Query 024799
Match_columns 262
No_of_seqs 132 out of 174
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:29:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024799.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024799hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2500 Uncharacterized conser 100.0 9.4E-88 2E-92 601.8 19.8 231 4-258 1-232 (253)
2 PF07933 DUF1681: Protein of u 100.0 2.8E-79 6E-84 524.1 6.3 158 8-173 1-160 (160)
3 cd00835 RanBD Ran-binding doma 92.7 2.9 6.2E-05 33.9 11.4 107 10-130 10-121 (122)
4 cd00837 EVH1 EVH1 (Enabled, Va 91.3 2.6 5.5E-05 33.6 9.4 94 17-128 7-102 (104)
5 PF00638 Ran_BP1: RanBP1 domai 88.9 7.9 0.00017 30.9 10.5 108 9-130 8-120 (122)
6 PF00568 WH1: WH1 domain; Int 88.6 4.6 0.0001 32.3 8.9 94 17-128 14-109 (111)
7 smart00160 RanBD Ran-binding d 69.3 64 0.0014 26.7 10.8 106 9-128 18-129 (130)
8 PF06058 DCP1: Dcp1-like decap 66.3 49 0.0011 27.5 8.3 100 6-126 16-118 (122)
9 smart00461 WH1 WASP homology r 60.8 41 0.00088 26.9 6.7 93 14-128 8-104 (106)
10 cd01205 WASP WASP-type EVH1 do 56.2 72 0.0016 26.2 7.5 79 36-128 22-103 (105)
11 TIGR00105 L31 ribosomal protei 50.5 15 0.00033 27.8 2.5 48 8-57 8-57 (68)
12 PF09157 TruB-C_2: Pseudouridi 49.9 15 0.00033 25.8 2.4 18 96-115 30-47 (58)
13 COG5216 Uncharacterized conser 45.4 12 0.00025 28.6 1.1 22 54-75 27-48 (67)
14 PRK00019 rpmE 50S ribosomal pr 45.2 19 0.0004 27.8 2.3 51 8-58 8-58 (72)
15 smart00835 Cupin_1 Cupin. This 34.4 2.3E+02 0.0049 23.2 7.3 86 18-110 31-121 (146)
16 PF09214 Prd1-P2: Bacteriophag 34.0 37 0.00081 33.9 3.0 65 45-113 295-373 (560)
17 PF00970 FAD_binding_6: Oxidor 33.8 1.6E+02 0.0035 21.9 5.9 12 160-171 81-92 (99)
18 COG0254 RpmE Ribosomal protein 32.7 35 0.00076 26.7 2.1 50 9-58 10-60 (75)
19 PRK13918 CRP/FNR family transc 32.6 1.1E+02 0.0024 25.4 5.3 53 44-99 32-87 (202)
20 COG5489 Uncharacterized conser 31.5 1.9E+02 0.0041 24.2 6.2 70 42-114 14-90 (107)
21 COG5443 FlbT Flagellar biosynt 29.2 27 0.00058 30.5 1.0 16 157-172 5-20 (148)
22 KOG3671 Actin regulatory prote 27.7 95 0.0021 32.3 4.7 86 36-133 55-142 (569)
23 PF04926 PAP_RNA-bind: Poly(A) 26.7 59 0.0013 27.1 2.7 31 105-135 84-119 (157)
24 PF00388 PI-PLC-X: Phosphatidy 26.6 25 0.00055 28.8 0.4 59 68-134 21-81 (146)
25 PF11732 Thoc2: Transcription- 24.3 11 0.00024 29.5 -2.0 16 81-96 23-38 (77)
26 PF13296 T6SS_Vgr: Putative ty 23.2 25 0.00055 29.0 -0.2 25 95-120 38-62 (109)
27 PHA02757 hypothetical protein; 22.9 81 0.0017 24.6 2.5 19 56-74 45-63 (75)
28 CHL00136 rpl31 ribosomal prote 21.9 99 0.0021 23.6 2.8 43 14-58 16-58 (68)
29 PF09671 Spore_GerQ: Spore coa 20.3 1E+02 0.0023 24.6 2.7 32 36-72 32-63 (81)
No 1
>KOG2500 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=9.4e-88 Score=601.82 Aligned_cols=231 Identities=50% Similarity=0.813 Sum_probs=190.2
Q ss_pred CcccceeEEEEeeceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeCCeEEEEEecCCCCceeeeeeccCCCCCC
Q 024799 4 DDEESLEHTLLVVREVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCKDRCEIRLEDPNSGELFAACFVQPGQREN 83 (262)
Q Consensus 4 ~~~~~iE~vL~v~~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g~~~~I~LeD~~tGeLFA~cpv~pg~~~~ 83 (262)
+++++||+||||++|||||+||||+|++||||+||++++|+||||||||++|+.|+|+|||++||+|||+|||++|.. +
T Consensus 1 ~e~~~yE~vL~v~pev~VY~IPPr~t~~gyra~eW~l~~~~WtGrlrvvakg~~~~ikLeD~tsg~LfA~c~id~~~~-~ 79 (253)
T KOG2500|consen 1 EEEEAYESVLFVKPEVFVYKIPPRATSRGYRAGEWNLDKPAWTGRLRVVAKGERCEIKLEDKTSGELFAQCPIDEGPG-N 79 (253)
T ss_pred CccccceeEEEecccEEEEECCCcccCCCccccccccCCccccceeEEEEcCcEEEEEeccCCchhhhhhCcccCCCC-c
Confidence 478899999999999999999999999999999999999999999999999999999999999999999999976533 8
Q ss_pred ceeEeccccceEEEEEecCCCCeEEEeeeecccCcccchhhhhhhHHHHHHHhhhhhcCCCCCCCCCCCCCCCcCCCCCC
Q 024799 84 SVETVLDSSRYFVLKIEDGTGKHAFIGLGFNERNEAFDFNVALSDHEKYVRRELEKESGEMSESDGHIDIHPAVNHRLKE 163 (262)
Q Consensus 84 aVE~V~DSSRYFVLRV~D~~Gr~AfIGiGF~eRsdAFDFnvaLqD~~K~l~r~~e~~~~~~~~~~~~~~~~P~~D~sLKe 163 (262)
+||+|+||||||||||+|++||||||||||.||+||||||||||||+||+++++++|+++ ++.+++|++||+|||
T Consensus 80 avEav~DSSRYFViRv~dgngr~AFiGlGF~eR~dafDfnvaLqDHfkyv~~~~e~ek~e-----q~~d~~pslDlgFKE 154 (253)
T KOG2500|consen 80 AVEAVSDSSRYFVIRVEDGNGRHAFIGLGFGERGDAFDFNVALQDHFKYVKRQKEAEKQE-----QHYDAGPSLDLGFKE 154 (253)
T ss_pred cceeecccceEEEEEEeCCCccEEEEeecccccccccchhhhHHHHHHHHHHHHHHHhhh-----cccCCCccccccccC
Confidence 999999999999999999999999999999999999999999999999999999988753 478899999999999
Q ss_pred CceEEEecCCCCCCCCCCccccCCCCCcccccccccccCCCCCCCCCCCCCCCCCC-CCChhhhhhcccccCCCccCCcc
Q 024799 164 GETIRINVKPKPTSGTGMLSAAGLSGAVSVSAKAKTVGLAPPPSGMGKIRAPLPPP-PNDPAAARINSASHNNGVRAPKE 242 (262)
Q Consensus 164 GeTI~Ini~~k~~~g~~~~s~~~~~g~~~~~~~~~~~~L~PPP~~~~~~~~plppP-P~~~~~a~~~~~~~~~~~~~~~~ 242 (262)
||||+|||+|.+. +.++.+. .+++.++...-+|||||++. +..|||| |.++.+-++.+.+ . ...
