61 QGVRNALQEYL 71 (76)
Q Consensus 61 ~~v~~al~~l~ 71 (76)
.++.+++..-.
T Consensus 193 ~Ai~et~~~~p 203 (240)
T PF09564_consen 193 SAIYETVYQNP 203 (240)
T ss_pred HHHHHHHHhCc
Confidence 88888886544
No 34
>PF00387 PI-PLC-Y: Phosphatidylinositol-specific phospholipase C, Y domain This entry is for the whole phospholipase C protein; InterPro: IPR001711 Phosphatidylinositol-specific phospholipase C (3.1.4.11 from EC), an eukaryotic intracellular enzyme, plays an important role in signal transduction processes [] (see IPR001192 from INTERPRO). It catalyzes the hydrolysis of 1-phosphatidyl-D-myo-inositol-3,4,5-triphosphate into the second messenger molecules diacylglycerol and inositol-1,4,5-triphosphate. This catalytic process is tightly regulated by reversible phosphorylation and binding of regulatory proteins [, , ]. In mammals, there are at least 6 different isoforms of PI-PLC, they differ in their domain structure, their regulation, and their tissue distribution. Lower eukaryotes also possess multiple isoforms of PI-PLC. All eukaryotic PI-PLCs contain two regions of homology, sometimes referred to as 'X-box' (see IPR000909 from INTERPRO) and 'Y-box'. The order of these two regions is always the same (NH2-X-Y-COOH), but the spacing is variable. In most isoforms, the distance between these two regions is only 50-100 residues but in the gamma isoforms one PH domain, two SH2 domains, and one SH3 domain are inserted between the two PLC-specific domains. The two conserved regions have been shown to be important for the catalytic activity. At the C-terminal of the Y-box, there is a C2 domain (see IPR000008 from INTERPRO) possibly involved in Ca-dependent membrane attachment.; GO: 0004435 phosphatidylinositol phospholipase C activity, 0006629 lipid metabolic process, 0007165 signal transduction, 0035556 intracellular signal transduction; PDB: 3OHM_B 2FJU_B 2ZKM_X 3QR1_D 3QR0_A 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=26.42 E-value=38 Score=22.16 Aligned_cols=27 Identities=26% Similarity=0.614 Sum_probs=17.7
Q ss_pred eeEeeCCeEEEeecCCHHHHHHHHHHH
Q psy11599 37 HHWQTGNKKFGLTFQAAADARAFDQGV 63 (76)
Q Consensus 37 HqWr~~~~~~GLnF~s~~eA~~F~~~v 63 (76)
.-|...=+.++|||++++++-..-.++
T Consensus 75 ~~W~~G~Q~vALN~Qt~d~~m~ln~g~ 101 (118)
T PF00387_consen 75 PFWNCGCQMVALNFQTPDEPMQLNQGM 101 (118)
T ss_dssp HHHTTT-SEEEB-TTS-SHHHHHHHHH
T ss_pred HHhhccCccceeeccCCChhHHHHHhh
Confidence 447777778999999999876655543
No 35
>PF12373 Msg2_C: Major surface glycoprotein 2 C terminal; InterPro: IPR021041 Pneumocystis can cause potentially fatal pneumonia infections in immunosuppressed people. The most abundant protein on the surface of Pneumocystis is the major surface glycoprotein (Msg), which is encoded by a multi-copy gene family. Variation in the expressed Msg is thought to help this organism evade the host immune response. The Msg sequences segregate into two distinct branches, with recombination further increasing the diversity of the Msg sequences []. This entry represents a conserved domain found towards the C terminus of Msg2, and is usually found in association with PF02349 from PFAM.
Probab=26.39 E-value=76 Score=16.43 Aligned_cols=12 Identities=33% Similarity=0.512 Sum_probs=10.3
Q ss_pred CCHHHHHHHHHH
Q psy11599 51 QAAADARAFDQG 62 (76)
Q Consensus 51 ~s~~eA~~F~~~ 62 (76)
-||.|+.+|+..
