Query 047538
Match_columns 293
No_of_seqs 135 out of 181
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 12:00:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047538hhsearch_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 1.6E-87 3.5E-92 608.6 21.8 249 24-289 2-253 (253)
2 PF07933 DUF1681: Protein of u 100.0 1.1E-78 2.4E-83 526.4 8.8 158 27-189 1-160 (160)
3 cd00835 RanBD Ran-binding doma 93.3 2.5 5.5E-05 34.7 11.9 110 29-151 10-121 (122)
4 PF00638 Ran_BP1: RanBP1 domai 85.9 17 0.00037 29.4 12.4 111 28-151 8-120 (122)
5 cd00837 EVH1 EVH1 (Enabled, Va 81.4 16 0.00034 29.5 8.8 92 38-149 9-102 (104)
6 smart00160 RanBD Ran-binding d 79.9 35 0.00076 28.7 11.3 108 29-149 19-129 (130)
7 PF00568 WH1: WH1 domain; Int 76.0 20 0.00043 29.1 7.9 93 37-149 15-109 (111)
8 smart00461 WH1 WASP homology r 72.3 11 0.00025 30.6 5.7 78 57-149 23-104 (106)
9 KOG3671 Actin regulatory prote 53.1 75 0.0016 33.7 8.6 84 55-153 55-141 (569)
10 TIGR00105 L31 ribosomal protei 50.8 13 0.00028 28.7 2.2 46 28-75 9-56 (68)
11 COG5216 Uncharacterized conser 48.6 9 0.00019 29.9 1.0 24 73-96 27-50 (67)
12 PF07935 SSV1_ORF_D-335: ORF D 43.0 26 0.00055 28.0 2.8 23 110-132 15-37 (72)
13 PRK00019 rpmE 50S ribosomal pr 41.1 26 0.00056 27.5 2.6 49 28-76 9-57 (72)
14 cd01205 WASP WASP-type EVH1 do 38.3 1.8E+02 0.004 24.4 7.3 79 55-149 22-103 (105)
15 COG0254 RpmE Ribosomal protein 35.4 36 0.00079 27.2 2.6 50 27-76 9-59 (75)
16 PRK14948 DNA polymerase III su 31.2 1.8E+02 0.0039 30.7 7.6 11 180-190 503-513 (620)
17 KOG2675 Adenylate cyclase-asso 30.6 43 0.00094 34.7 2.9 20 99-118 156-175 (480)
18 PF00018 SH3_1: SH3 domain; I 30.2 37 0.0008 23.2 1.7 17 170-186 9-25 (48)
19 PF04926 PAP_RNA-bind: Poly(A) 29.2 56 0.0012 27.7 3.0 31 126-156 84-119 (157)
20 PF07653 SH3_2: Variant SH3 do 28.3 38 0.00081 23.8 1.5 17 170-186 11-27 (55)
21 PF00970 FAD_binding_6: Oxidor 28.2 1.1E+02 0.0023 23.2 4.1 12 176-187 81-92 (99)
22 COG5443 FlbT Flagellar biosynt 27.5 32 0.00069 30.6 1.2 15 172-186 4-18 (148)
23 CHL00136 rpl31 ribosomal prote 24.8 73 0.0016 24.8 2.6 35 40-76 23-57 (68)
24 PF06863 DUF1254: Protein of u 23.7 1.5E+02 0.0033 24.5 4.6 38 84-121 21-60 (128)
25 PF06058 DCP1: Dcp1-like decap 23.2 1.6E+02 0.0036 24.8 4.7 98 27-147 18-118 (122)
26 PF09214 Prd1-P2: Bacteriophag 23.2 1.4E+02 0.0031 30.4 5.0 48 85-134 312-373 (560)
27 cd01268 Numb Numb Phosphotyros 22.4 3.3E+02 0.0071 23.7 6.5 78 65-152 51-129 (138)
28 cd01800 SF3a120_C Ubiquitin-li 22.1 71 0.0015 24.0 2.1 19 174-192 55-73 (76)
29 PF03664 Glyco_hydro_62: Glyco 22.1 2.7E+02 0.0059 27.2 6.3 62 38-100 91-168 (271)
30 COG5558 Transposase [DNA repli 21.2 1.1E+02 0.0024 29.1 3.5 31 113-147 117-147 (261)
31 KOG1924 RhoA GTPase effector D 21.0 86 0.0019 35.1 3.1 14 219-232 550-563 (1102)
No 1
>KOG2500 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.6e-87 Score=608.57 Aligned_cols=249 Identities=44% Similarity=0.722 Sum_probs=202.9
Q ss_pred cccceeeEEEeecceEEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEeCCeeEEEEeeCCcccceeeeeccCCCCCCe
Q 047538 24 ETEAIEFVLFQVSECYVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSKGEECIIKLEDKSTGELYARAFLRKGELHPV 103 (293)
Q Consensus 24 ~~d~iE~VL~v~~eV~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvekG~~~~IkLED~~TGeLFA~cP~~~~~~~aV 103 (293)