T Consensus 155 GeTIkinikn~tk-k~g~~s~-----pr~~~gk~gl~llPPPpggt---~~ilPPP~p~a~v~t~~~Spg----~--sp~ 219 (253)
T KOG2500|consen 155 GETIKINIKNITK-KKGAASW-----PRTGPGKGGLGLLPPPPGGT---SIILPPPPPLAPVTTAQSSPG----S--SPA 219 (253)
T ss_pred CcEEEEEeecccc-ccccccc-----cccCCCCCcccccCCCCCCc---ccccCCCCCCCccceeccCCC----C--CCC
Confidence 9999999997322 2223322 23334442222355555553 3458888 8888877777764 2 122
Q ss_pred ccCCCCCCCCCCcchh
Q 024799 243 TTRHSTTDPSSDLSQI 258 (262)
Q Consensus 243 ~~~~~~~~~~~~~~~~ 258 (262)
+.+.-+++||.+.
T Consensus 220 ---~~p~s~~sDlw~d 232 (253)
T KOG2500|consen 220 ---PQPSSALSDLWTD 232 (253)
T ss_pred ---CCCCccccccccc
Confidence 2224567777654
No 2
>PF07933 DUF1681: Protein of unknown function (DUF1681); InterPro: IPR012466 NECAP 1 localises to clathrin-coated pits and direct binding to the globular ear domain of the alpha-adaptin subunit (alpha-ear) of the adaptor protein 2 (AP-2) complex. This interaction is mediated by a specific motif, WVQF, that uses a distinct alpha-ear interface relative to known alpha-ear-binding partners. Disruption of this interaction blocks clathrin-mediated endocytosis [].; GO: 0006897 endocytosis, 0016020 membrane; PDB: 1TQZ_A.
Probab=100.00 E-value=2.8e-79 Score=524.07 Aligned_cols=158 Identities=55% Similarity=0.982 Sum_probs=90.5
Q ss_pred ceeEEEEeeceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeCCeE--EEEEecCCCCceeeeeeccCCCCCCce
Q 024799 8 SLEHTLLVVREVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCKDRC--EIRLEDPNSGELFAACFVQPGQRENSV 85 (262)
Q Consensus 8 ~iE~vL~v~~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g~~~--~I~LeD~~tGeLFA~cpv~pg~~~~aV 85 (262)
+||+|||++++||||+|||++|++||||+||++++|||||||||+++|++| .|+|||++||+|||+|||..+ .+|
T Consensus 1 ~ie~vL~~~~ev~VY~IPP~~s~~GyrAadW~~~~~iwtGrlrV~~~g~~~~v~i~leD~~tgeLFA~~P~~~~---~~V 77 (160)
T PF07933_consen 1 AIERVLFVIPEVHVYKIPPRTSNKGYRAADWTLDKPIWTGRLRVVEKGDKCKVDIRLEDPSTGELFAQCPYDDY---AAV 77 (160)
T ss_dssp --S---B--SSEEEEE--S--SSSS--HHHH--SSS-EEEEEEEE--SSSE--EEEEE-SS--SS-EEEEE-SS-----E
T ss_pred CeeEEEEEcCcEEEEECCCCCCCCCeecccCCCCCceeeeEEEEEEcCCeeEEEEEecCCCCcceEEECcccCC---Cce
Confidence 599999999999999999999999999999999999999999999999999 999999999999999999654 799
Q ss_pred eEeccccceEEEEEecCCCCeEEEeeeecccCcccchhhhhhhHHHHHHHhhhhhcCCCCCCCCCCCCCCCcCCCCCCCc
Q 024799 86 ETVLDSSRYFVLKIEDGTGKHAFIGLGFNERNEAFDFNVALSDHEKYVRRELEKESGEMSESDGHIDIHPAVNHRLKEGE 165 (262)
Q Consensus 86 E~V~DSSRYFVLRV~D~~Gr~AfIGiGF~eRsdAFDFnvaLqD~~K~l~r~~e~~~~~~~~~~~~~~~~P~~D~sLKeGe 165 (262)
|+|+||||||||||+|++||||||||||+||+||||||||||||+||++++.+.+... .+.+.+|++||||||||
T Consensus 78 E~v~DSSRYFvlRv~d~~Gr~AfiGiGF~eRsdAFDF~vaLqd~~k~~~~~~~~~~~~-----~~~~~~p~~D~sLKeGe 152 (160)
T PF07933_consen 78 EPVIDSSRYFVLRVQDPSGRHAFIGIGFRERSDAFDFNVALQDHRKYLKREKEAEEQS-----QAAESQPKKDYSLKEGE 152 (160)
T ss_dssp EE-TT--S-EEEEEEETTTEEEEEEEE-S-HHHHHHHHHHHHHHHS-SS-------------------------------
T ss_pred EEeecccceEEEEEEcCCCcEEEEEEeeccccccccHHHHHHHHHHHhhchhhhhhhh-----cccCCCCccCCcCCCCC
Confidence 9999999999999999999999999999999999999999999999999887765432 23456899999999999
Q ss_pred eEEEecCC
Q 024799 166 TIRINVKP 173 (262)
Q Consensus 166 TI~Ini~~ 173 (262)
||+|||++
T Consensus 153 tI~ini~g 160 (160)
T PF07933_consen 153 TIKINIGG 160 (160)
T ss_dssp --------
T ss_pred EEEEecCC
Confidence 99999974
No 3
>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=92.71 E-value=2.9 Score=33.93 Aligned_cols=107 Identities=19% Similarity=0.304 Sum_probs=76.9
Q ss_pred eEEEEeeceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeC--CeEEEEEecCCCCceeeeeeccCCCCCCceeE
Q 024799 10 EHTLLVVREVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCK--DRCEIRLEDPNSGELFAACFVQPGQRENSVET 87 (262)
Q Consensus 10 E~vL~v~~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g--~~~~I~LeD~~tGeLFA~cpv~pg~~~~aVE~ 87 (262)
|.+||.++ |-+|+.=.- ..+|. .-=.|-|+|.... .++-|.+....+|.|...+++.|+- .+..
T Consensus 10 E~~if~~r-~KLy~~~~~-------~~~Wk---erG~G~lki~~~k~~~~~RivmR~d~~~kv~lN~~i~~~~---~~~~ 75 (122)
T cd00835 10 EEVIFSVR-AKLYRFDDE-------TKEWK---ERGVGELKILKHKDTGKYRLLMRRDQVLKLCLNHKLVPGM---KLQP 75 (122)
T ss_pred cEEEEEEE-eEEEEEcCC-------CCCCe---eceEEEEEEEEcCCCCcEEEEEEeCCccEEEEeeEecCCc---EEee
Confidence 55667654 667765221 34684 3336889998775 5777777776799999999998873 5666
Q ss_pred eccccceEEEEEecC---CCCeEEEeeeecccCcccchhhhhhhHH
Q 024799 88 VLDSSRYFVLKIEDG---TGKHAFIGLGFNERNEAFDFNVALSDHE 130 (262)
Q Consensus 88 V~DSSRYFVLRV~D~---~Gr~AfIGiGF~eRsdAFDFnvaLqD~~ 130 (262)
.--|.+++++-..|. .+......|-|..=.+|=.|.-+++++.