T Consensus 14 VtE~E~kAFDl~ 25 (30)
T PF12373_consen 14 VTEAEVKAFDLT 25 (30)
T ss_pred cCHHHHHHHHHH
Confidence 589999999876
No 36
>cd05756 Ig1_IL1R_like First immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R) and similar proteins. Ig1_IL1R_like: domain similar to the first immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with an accessory protein, IL1RAP. IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three Ig-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta.
Probab=26.09 E-value=73 Score=19.19 Aligned_cols=30 Identities=13% Similarity=0.242 Sum_probs=22.9
Q ss_pred CCeEEEeEeeecCeEEeecCCceeeEeeCCe
Q psy11599 14 FTGVVLSCTITRDFTYNKVMPTFHHWQTGNK 44 (76)
Q Consensus 14 D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~ 44 (76)
...+.++|.+.....|+.+.|. ..|..++.
T Consensus 14 G~~~~L~C~~~g~~~~~~p~~~-v~Wyk~~~ 43 (94)
T cd05756 14 GEPVVIKCPLFYSYIAQSPGLN-LTWYKSDG 43 (94)
T ss_pred CCCeEEECCCCCcccccCCCce-EEEEEcCC
Confidence 4457899998887777777777 78887764
No 37
>TIGR03642 cas_csx13 CRISPR-associated protein, Csx13 family. This model describes a protein N-terminal protein sequence domain strictly associated with CRISPR and CRISPR-associated protein systems. This model and TIGR02584 identify two separate clades from a larger homology domain family, both CRISPR-associated, while other homologs are found that may not be. Members are found in bacteria that include Pelotomaculum thermopropionicum SI, Thermoanaerobacter tengcongensis MB4, and Roseiflexus sp. RS-1, and in archaea that include Thermoplasma volcanium, Picrophilus torridus, and Methanospirillum hungatei. The molecular function is unknown.
Probab=25.74 E-value=94 Score=20.63 Aligned_cols=23 Identities=9% Similarity=0.039 Sum_probs=20.3
Q ss_pred cCCHHHHHHHHHHHHHHhhhhhc
Q psy11599 50 FQAAADARAFDQGVRNALQEYLH 72 (76)
Q Consensus 50 F~s~~eA~~F~~~v~~al~~l~~ 72 (76)
+.|++|+..|...+...+.++..
T Consensus 64 I~t~~d~~~~~~~I~~~i~~l~~ 86 (124)
T TIGR03642 64 ILSDEDILTFMSIAAKEVKKERE 86 (124)
T ss_pred cCCHHHHHHHHHHHHHHHHHHhh
Confidence 47899999999999999988864
No 38
>PF05996 Fe_bilin_red: Ferredoxin-dependent bilin reductase; InterPro: IPR009249 This family consists of several different but closely related proteins which include phycocyanobilin:ferredoxin oxidoreductase 1.3.7.5 from EC (PcyA), 15,16-dihydrobiliverdin:ferredoxin oxidoreductase 1.3.7.2 from EC (PebA) and phycoerythrobilin:ferredoxin oxidoreductase 1.3.7.3 from EC (PebB). Phytobilins are linear tetrapyrrole precursors of the light-harvesting prosthetic groups of the phytochrome photoreceptors of plants and the phycobiliprotein photosynthetic antennae of cyanobacteria, red algae, and cryptomonads. It is known that that phytobilins are synthesised from haem via the intermediacy of biliverdin IX alpha (BV), which is reduced subsequently by ferredoxin-dependent bilin reductases with different double-bond specificities [].; GO: 0016636 oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor, 0050897 cobalt ion binding, 0010024 phytochromobilin biosynthetic process, 0055114 oxidation-reduction process; PDB: 3I8U_X 3AJH_A 3NB9_A 3I94_A 2DKE_A 3NB8_A 3F0M_A 3AJG_A 3I95_A 2D1E_A ....