T Consensus 76 ~~~~~k~~~~~~~d~~~~~~~~~~~~lrfk~~~~a~~f~~~~~~~~ 121 (122)
T cd00835 76 MGNSDKSIVWAAMDFSDDEPKPETFAIRFKTEEIADEFKEAIEEAK 121 (122)
T ss_pred cCCCCcEEEEEeeecCCCCCcEEEEEEEECCHHHHHHHHHHHHHhh
Confidence 665577777766663 3688899999988888888888888764
No 4
>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=91.30 E-value=2.6 Score=33.62 Aligned_cols=94 Identities=19% Similarity=0.309 Sum_probs=69.6
Q ss_pred ceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEe--CCeEEEEEecCCCCceeeeeeccCCCCCCceeEeccccce
Q 024799 17 REVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSC--KDRCEIRLEDPNSGELFAACFVQPGQRENSVETVLDSSRY 94 (262)
Q Consensus 17 ~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~--g~~~~I~LeD~~tGeLFA~cpv~pg~~~~aVE~V~DSSRY 94 (262)
--+.||..-|. .+ .|.... --.|.|.++.- .....|++.|..++.+==.|.++++ .+---++.-|
T Consensus 7 ~~a~v~~~~~~--~~-----~W~~~~-~~~g~v~~~~d~~~~~y~i~~~~~~~~~vv~~~~l~~~-----~~y~~~~~~F 73 (104)
T cd00837 7 AVAQVYTADPS--TG-----KWVPAS-GGTGAVSLVKDSTRNTYRIRGVDIQDQKVIWNQEIYKG-----LKYTQATPFF 73 (104)
T ss_pred EEEEEEEECCC--CC-----ceEECC-CCeEEEEEEEECCCCEEEEEEEecCCCeEEEEEEecCC-----cEEeecCCeE
Confidence 45778887665 22 375432 46799999864 4568999999998887778888775 5666677777
Q ss_pred EEEEEecCCCCeEEEeeeecccCcccchhhhhhh
Q 024799 95 FVLKIEDGTGKHAFIGLGFNERNEAFDFNVALSD 128 (262)
Q Consensus 95 FVLRV~D~~Gr~AfIGiGF~eRsdAFDFnvaLqD 128 (262)
+.-+.. ...+|+.|.+-.||-.|.-++++
T Consensus 74 h~w~~~-----~~~~GL~F~se~eA~~F~~~v~~ 102 (104)
T cd00837 74 HQWEDD-----NCVYGLNFASEEEAAQFRKKVLE 102 (104)
T ss_pred EEEEcC-----CcEEEEeeCCHHHHHHHHHHHHh
Confidence 777754 33899999999999998877664
No 5
>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=88.87 E-value=7.9 Score=30.93 Aligned_cols=108 Identities=19% Similarity=0.345 Sum_probs=75.2
Q ss_pred eeEEEEeeceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeC--CeEEEEEecCCCCceeeeeeccCCCCCCcee
Q 024799 9 LEHTLLVVREVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCK--DRCEIRLEDPNSGELFAACFVQPGQRENSVE 86 (262)
Q Consensus 9 iE~vL~v~~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g--~~~~I~LeD~~tGeLFA~cpv~pg~~~~aVE 86 (262)
=|.+||-.+ |-+|+.=.- + ..| ...=+|.|||.... .++-|.+-...+|.|-..+++.++ -.+.
T Consensus 8 ~E~~l~~~r-~Kl~~~~~~--~-----~~W---~erG~G~l~i~~~k~~~~~RlvmR~d~~~kv~lN~~i~~~---m~~~ 73 (122)
T PF00638_consen 8 DEEILFEVR-AKLYRFDKE--D-----KEW---KERGVGTLKILKHKETGKYRLVMRRDGTGKVLLNHPIFKG---MKLK 73 (122)
T ss_dssp SEEEEEEEE-EEEEEEETT--T-----TEE---EEEEEEEEEEEEETTSCEEEEEEEETTTTEEEEEEE--TT---C-EE
T ss_pred CcEEEEEEE-EEEEEEeCC--C-----CCc---cccceeEEEEEEccCCcceEEEEEEcccCceeEEEEecCC---ceec
Confidence 466888877 888887331 2 346 23447999999875 577788887779999999999876 3567
Q ss_pred EeccccceEEEE---EecCCCCeEEEeeeecccCcccchhhhhhhHH
Q 024799 87 TVLDSSRYFVLK---IEDGTGKHAFIGLGFNERNEAFDFNVALSDHE 130 (262)
Q Consensus 87 ~V~DSSRYFVLR---V~D~~Gr~AfIGiGF~eRsdAFDFnvaLqD~~ 130 (262)
+.-.|.+.++.- ..|+.|....+=|=|.+=.+|=.|.-+++++.