Probab=25.47 E-value=38 Score=24.35 Aligned_cols=59 Identities=22% Similarity=0.233 Sum_probs=32.3
Q ss_pred EEeccccCCeEEEeEeeecCeEEeecCCceee--EeeCCe-EE--EeecCCHHHHHHHHHHHHHHhhhhh
Q psy11599 7 WLGSEISFTGVVLSCTITRDFTYNKVMPTFHH--WQTGNK-KF--GLTFQAAADARAFDQGVRNALQEYL 71 (76)
Q Consensus 7 i~G~~l~D~~vvlnc~l~~~l~Yn~atp~FHq--Wr~~~~-~~--GLnF~s~~eA~~F~~~v~~al~~l~ 71 (76)
..|..++ |+||.+|+...| .-|+|-- -..... +. .|-|+...............|..|.
T Consensus 56 ~~g~~lq----VL~~V~yP~~~y--dLPiFG~Dlv~~~~~~~~~ailDl~P~~~~~~l~~~y~~~L~~l~ 119 (228)
T PF05996_consen 56 DAGEGLQ----VLNCVIYPRPEY--DLPIFGADLVAFPGKRISAAILDLQPLSQDRDLPEKYYSKLAPLP 119 (228)
T ss_dssp EETTTEE----EEEEEEEE-TTS-----EEEEEEEEETTETEEEEEEEEE-SSTTSHHCHHHHHHHHTSH
T ss_pred hcCCCcE----EEEEEEcCCCCC--CCCcccceeeeeCCccEEEEEEeCCCCCCcccchHHHHHHHHHHH
Confidence 3456666 999999999988 6788753 112233 33 3777665555445555555555553
No 39
>KOG1890|consensus
Probab=25.44 E-value=67 Score=27.68 Aligned_cols=39 Identities=10% Similarity=0.380 Sum_probs=27.4
Q ss_pred EeecCCceeeEeeCCeE----EEeecCCHHHHHHHHHHHHHHh
Q psy11599 29 YNKVMPTFHHWQTGNKK----FGLTFQAAADARAFDQGVRNAL 67 (76)
Q Consensus 29 Yn~atp~FHqWr~~~~~----~GLnF~s~~eA~~F~~~v~~al 67 (76)
|.....+||.||...-+ ...-.-++|||......+.+-+
T Consensus 665 ~~e~eGyFh~~R~a~~R~fNn~a~~~k~~Ee~~e~~~siaEm~ 707 (949)
T KOG1890|consen 665 VDELEGYFHIWRPATVRLFNNTAIRLKSLEEANEYISSIAEMI 707 (949)
T ss_pred hhhccceeEEeehhhhhhccccceeeccHHHHHHHHHHHHHHH
Confidence 34577799999966443 2233469999998887776655
No 40
>PF15465 DUF4634: Domain of unknown function (DUF4634)
Probab=25.33 E-value=1e+02 Score=20.85 Aligned_cols=62 Identities=16% Similarity=0.272 Sum_probs=43.7
Q ss_pred EEeccccCCeEEEeEeeecCeEEeecCCceeeEeeCCeE-EEeecCCHHHHHHHHHHHHHHhhh
Q psy11599 7 WLGSEISFTGVVLSCTITRDFTYNKVMPTFHHWQTGNKK-FGLTFQAAADARAFDQGVRNALQE 69 (76)
Q Consensus 7 i~G~~l~D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~-~GLnF~s~~eA~~F~~~v~~al~~ 69 (76)
|.|..-.|.+..=|-.-|.=.-|..+||+.--|-.+=.. |++ |.|++--.++...+.+|.+.
T Consensus 14 ILGQEYEdEe~leEdeyYQV~YyYTVTP~YDdf~~nFt~dYs~-fesEdrln~ldk~vtEavet 76 (129)
T PF15465_consen 14 ILGQEYEDEERLEEDEYYQVVYYYTVTPNYDDFGANFTVDYSM-FESEDRLNRLDKEVTEAVET 76 (129)
T ss_pred hccccccchhhcccccceeEEEEEEeCCCccccceeEEEEEee-eeehhhhhhhhhHHHHhhhc
Confidence 667777777766665555333458999998776666443 554 78888888888888877753
No 41
>PLN02837 threonine-tRNA ligase
Probab=24.71 E-value=93 Score=25.38 Aligned_cols=29 Identities=14% Similarity=0.408 Sum_probs=23.7
Q ss_pred EeeCC------eEEEeecCCHHHHHHHHHHHHHHh
Q psy11599 39 WQTGN------KKFGLTFQAAADARAFDQGVRNAL 67 (76)
Q Consensus 39 Wr~~~------~~~GLnF~s~~eA~~F~~~v~~al 67 (76)
||.+. ..||..|+++++-+++..-+++|-
T Consensus 181 wrg~~~~~~l~ri~g~~~~~~~~l~~~~~~~~e~~ 215 (614)
T PLN02837 181 WRGDEKNQMLQRIYGTAWESEEQLKAYLHFKEEAK 215 (614)
T ss_pred hcccccCcceEEEEEEecCCHHHHHHHHHHHHHhh
Confidence 78762 349999999999999988887764
No 42
>COG5171 YRB1 Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]
Probab=24.23 E-value=1.3e+02 Score=21.79 Aligned_cols=25 Identities=16% Similarity=0.469 Sum_probs=20.5
Q ss_pred eEEEeecCCHHHHHHHHHHHHHHhh
Q psy11599 44 KKFGLTFQAAADARAFDQGVRNALQ 68 (76)
Q Consensus 44 ~~~GLnF~s~~eA~~F~~~v~~al~ 68 (76)
+-|.+-|.|+|+|..|..-++..-+
T Consensus 178 ~tFairF~s~Ena~~FkEefek~qe 202 (211)
T COG5171 178 QTFAIRFYSEENAKRFKEEFEKGQE 202 (211)
T ss_pred eEEEEeeccHHHHHHHHHHHHHHHH
Confidence 3499999999999999887766543
No 43
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=24.21 E-value=74 Score=17.28 Aligned_cols=17 Identities=18% Similarity=0.055 Sum_probs=13.3
Q ss_pred EEeecCCHHHHHHHHHH
Q psy11599 46 FGLTFQAAADARAFDQG 62 (76)
Q Consensus 46 ~GLnF~s~~eA~~F~~~ 62 (76)
.=+.|.|+++|......
T Consensus 42 a~v~f~~~~~a~~al~~ 58 (70)
T PF14259_consen 42 AFVEFSSEEDAKRALEL 58 (70)
T ss_dssp EEEEESSHHHHHHHHHH
T ss_pred EEEEeCCHHHHHHHHHH
Confidence 33689999999887655
No 44
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=22.81 E-value=1.1e+02 Score=17.62 Aligned_cols=19 Identities=16% Similarity=0.237 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHhhhhhc
Q psy11599 54 ADARAFDQGVRNALQEYLH 72 (76)
Q Consensus 54 ~eA~~F~~~v~~al~~l~~ 72 (76)
.||-.|-+.|+..|..|.+
T Consensus 34 ~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 34 QEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred HHHHHHHHHHHHHHHHHhC
Confidence 3788888888888887753
No 45
>PF12006 DUF3500: Protein of unknown function (DUF3500); InterPro: IPR021889 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 335 to 438 amino acids in length. This protein has a conserved GHH sequence motif. This protein has two completely conserved G residues that may be functionally important.
Probab=22.25 E-value=1.1e+02 Score=23.15 Aligned_cols=27 Identities=26% Similarity=0.447 Sum_probs=21.5
Q ss_pred eccccCCeEEEeEeeecCeEEeecCCcee
Q psy11599 9 GSEISFTGVVLSCTITRDFTYNKVMPTFH 37 (76)
Q Consensus 9 G~~l~D~~vvlnc~l~~~l~Yn~atp~FH 37 (76)
|.++--+++.+||.+..+=+ ..||+|.