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~irf~~~e~a~~f~~~i~e~~ 120 (122)
T PF00638_consen 74 PMKGSEKSLVWTAIDYADEEGKPETYLIRFKSAEDADEFKKKIEEAK 120 (122)
T ss_dssp ESTTTTTEEEEEEEECTTSSSEEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccccCCcEEEEEeccccCCCCceEEEEEEECCHHHHHHHHHHHHHHh
Confidence 777666655543 23456788888899988788888888887764
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=88.64 E-value=4.6 Score=32.33 Aligned_cols=94 Identities=23% Similarity=0.301 Sum_probs=65.6
Q ss_pred ceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeC--CeEEEEEecCCCCceeeeeeccCCCCCCceeEeccccce
Q 024799 17 REVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCK--DRCEIRLEDPNSGELFAACFVQPGQRENSVETVLDSSRY 94 (262)
Q Consensus 17 ~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g--~~~~I~LeD~~tGeLFA~cpv~pg~~~~aVE~V~DSSRY 94 (262)
-.++||.+=|.+ .+ .|... .-+|.|.++.-- ....|++.|-.++.+--.|-++++ .+-.-++.-|
T Consensus 14 ~vA~v~~~~p~~-~~-----~W~~~--~~~g~v~~v~d~~~~~y~I~~~~~~~~~~v~e~~l~~~-----~~Y~~~~~~F 80 (111)
T PF00568_consen 14 AVAQVYQADPDT-KR-----QWSPV--KGTGVVCFVKDNSRRSYFIRLYDLQDGKVVWEQELYPG-----FVYTKARPFF 80 (111)
T ss_dssp EEEEEEEEETTT-SE-----SEEES--SSEEEEEEEEETTTTEEEEEEEETTTTEEEEEEEESTT------EEEEESSSE
T ss_pred EEEEEEEEEcCC-CC-----cEeeC--CeEEEEEEEEECCCCEEEEEEEEccccEEEEEeEecCC-----CEEEeCCCcE
Confidence 456777774432 22 27422 668899988653 678899999889998889988876 3333345555
Q ss_pred EEEEEecCCCCeEEEeeeecccCcccchhhhhhh
Q 024799 95 FVLKIEDGTGKHAFIGLGFNERNEAFDFNVALSD 128 (262)
Q Consensus 95 FVLRV~D~~Gr~AfIGiGF~eRsdAFDFnvaLqD 128 (262)
..-+ +++ ..+||+|.+-.||-.|.-.+++
T Consensus 81 h~f~--~~~---~~~GLnF~se~eA~~F~~~v~~ 109 (111)
T PF00568_consen 81 HQFE--DDD---CVYGLNFASEEEADQFYKKVQE 109 (111)
T ss_dssp EEEE--ETT---CEEEEEESSHHHHHHHHHHHHH
T ss_pred EEEE--eCC---eEEEEecCCHHHHHHHHHHHhc
Confidence 5555 332 2999999999999999877765
No 7
>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=69.33 E-value=64 Score=26.71 Aligned_cols=106 Identities=17% Similarity=0.268 Sum_probs=70.6
Q ss_pred eeEEEEeeceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeC---CeEEEEEecCCCCceeeeeeccCCCCCCce
Q 024799 9 LEHTLLVVREVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCK---DRCEIRLEDPNSGELFAACFVQPGQRENSV 85 (262)
Q Consensus 9 iE~vL~v~~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g---~~~~I~LeD~~tGeLFA~cpv~pg~~~~aV 85 (262)
=|.+||. ..|-+|+.-. ....|.. -=.|-|||.... .+.-|.+....+|.+.+.+++.++- .+
T Consensus 18 ~E~~lf~-~r~KL~~~~~-------~~~~Wke---rG~G~lki~~~~~~~~~~RivmR~~~~~kv~lN~~i~~~~---~~ 83 (130)
T smart00160 18 DEEVIFS-ARAKLYRFAN-------DKKEWKE---RGVGDLKILKSKDNGGKVRIVMRRDGVLKVCANHPIFKSM---TL 83 (130)
T ss_pred CeEEEEE-EEeEEEEEcC-------CCCCCee---ccEEEEEEEEcCCCCCeEEEEEEECCCceEEeccEecCCc---EE
Confidence 3556666 3456666632 1236852 235999997654 5688888887899999999998873 46
Q ss_pred eEeccccceEEEEEec---CCCCeEEEeeeecccCcccchhhhhhh
Q 024799 86 ETVLDSSRYFVLKIED---GTGKHAFIGLGFNERNEAFDFNVALSD 128 (262)
Q Consensus 86 E~V~DSSRYFVLRV~D---~~Gr~AfIGiGF~eRsdAFDFnvaLqD 128 (262)
+++--|-+.++.-..| +.++-....|-|..=.+|=-|.-++++
T Consensus 84 ~~~~~~~~~~~~~~~d~~d~~~~~~~~~irfk~~e~a~~f~~~~~e 129 (130)
T smart00160 84 KPLAGSNRALKWTPEDFADDIPKLVLYAVRFKTKEEADSFKNIFEE 129 (130)
T ss_pred eecCCCcceEEEeeeecCCCCCceEEEEEEeCCHHHHHHHHHHHHh
Confidence 6665554555443333 446777888888887777777777665
No 8
>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=66.27 E-value=49 Score=27.47 Aligned_cols=100 Identities=21% Similarity=0.307 Sum_probs=62.5
Q ss_pred ccceeEEEEeeceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeC---CeEEEEEecCCCCceeeeeeccCCCCC
Q 024799 6 EESLEHTLLVVREVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCK---DRCEIRLEDPNSGELFAACFVQPGQRE 82 (262)
Q Consensus 6 ~~~iE~vL~v~~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g---~~~~I~LeD~~tGeLFA~cpv~pg~~~ 82 (262)
|..|++||.++.-|.||+.=+.+ .+|. +.--.|.|=|+++. .-+.|.|--.++..+ -. ++.++
T Consensus 16 Dp~I~~Il~~a~~v~vY~f~~~~-------~~W~--K~~iEG~LFv~~r~~~p~~~~~vlNR~~~~n~-~~-~i~~~--- 81 (122)
T PF06058_consen 16 DPSIESILDTASHVVVYKFDHET-------NEWE--KTDIEGTLFVYKRSSSPRYGLIVLNRRSTENF-VE-PITPD--- 81 (122)
T ss_dssp -TTEEEEEEEEEEEEEEEEETTT-------TEEE--EEEEEEEEEEEEEETTS-ECEEEEESSSS--E-EE-EE-SG---
T ss_pred CchHHHHHhhCCeEEEEeecCCC-------CcEe--ecCcEeeEEEEEeecccceEEEEecCCCCCce-ee-ecCCC---
Confidence 34799999999999999986653 3595 56669999999874 344455555444333 22 23332
Q ss_pred CceeEeccccceEEEEEecCCCCeEEEeeeecccCcccchhhhh
Q 024799 83 NSVETVLDSSRYFVLKIEDGTGKHAFIGLGFNERNEAFDFNVAL 126 (262)
Q Consensus 83 ~aVE~V~DSSRYFVLRV~D~~Gr~AfIGiGF~eRsdAFDFnvaL 126 (262)
.-+| +. -.|..+| ++++-..||.|-+-.|.=+..-.|
T Consensus 82 ~~~e-~~--~~~l~~r----~~~~~I~GiWf~~~~d~~ri~~~l 118 (122)
T PF06058_consen 82 LDFE-LQ--DPYLIYR----NDNQEIYGIWFYDDEDRQRIYNLL 118 (122)
T ss_dssp GGEE-EE--TTEEEEE----ETTTEEEEEEESSHHHHHHHHHHH
T ss_pred cEEE-Ee--CCEEEEE----cCCceEEEEEEEeHHHHHHHHHHH
Confidence 2344 22 2477777 335588999998877655444433
No 9
>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=60.77 E-value=41 Score=26.94 Aligned_cols=93 Identities=15% Similarity=0.210 Sum_probs=58.2
Q ss_pred EeeceeEEEEcCCCCCCCCeecCCCCCCCceeeE-EEEEEE--eCCeEEEEEecCCCC-ceeeeeeccCCCCCCceeEec
Q 024799 14 LVVREVCVYKIPPRTTSGGYKCGEWLQSDKIWTG-RLRVVS--CKDRCEIRLEDPNSG-ELFAACFVQPGQRENSVETVL 89 (262)
Q Consensus 14 ~v~~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtG-RLrVv~--~g~~~~I~LeD~~tG-eLFA~cpv~pg~~~~aVE~V~ 89 (262)
...--|.+|.=-|. .|. +...| -+.|+- ......+++.|-..+ .+-=.|.++++ .+---
T Consensus 8 ~~~avV~~y~~~~~---------~W~---~~~~gg~~~~~~~~~~~~~~~ri~~~~~~~~vv~e~ely~~-----~~y~~ 70 (106)
T smart00461 8 LARAVVQLYDADTK---------KWV---PTGEGGAANLVIDKNQRSYFFRIVGIKGQDKVIWNQELYKN-----FKYNQ 70 (106)
T ss_pred EEEEEEEEEeCCCC---------CeE---ECCCCCEEEEEEEecCCeEEEEEEEecCCCeEEEEEeccCC-----CEEee
Confidence 34455667753222 284 33445 344443 357889999998776 66667888776 33223
Q ss_pred cccceEEEEEecCCCCeEEEeeeecccCcccchhhhhhh
Q 024799 90 DSSRYFVLKIEDGTGKHAFIGLGFNERNEAFDFNVALSD 128 (262)
Q Consensus 90 DSSRYFVLRV~D~~Gr~AfIGiGF~eRsdAFDFnvaLqD 128 (262)
++.=|..-+ + ...++|+.|.+-.||-.|.-++++
T Consensus 71 ~~~~Fh~f~--~---~~~~~GLnF~se~EA~~F~~~v~~ 104 (106)
T smart00461 71 ATPTFHQWA--D---DKCVYGLNFASEEEAKKFRKKVLK 104 (106)
T ss_pred cCCceEEEE--e---CCeEEEeecCCHHHHHHHHHHHHh
Confidence 444344444 2 345899999999999999877664
No 10
>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=56.19 E-value=72 Score=26.25 Aligned_cols=79 Identities=27% Similarity=0.431 Sum_probs=53.1
Q ss_pred CCCCCCCceeeEEEEEEEe--CCeEEEEEecCCCCc-eeeeeeccCCCCCCceeEeccccceEEEEEecCCCCeEEEeee
Q 024799 36 GEWLQSDKIWTGRLRVVSC--KDRCEIRLEDPNSGE-LFAACFVQPGQRENSVETVLDSSRYFVLKIEDGTGKHAFIGLG 112 (262)
Q Consensus 36 ~dW~~~~~iwtGRLrVv~~--g~~~~I~LeD~~tGe-LFA~cpv~pg~~~~aVE~V~DSSRYFVLRV~D~~Gr~AfIGiG 112 (262)
+.|. .. ++|-|-++.- +....|+|.|..++. ||-|= ++.+ .+---| |=|=+..+ |...++|+-
T Consensus 22 ~~W~--~~-~~Gvl~~vkD~~~~sy~lrl~D~~~~~v~weqE-lY~~-----f~y~~~--r~fFhtFe---~d~c~~GL~ 87 (105)
T cd01205 22 GRWT--KT-LTGAVCLVKDNVQKSYFIRLFDIKANRIIWEQE-LYDN-----FEYQQP--RPFFHTFE---GDDCVVGLN 87 (105)
T ss_pred CeeE--EE-eEEEEEEEEECCCCEEEEEEEEccCCcEEEEEE-cccC-----cEEccC--CCcEEEEe---ccCcEEEEE
Confidence 3585 23 7899888866 678999999988754 55543 2222 222222 33334444 567899999
Q ss_pred ecccCcccchhhhhhh
Q 024799 113 FNERNEAFDFNVALSD 128 (262)
Q Consensus 113 F~eRsdAFDFnvaLqD 128 (262)
|.|.+||-.|.-.+++
T Consensus 88 Fade~EA~~F~k~v~~ 103 (105)
T cd01205 88 FADETEAAEFRKKVLD 103 (105)
T ss_pred ECCHHHHHHHHHHHHh
Confidence 9999999999876654
No 11
>TIGR00105 L31 ribosomal protein L31. This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc.
Probab=50.45 E-value=15 Score=27.76 Aligned_cols=48 Identities=17% Similarity=0.245 Sum_probs=34.2
Q ss_pred ceeEEEEeeceeEEEEcCCCCCCCC--eecCCCCCCCceeeEEEEEEEeCCe
Q 024799 8 SLEHTLLVVREVCVYKIPPRTTSGG--YKCGEWLQSDKIWTGRLRVVSCKDR 57 (262)
Q Consensus 8 ~iE~vL~v~~eV~VY~IPP~~s~~G--yrA~dW~~~~~iwtGRLrVv~~g~~ 57 (262)
.|..|++++.-=.+|.+ +++... ++-+=|....|.|||.-+++.++.+
T Consensus 8 ~y~~v~~~~s~g~~f~~--~ST~~~~~i~vdi~s~~HPfyTG~~~~~~~~GR 57 (68)
T TIGR00105 8 DYHEITVTCTCGNVFTT--RSTWGKETLNLDICSKCHPFYTGKQKIVDTGGR 57 (68)
T ss_pred CCEEEEEEECCCCEEEE--eeecCCceEEEEECCCCcccCCCceEEeccCCc
Confidence 37778877755566666 333333 8888888789999999888876544
No 12
>PF09157 TruB-C_2: Pseudouridine synthase II TruB, C-terminal; InterPro: IPR015240 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1ZL3_A 1K8W_A 1R3F_A.
Probab=49.91 E-value=15 Score=25.83 Aligned_cols=18 Identities=28% Similarity=0.772 Sum_probs=13.3
Q ss_pred EEEEecCCCCeEEEeeeecc
Q 024799 96 VLKIEDGTGKHAFIGLGFNE 115 (262)
Q Consensus 96 VLRV~D~~Gr~AfIGiGF~e 115 (262)
.+||-|++|+ |||||--+
T Consensus 30 ~vrvy~~~~~--FlGig~~~ 47 (58)
T PF09157_consen 30 LVRVYDEDGR--FLGIGEID 47 (58)
T ss_dssp EEEEETTTTE--EEEEEEE-
T ss_pred eEEEECCCCE--EEEEEEEc
Confidence 7888876554 99999755
No 13
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=45.38 E-value=12 Score=28.65 Aligned_cols=22 Identities=55% Similarity=0.896 Sum_probs=20.7
Q ss_pred eCCeEEEEEecCCCCceeeeee
Q 024799 54 CKDRCEIRLEDPNSGELFAACF 75 (262)
Q Consensus 54 ~g~~~~I~LeD~~tGeLFA~cp 75 (262)
.|++..|.|||-..||.-|.||
T Consensus 27 CGDRFeIsLeDl~~GE~VArCP 48 (67)
T COG5216 27 CGDRFEISLEDLRNGEVVARCP 48 (67)
T ss_pred CCCEeEEEHHHhhCCceEEEcC
Confidence 5899999999999999999997
No 14
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=45.16 E-value=19 Score=27.81 Aligned_cols=51 Identities=12% Similarity=0.175 Sum_probs=36.8
Q ss_pred ceeEEEEeeceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeCCeE
Q 024799 8 SLEHTLLVVREVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCKDRC 58 (262)
Q Consensus 8 ~iE~vL~v~~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g~~~ 58 (262)
+|..|++++.-=.+|.+-......-++.+=|....|.|||.-|++.++.++
T Consensus 8 ~y~~v~~~c~~g~~f~~~ST~~~~~i~vdi~s~~HPFyTG~q~~~dt~GRv 58 (72)
T PRK00019 8 KYEEVTVTCSCGNVFETRSTLGKDEINVDVCSKCHPFYTGKQKIVDTGGRV 58 (72)
T ss_pred CCEEEEEEECCCCEEEEeecCCCCcEEEEeCCCCCCcCcCCEeEeccCCcH
Confidence 467777777644556654433344488988988899999999999887653
No 15
>smart00835 Cupin_1 Cupin. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.