T Consensus 124 g~~f~GHHlsln~~~~~~~v--~~tP~F~ 150 (313)
T PF12006_consen 124 GWQFEGHHLSLNCTFVGGQV--SITPTFF 150 (313)
T ss_pred eEEecccEEEEEEEEeCCCE--EECceee
Confidence 55666678999999987766 8899885
No 46
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=22.23 E-value=1.5e+02 Score=24.10 Aligned_cols=30 Identities=17% Similarity=0.453 Sum_probs=24.4
Q ss_pred eEeeCC------eEEEeecCCHHHHHHHHHHHHHHh
Q psy11599 38 HWQTGN------KKFGLTFQAAADARAFDQGVRNAL 67 (76)
Q Consensus 38 qWr~~~------~~~GLnF~s~~eA~~F~~~v~~al 67 (76)
-|+.+. +.||.-|++++++..|..-+++|-
T Consensus 208 ~~~g~~~~~~l~Ri~g~a~~~~~~l~~~~~~~~~~~ 243 (639)
T PRK12444 208 YWRGDSNNQVLQRIYGVAFSSQKELEEYLHFVEEAA 243 (639)
T ss_pred EEcCCCCCcceEEEEEEecCCHHHHHHHHHHHHHhc
Confidence 477763 349999999999999998877664
No 47
>COG3691 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.19 E-value=2e+02 Score=18.64 Aligned_cols=29 Identities=10% Similarity=0.104 Sum_probs=23.2
Q ss_pred eEEEeecCCHHHHHHHHHHHHHHhhhhhc
Q psy11599 44 KKFGLTFQAAADARAFDQGVRNALQEYLH 72 (76)
Q Consensus 44 ~~~GLnF~s~~eA~~F~~~v~~al~~l~~ 72 (76)
..|-+-|+|+++|..+...+.++-..+.+
T Consensus 32 ~~~s~~~as~a~ae~~La~lt~kAr~veS 60 (98)
T COG3691 32 AEYSRFFATRAEAEEALAALTEKARAVES 60 (98)
T ss_pred EEEEEEecCHHHHHHHHHHHHHHHHhhcc
Confidence 35999999999999998887777665543
No 48
>PRK08153 histidinol-phosphate aminotransferase; Provisional
Probab=21.36 E-value=1.4e+02 Score=21.99 Aligned_cols=28 Identities=11% Similarity=0.200 Sum_probs=22.5
Q ss_pred EEeecCCHHHHHHHHHHHHHHhhhhhcc
Q psy11599 46 FGLTFQAAADARAFDQGVRNALQEYLHD 73 (76)
Q Consensus 46 ~GLnF~s~~eA~~F~~~v~~al~~l~~g 73 (76)
+=++|.+++|.+.|..++.++++.+..|
T Consensus 342 iRis~~~~~~~~~~~~al~~~~~~~~~~ 369 (369)
T PRK08153 342 IRVSCGPDEELDLFAEALPEALEAARKG 369 (369)
T ss_pred EEEecCCHHHHHHHHHHHHHHHHHhhcC
Confidence 3466789999999999999998766543
No 49
>cd05722 Ig1_Neogenin First immunoglobulin (Ig)-like domain in neogenin and similar proteins. Ig1_Neogenin: first immunoglobulin (Ig)-like domain in neogenin and related proteins. Neogenin is a cell surface protein which is expressed in the developing nervous system of vertebrate embryos in the growing nerve cells. It is also expressed in other embryonic tissues, and may play a general role in developmental processes such as cell migration, cell-cell recognition, and tissue growth regulation. Included in this group is the tumor suppressor protein DCC, which is deleted in colorectal carcinoma . DCC and neogenin each have four Ig-like domains followed by six fibronectin type III domains, a transmembrane domain, and an intracellular domain.
Probab=21.32 E-value=1.6e+02 Score=17.04 Aligned_cols=28 Identities=21% Similarity=0.428 Sum_probs=19.3
Q ss_pred CCeEEEeEeeecCeEEeecCCceeeEeeCCeEEE
Q psy11599 14 FTGVVLSCTITRDFTYNKVMPTFHHWQTGNKKFG 47 (76)
Q Consensus 14 D~~vvlnc~l~~~l~Yn~atp~FHqWr~~~~~~G 47 (76)
.+.++++|.+.- .+.|.+ +|..++..+.