Probab=34.43 E-value=2.3e+02 Score=23.18 Aligned_cols=86 Identities=13% Similarity=0.126 Sum_probs=43.8
Q ss_pred eeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeCCeE----EEEEecCCCCceeeeeeccCCCCCCceeEe-cccc
Q 024799 18 EVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCKDRC----EIRLEDPNSGELFAACFVQPGQRENSVETV-LDSS 92 (262)
Q Consensus 18 eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g~~~----~I~LeD~~tGeLFA~cpv~pg~~~~aVE~V-~DSS 92 (262)
.+....|+|......|.-.....--.+.+|++++.-.+..+ .+.|. .|++|.-- ++. ...++.. -+..
T Consensus 31 ~~~~~~i~pg~~~~~h~H~~~~e~~~Vl~G~~~~~~~~~~~~~~~~~~l~---~GD~~~ip---~g~-~H~~~n~~~~~~ 103 (146)
T smart00835 31 SAARVNLEPGGMLPPHYHPRATELLYVVRGEGRVGVVDPNGNKVYDARLR---EGDVFVVP---QGH-PHFQVNSGDENL 103 (146)
T ss_pred EEEEEEecCCcCcCCeeCCCCCEEEEEEeCeEEEEEEeCCCCeEEEEEec---CCCEEEEC---CCC-EEEEEcCCCCCE
Confidence 34556678876554443111100025677888886544321 33343 47776553 332 1222222 2456
Q ss_pred ceEEEEEecCCCCeEEEe
Q 024799 93 RYFVLKIEDGTGKHAFIG 110 (262)
Q Consensus 93 RYFVLRV~D~~Gr~AfIG 110 (262)
+|++++..|....-.+.|
T Consensus 104 ~~l~~~~~~~~~~~~~~~ 121 (146)
T smart00835 104 EFVAFNTNDPNRRFFLAG 121 (146)
T ss_pred EEEEEecCCCCceeEeec
Confidence 788888887654444445
No 16
>PF09214 Prd1-P2: Bacteriophage Prd1, adsorption protein P2; InterPro: IPR015297 This entry represents absorption protein P2 (synonym: receptor-binding protein P2) from the bacteriophage PRD1. Absorption protein P2 is a multi-beta-sheet protein whose complicated topology forms an elongated seahorse-shaped molecule with a distinct head, containing a pseudo-beta propeller structure with approximate 6-fold symmetry, and tail (beta-sandwich). They are required for the attachment of the phage to the host conjugative DNA transfer complex. This is a poorly understood large transmembrane complex of unknown architecture, with at least 11 different proteins []. ; PDB: 1N7U_A 1N7V_A.
Probab=33.98 E-value=37 Score=33.85 Aligned_cols=65 Identities=31% Similarity=0.334 Sum_probs=34.3
Q ss_pred eeEEEEEEEeCCeEEEEEecCCCCceeeeeecc-CCC----CCCceeEe--------ccccceEEEEEecCC-CCeEEEe
Q 024799 45 WTGRLRVVSCKDRCEIRLEDPNSGELFAACFVQ-PGQ----RENSVETV--------LDSSRYFVLKIEDGT-GKHAFIG 110 (262)
Q Consensus 45 wtGRLrVv~~g~~~~I~LeD~~tGeLFA~cpv~-pg~----~~~aVE~V--------~DSSRYFVLRV~D~~-Gr~AfIG 110 (262)
-.|||--.--.-.++|-| ||+.|+-||-+ -.+ .+.+-|-. .=||-||.+--.|+- |-++|||
T Consensus 295 vagrlvp~v~di~vdifl----tgkff~l~pp~ritnnyfad~~v~e~tvt~gn~~~~~~~~y~~vy~tdg~g~a~~fi~ 370 (560)
T PF09214_consen 295 VAGRLVPYVEDITVDIFL----TGKFFALCPPYRITNNYFADEEVNEFTVTRGNWRGAMSSVYWQVYQTDGYGMAKCFIG 370 (560)
T ss_dssp EEEEEEEEEEEEEEEEEE----EEEEEEE---EEEEEEEEETTCEE--EEEES---SEEEE-SEEEEEE-SSSEEEEEEE
T ss_pred hhhccccceeeeeEEEEe----ecceeeeCCceEeccccccccccccceEEecceechhhheeeeeEeccCCCceeEEEe
Confidence 346654333334455555 79999999731 000 01222322 237789999888875 5699999
Q ss_pred eee
Q 024799 111 LGF 113 (262)
Q Consensus 111 iGF 113 (262)
.|=
T Consensus 371 ~gg 373 (560)
T PF09214_consen 371 FGG 373 (560)
T ss_dssp SSS
T ss_pred cCC
Confidence 873
No 17
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=33.82 E-value=1.6e+02 Score=21.90 Aligned_cols=12 Identities=33% Similarity=0.609 Sum_probs=9.5
Q ss_pred CCCCCceEEEec
Q 024799 160 RLKEGETIRINV 171 (262)
Q Consensus 160 sLKeGeTI~Ini 171 (262)
.|++|++|.|.-
T Consensus 81 ~l~~Gd~v~i~g 92 (99)
T PF00970_consen 81 QLKPGDEVEIRG 92 (99)
T ss_dssp TSCTTSEEEEEE
T ss_pred hCCCCCEEEEEE
Confidence 488999988864
No 18
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=32.68 E-value=35 Score=26.69 Aligned_cols=50 Identities=10% Similarity=0.216 Sum_probs=32.5
Q ss_pred eeEEEEeecee-EEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeCCeE
Q 024799 9 LEHTLLVVREV-CVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCKDRC 58 (262)
Q Consensus 9 iE~vL~v~~eV-~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g~~~ 58 (262)
++.|++++..| .+|.|=......--+.+=|....|.|||+.|++.++.++
T Consensus 10 ~~~v~~~~~s~g~~f~~~ST~~~~~i~vdV~s~~HPFyTG~qk~~d~~Grv 60 (75)
T COG0254 10 YRPVVFVCSSCGNEFTTRSTKGTDEINLDVCSKCHPFYTGKQKIVDTEGRV 60 (75)
T ss_pred cceEEEEeCCCCCEEEEEeccCCceEEEEeCCCCCCcCcCceeEeeccccH
Confidence 47788887633 444443322222355666766799999999999987543
No 19
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=32.62 E-value=1.1e+02 Score=25.45 Aligned_cols=53 Identities=28% Similarity=0.382 Sum_probs=35.3
Q ss_pred eeeEEEEEEEe---CCeEEEEEecCCCCceeeeeeccCCCCCCceeEeccccceEEEEE
Q 024799 44 IWTGRLRVVSC---KDRCEIRLEDPNSGELFAACFVQPGQRENSVETVLDSSRYFVLKI 99 (262)
Q Consensus 44 iwtGRLrVv~~---g~~~~I~LeD~~tGeLFA~cpv~pg~~~~aVE~V~DSSRYFVLRV 99 (262)
|-+|++|+... |....+.+..+ |++|..+.+....+...++.+.| ++-+.|..
T Consensus 32 I~~G~vr~~~~~~~G~e~~l~~~~~--Gd~~G~~~~~~~~~~~~~~A~~~-~~v~~i~~ 87 (202)
T PRK13918 32 VRSGLVRLHTVDDEGNALTLRYVRP--GEYFGEEALAGAERAYFAEAVTD-SRIDVLNP 87 (202)
T ss_pred EEeeEEEEEEECCCCCEEEEEEecC--CCeechHHhcCCCCCceEEEcCc-eEEEEEEH
Confidence 45899999875 67787887765 89999875532233455776666 55555553
No 20
>COG5489 Uncharacterized conserved protein [Function unknown]
Probab=31.48 E-value=1.9e+02 Score=24.23 Aligned_cols=70 Identities=17% Similarity=0.318 Sum_probs=47.0
Q ss_pred CceeeEEEEEEEeCCeEEEEEecCCCCceeeeeec---cCCCC--CCceeEeccccc-eEEEEEecCC-CCeEEEeeeec
Q 024799 42 DKIWTGRLRVVSCKDRCEIRLEDPNSGELFAACFV---QPGQR--ENSVETVLDSSR-YFVLKIEDGT-GKHAFIGLGFN 114 (262)
Q Consensus 42 ~~iwtGRLrVv~~g~~~~I~LeD~~tGeLFA~cpv---~pg~~--~~aVE~V~DSSR-YFVLRV~D~~-Gr~AfIGiGF~ 114 (262)
+-.|+|.+|-+...-++.|.=.+..+|+ .+|- .-|.. ..+-+.+-++-| |+-|++.|+. |+.-|-++.=.
T Consensus 14 ~~~~~G~irTL~vnakv~lvPn~~~s~~---~aPdfRV~~gg~eiGAaW~k~s~~G~dYlsvkLddP~f~~~i~A~L~~~ 90 (107)
T COG5489 14 NGGFEGTIRTLTVNAKVRLVPNESKSGD---NAPDFRVTAGGVEIGAAWNKTSNSGRDYLSVKLDDPSFGAPIYANLFPA 90 (107)
T ss_pred CCceEEEEEEEEEcceEEEcccCCCCCC---CCCcEEEEecCcchhhhhhhhcccCcceEEEEecCCcCCCeeEeeeeec
Confidence 5678999999999888777666666654 2442 11110 145566677777 9999999987 77666665433
No 21
>COG5443 FlbT Flagellar biosynthesis regulator FlbT [Cell motility and secretion]
Probab=29.17 E-value=27 Score=30.45 Aligned_cols=16 Identities=44% Similarity=0.451 Sum_probs=13.7
Q ss_pred cCCCCCCCceEEEecC
Q 024799 157 VNHRLKEGETIRINVK 172 (262)
Q Consensus 157 ~D~sLKeGeTI~Ini~ 172 (262)
+-.|||.||+|-||-.
T Consensus 5 lriSLk~gEki~iNGA 20 (148)
T COG5443 5 LRISLKPGEKIFINGA 20 (148)
T ss_pred eEEeecCCCEEEEecc
Confidence 4689999999999964
No 22
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=27.70 E-value=95 Score=32.34 Aligned_cols=86 Identities=22% Similarity=0.213 Sum_probs=57.1
Q ss_pred CCCCCCCceeeEEEEEEEe--CCeEEEEEecCCCCceeeeeeccCCCCCCceeEeccccceEEEEEecCCCCeEEEeeee
Q 024799 36 GEWLQSDKIWTGRLRVVSC--KDRCEIRLEDPNSGELFAACFVQPGQRENSVETVLDSSRYFVLKIEDGTGKHAFIGLGF 113 (262)
Q Consensus 36 ~dW~~~~~iwtGRLrVv~~--g~~~~I~LeD~~tGeLFA~cpv~pg~~~~aVE~V~DSSRYFVLRV~D~~Gr~AfIGiGF 113 (262)
+.|+.+ .-.|-|-+|-- +..|.+||.|-+.+.|-=.--+|- ..|-.- .|-|-+..+.+++ ++|+-|
T Consensus 55 ~~W~~~--~~~Gal~lVkD~~~rsyFlrl~di~~~rliWdqELY~-----nf~y~q--~r~ffhtFegddc---~aGLnF 122 (569)
T KOG3671|consen 55 NHWNKT--GLCGALCLVKDNAQRSYFLRLVDIVNNRLIWDQELYQ-----NFEYRQ--PRTFFHTFEGDDC---QAGLNF 122 (569)
T ss_pred hhhccc--cCceeEEEeeccccceeeeEEeeecCceeeehHHhhh-----hceecc--Cccceeeeccccc---eeeecc
Confidence 478631 12254544433 478999999988887643333322 244443 6777788885444 999999
Q ss_pred cccCcccchhhhhhhHHHHH
Q 024799 114 NERNEAFDFNVALSDHEKYV 133 (262)
Q Consensus 114 ~eRsdAFDFnvaLqD~~K~l 133 (262)
.+-.||--|.-.+||-..+-
T Consensus 123 ~~E~EA~~F~k~V~~r~~~~ 142 (569)
T KOG3671|consen 123 ASEEEAQKFRKKVQDRICHR 142 (569)
T ss_pred cCHHHHHHHHHHHHHHhhhh
Confidence 99999999999988854443
No 23
>PF04926 PAP_RNA-bind: Poly(A) polymerase predicted RNA binding domain; InterPro: IPR007010 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analogue at 2.5 A resolution has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The C-terminal domain unexpectedly folds into a compact domain reminiscent of the RNA-recognition motif fold. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase. ; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0043631 RNA polyadenylation, 0005634 nucleus; PDB: 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A 1Q79_A 1Q78_A 1F5A_A.
Probab=26.69 E-value=59 Score=27.15 Aligned_cols=31 Identities=29% Similarity=0.618 Sum_probs=23.2
Q ss_pred CeEEEeeeecccCc-----ccchhhhhhhHHHHHHH
Q 024799 105 KHAFIGLGFNERNE-----AFDFNVALSDHEKYVRR 135 (262)
Q Consensus 105 r~AfIGiGF~eRsd-----AFDFnvaLqD~~K~l~r 135 (262)
..-||||-|..-.. ..|+.-++|+|...++.
T Consensus 84 ~~~fIGL~~~~~~~~~~~~~~dL~~~i~~F~~~v~~ 119 (157)
T PF04926_consen 84 SSFFIGLEFDSKESNEGSKKLDLTYAIQEFKDLVRN 119 (157)
T ss_dssp EEEEEEEEE--SSSS---S-EE-HHHHHHHHHHHHC
T ss_pred EEEEEEEEECCCCccccceEEehHHHHHHHHHHHHh
Confidence 46799999998764 49999999999998875
No 24
>PF00388 PI-PLC-X: Phosphatidylinositol-specific phospholipase C, X domain This entry is for the whole phospholipase C protein; InterPro: IPR000909 Phosphatidylinositol-specific phospholipase C (3.1.4.11 from EC), a eukaryotic intracellular enzyme, plays an important role in signal transduction processes []. 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 the 'X-box' 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. By profile analysis, we could show that sequences with significant similarity to the X-box domain occur also in prokaryotic and trypanosome PI-specific phospholipases C. Apart from this region, the prokaryotic enzymes show no similarity to their eukaryotic counterparts.; GO: 0004629 phospholipase C activity, 0006629 lipid metabolic process, 0035556 intracellular signal transduction; PDB: 2FJU_B 2ZKM_X 3V18_A 3V1H_A 3V16_A 3QR1_D 3EA3_A 3EA1_A 2OR2_A 1T6M_B ....