T Consensus 14 g~~v~l~C~v~g-----~P~p~i-~W~k~g~~l~ 41 (95)
T cd05722 14 GGPVVLNCSAEG-----EPPPKI-EWKKDGVLLN 41 (95)
T ss_pred CCCEEEeeeccc-----CCCCEE-EEEECCeECc
Confidence 446899999663 246666 8988876543
No 50
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=21.07 E-value=1.6e+02 Score=16.00 Aligned_cols=18 Identities=11% Similarity=0.294 Sum_probs=12.6
Q ss_pred ecCCHHHHHHHHHHHHHH
Q psy11599 49 TFQAAADARAFDQGVRNA 66 (76)
Q Consensus 49 nF~s~~eA~~F~~~v~~a 66 (76)
.|.++++|+.+...+...
T Consensus 11 s~~~~~~A~~~~~~l~~~ 28 (76)
T PF05036_consen 11 SFSSEENAERLLAKLKKK 28 (76)
T ss_dssp EES-HHHHHHHHHHHHHH
T ss_pred EcCCHHHHHHHHHHHHhc
Confidence 578888888887776655
No 51
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=20.44 E-value=50 Score=24.87 Aligned_cols=30 Identities=23% Similarity=0.327 Sum_probs=23.1
Q ss_pred ceeeEeeCCeEEEeecCCHHHHHHHHHHHHHHhhhhhcc
Q psy11599 35 TFHHWQTGNKKFGLTFQAAADARAFDQGVRNALQEYLHD 73 (76)
Q Consensus 35 ~FHqWr~~~~~~GLnF~s~~eA~~F~~~v~~al~~l~~g 73 (76)
+||.|++.+. ...+.|...+..||++|...
T Consensus 236 tl~~lcGS~~---------~~l~~FR~~Lk~AL~eL~~~ 265 (282)
T PF07042_consen 236 TLRELCGSES---------SRLRKFRQQLKKALDELVAV 265 (282)
T ss_pred HHHHHcCCCc---------cCHHHHHHHHHHHHHHHHhc
Confidence 6777766543 26889999999999999753
No 52
>PF08553 VID27: VID27 cytoplasmic protein; InterPro: IPR013863 This entry represents fungal and plant proteins and contains many hypothetical proteins. Vid27p is a cytoplasmic protein of unknown function, possibly regulates import of fructose-1,6-bisphosphatase into Vacuolar Import and Degradation (Vid) vesicles and is not essential for proteasome-dependent degradation of fructose-1,6-bisphosphatase (FBPase) [, ].
Probab=20.25 E-value=3e+02 Score=23.77 Aligned_cols=53 Identities=15% Similarity=0.261 Sum_probs=36.6
Q ss_pred EEeEeeecCeEE----eecCCceeeEeeC--CeEEEeecCCHHHHHHHHHHHHHHh-hhh
Q psy11599 18 VLSCTITRDFTY----NKVMPTFHHWQTG--NKKFGLTFQAAADARAFDQGVRNAL-QEY 70 (76)
Q Consensus 18 vlnc~l~~~l~Y----n~atp~FHqWr~~--~~~~GLnF~s~~eA~~F~~~v~~al-~~l 70 (76)
+|...|...+.+ ..-+=+|-+...+ ...|-|-|.+.++-..|...+..+| |.+
T Consensus 297 ~l~~~v~s~mNp~F~~e~lSFiFN~~~~~~~~~sw~lkF~~~~~~~~F~~~~~~~l~E~~ 356 (794)
T PF08553_consen 297 WLGQPVSSDMNPVFNFEHLSFIFNYYTEDGSAYSWLLKFKDQEDYERFQEKFMKCLWENL 356 (794)
T ss_pred EEeeeccCCcCeEEEcceeEEEEEeEcCCCceEEEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence 466666555532 2223356565554 3459999999999999999999998 444
Done!