Probab=26.59 E-value=25 Score=28.82 Aligned_cols=59 Identities=22% Similarity=0.379 Sum_probs=33.4
Q ss_pred CceeeeeeccCCCCCCceeEeccccceEEEEEecCCCC--eEEEeeeecccCcccchhhhhhhHHHHHH
Q 024799 68 GELFAACFVQPGQRENSVETVLDSSRYFVLKIEDGTGK--HAFIGLGFNERNEAFDFNVALSDHEKYVR 134 (262)
Q Consensus 68 GeLFA~cpv~pg~~~~aVE~V~DSSRYFVLRV~D~~Gr--~AfIGiGF~eRsdAFDFnvaLqD~~K~l~ 134 (262)
|.+++.| +....-+..-.--|||=|||.+..+. +.+=|.-+. ....|..+|.+..+|+.
T Consensus 21 ~~~~~~~-----Q~~~i~~QL~~GiR~lDlrv~~~~~~~~~v~Hg~~~~---~~~~~~dvL~~i~~fl~ 81 (146)
T PF00388_consen 21 GQLWSKT-----QSWSIREQLESGIRYLDLRVWDGNDGELVVYHGITST---SGITFEDVLNDIRDFLF 81 (146)
T ss_dssp TSHHC-B------SHHHHHHHHTT--EEEEEEEEETTSSEEEEETTSEE----EEEHHHHHHHHHHHTT
T ss_pred cccccCc-----chHhHHHHHhccCceEEEEEEcCCCCceEEEeCCEee---eeEeHHHHHHHHHHHHh
Confidence 4566666 32334556667789999999975544 444444433 33556667777766664
No 25
>PF11732 Thoc2: Transcription- and export-related complex subunit; InterPro: IPR021726 The THO/TREX complex is the transcription- and export-related complex associated with spliceosomes that preferentially deal with spliced mRNAs as opposed to unspliced mRNAs. Thoc2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats []. In humans, the TRE complex is comprised of the exon-junction-associated proteins Aly/REF and UAP56 together with the THO proteins THOC1 (hHpr1/p84), Thoc2 (hRlr1), THOC3 (hTex1), THOC5 (fSAP79), THOC6 (fSAP35), and THOC7 (fSAP24). Although much evidence indicates that the function of the TREX complex as an adaptor between the mRNA and components of the export machinery is conserved among eukaryotes, in Drosophila the majority of mRNAs can be exported from the nucleus independently of the THO complex []. This entry represents a conserved domain found towards the N terminus of these proteins.
Probab=24.32 E-value=11 Score=29.47 Aligned_cols=16 Identities=38% Similarity=0.727 Sum_probs=13.8
Q ss_pred CCCceeEeccccceEE
Q 024799 81 RENSVETVLDSSRYFV 96 (262)
Q Consensus 81 ~~~aVE~V~DSSRYFV 96 (262)
+++-+|+|+|+.|||-
T Consensus 23 YdNli~~vVe~~ky~t 38 (77)
T PF11732_consen 23 YDNLIEPVVESLKYFT 38 (77)
T ss_pred hhhhHHHHHHHHhhcc
Confidence 4578999999999995
No 26
>PF13296 T6SS_Vgr: Putative type VI secretion system Rhs element Vgr
Probab=23.23 E-value=25 Score=29.04 Aligned_cols=25 Identities=28% Similarity=0.480 Sum_probs=20.1
Q ss_pred EEEEEecCCCCeEEEeeeecccCccc
Q 024799 95 FVLKIEDGTGKHAFIGLGFNERNEAF 120 (262)
Q Consensus 95 FVLRV~D~~Gr~AfIGiGF~eRsdAF 120 (262)
+.+++ +++||.++.|-||+=|+|+.
T Consensus 38 ~l~~~-~~~~R~~~RG~GfELrTD~~ 62 (109)
T PF13296_consen 38 HLVDQ-RDNGRGAPRGEGFELRTDAW 62 (109)
T ss_pred cccCc-ccccccCccccceEEecchh
Confidence 44555 45799999999999999874
No 27
>PHA02757 hypothetical protein; Provisional
Probab=22.89 E-value=81 Score=24.57 Aligned_cols=19 Identities=42% Similarity=0.660 Sum_probs=15.4
Q ss_pred CeEEEEEecCCCCceeeee
Q 024799 56 DRCEIRLEDPNSGELFAAC 74 (262)
Q Consensus 56 ~~~~I~LeD~~tGeLFA~c 74 (262)
+++.|.=.|+.+|-||.+|
T Consensus 45 dK~CiiE~de~sGml~s~C 63 (75)
T PHA02757 45 DKACIIEIDEDSGMLFSQC 63 (75)
T ss_pred cceEEEEEcCCCCcEEEec
Confidence 5566666788899999999
No 28
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=21.85 E-value=99 Score=23.59 Aligned_cols=43 Identities=14% Similarity=0.319 Sum_probs=29.3
Q ss_pred EeeceeEEEEcCCCCCCCCeecCCCCCCCceeeEEEEEEEeCCeE
Q 024799 14 LVVREVCVYKIPPRTTSGGYKCGEWLQSDKIWTGRLRVVSCKDRC 58 (262)
Q Consensus 14 ~v~~eV~VY~IPP~~s~~GyrA~dW~~~~~iwtGRLrVv~~g~~~ 58 (262)
+.+.--.+|.+ +++..-++.+=|....|.|||..+++.++.++
T Consensus 16 v~c~~~~~~~~--~ST~~~i~vdv~s~~HPfyTG~~~~~~~~Grv 58 (68)
T CHL00136 16 VYCDGQLVMTV--GSTKPELNVDIWSGNHPFYTGSQKIIDTEGRV 58 (68)
T ss_pred EEEcCCCEEEE--eecCCCEEEEeCCCCCccCcCCeeEecccccH
Confidence 33333334554 34445588888887899999999999887653
No 29
>PF09671 Spore_GerQ: Spore coat protein (Spore_GerQ); InterPro: IPR014099 Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=20.27 E-value=1e+02 Score=24.57 Aligned_cols=32 Identities=28% Similarity=0.657 Sum_probs=23.8
Q ss_pred CCCCCCCceeeEEEEEEEeCCeEEEEEecCCCCceee
Q 024799 36 GEWLQSDKIWTGRLRVVSCKDRCEIRLEDPNSGELFA 72 (262)
Q Consensus 36 ~dW~~~~~iwtGRLrVv~~g~~~~I~LeD~~tGeLFA 72 (262)
.+|+ ..+|+|.+ |...+=.|.|-||+||.=|-
T Consensus 32 ~ewn--akvf~Gvi---E~aGRDhiiisDp~tg~ryL 63 (81)
T PF09671_consen 32 SEWN--AKVFRGVI---EAAGRDHIIISDPKTGKRYL 63 (81)
T ss_pred hhhh--heeeEEEe---hhcCcceEEEeCCCCCcEEE
Confidence 3696 88999965 45555678899999998443
Done!