+.++||+||||+++||||+||||+|++||||+||++++|+||||||||++|+.|+|||||++||+|||+||++.+++++|
T Consensus 2 e~~~yE~vL~v~pev~VY~IPPr~t~~gyra~eW~l~~~~WtGrlrvvakg~~~~ikLeD~tsg~LfA~c~id~~~~~av 81 (253)
T KOG2500|consen 2 EEEAYESVLFVKPEVFVYKIPPRATSRGYRAGEWNLDKPAWTGRLRVVAKGERCEIKLEDKTSGELFAQCPIDEGPGNAV 81 (253)
T ss_pred ccccceeEEEecccEEEEECCCcccCCCccccccccCCccccceeEEEEcCcEEEEEeccCCchhhhhhCcccCCCCccc
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEcccccceeEEEEEeCCCCceeeEEEeeeeccCcccchhHHHHhHHHHhhhhhhhHHHHHhhhcCCCCCCCcCCCCceE
Q 047538 104 EPVIDSSRYFVLRIEENIGGRLRHAFIGIGFRERTEAYDFQAALHDHMKYLDKKKTAEEMEQQFQSTSAVDYSLKEGETL 183 (293)
Q Consensus 104 E~ViDSSRYFVLRV~D~~~G~gR~AfIGiGF~ERsdAFDFnVALQD~~K~l~~~k~aee~~~~~~~~p~~DySLKEGETI 183 (293)
|+|+||||||||||+| |+||||||||||+||+||||||||||||+||+++++++++++++++..|++||+|||||||
T Consensus 82 Eav~DSSRYFViRv~d---gngr~AFiGlGF~eR~dafDfnvaLqDHfkyv~~~~e~ek~eq~~d~~pslDlgFKEGeTI 158 (253)
T KOG2500|consen 82 EAVSDSSRYFVIRVED---GNGRHAFIGLGFGERGDAFDFNVALQDHFKYVKRQKEAEKQEQHYDAGPSLDLGFKEGETI 158 (253)
T ss_pred eeecccceEEEEEEeC---CCccEEEEeecccccccccchhhhHHHHHHHHHHHHHHHhhhcccCCCccccccccCCcEE
Confidence 9999999999999996 6679999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCC---CCCCCccccccccCCCCCCccccCCCCCCccccCCCCCCCCCCCcchhcCCCCCCCCCCCCCCCCCCCCCC
Q 047538 184 HLHLKN---KSSGRVKSKFFEQGLNDLSLDDKGNRKEPVICLKPLPPPPAPLSPATAARMSPSNSPQKFSLEGSSKDASP 260 (293)
Q Consensus 184 ~Ini~~---k~g~~~~s~~~~~g~~~~s~~~~~~~~~~~~~~~lpppp~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~ 260 (293)
+|||+| ++|.-..+++.... +.|++-.- +. ...+..||||| |..|+++.+.||++.| ....++...+.
T Consensus 159 kinikn~tkk~g~~s~pr~~~gk-~gl~llPP--Pp-ggt~~ilPPP~--p~a~v~t~~~Spg~sp---~~~p~s~~sDl 229 (253)
T KOG2500|consen 159 KINIKNITKKKGAASWPRTGPGK-GGLGLLPP--PP-GGTSIILPPPP--PLAPVTTAQSSPGSSP---APQPSSALSDL 229 (253)
T ss_pred EEEeeccccccccccccccCCCC-CcccccCC--CC-CCcccccCCCC--CCCccceeccCCCCCC---CCCCCcccccc
Confidence 999995 45655555543322 33333111 11 11355555554 7788888888888632 22222222233
Q ss_pred CCCccCccCCCCCCCCCCCCCCCCCcccc
Q 047538 261 DSTKEDSKEQHSPESPNTEDIPDDDFGDF 289 (293)
Q Consensus 261 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 (293)
....+.+. .++..|-.++|+|++|
T Consensus 230 w~d~~~As-----~s~~~q~~~~~nwvqF 253 (253)
T KOG2500|consen 230 WTDFEEAS-----GSKKSQTAPSDNWVQF 253 (253)
T ss_pred cccccccc-----cccccccCCCCCcccC
Confidence 33332222 3445566889999998
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=1.1e-78 Score=526.40 Aligned_cols=158 Identities=56% Similarity=0.939 Sum_probs=89.5
Q ss_pred ceeeEEEeecceEEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEeCCee--EEEEeeCCcccceeeeeccCCCCCCee
Q 047538 27 AIEFVLFQVSECYVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSKGEEC--IIKLEDKSTGELYARAFLRKGELHPVE 104 (293)
Q Consensus 27 ~iE~VL~v~~eV~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvekG~~~--~IkLED~~TGeLFA~cP~~~~~~~aVE 104 (293)
+||+|||++++||||+|||++|++||||++|++++|||||||||+++|+.| .|+|||++||+|||+|||+.+ .+||
T Consensus 1 ~ie~vL~~~~ev~VY~IPP~~s~~GyrAadW~~~~~iwtGrlrV~~~g~~~~v~i~leD~~tgeLFA~~P~~~~--~~VE 78 (160)
T PF07933_consen 1 AIERVLFVIPEVHVYKIPPRTSNKGYRAADWTLDKPIWTGRLRVVEKGDKCKVDIRLEDPSTGELFAQCPYDDY--AAVE 78 (160)
T ss_dssp --S---B--SSEEEEE--S--SSSS--HHHH--SSS-EEEEEEEE--SSSE--EEEEE-SS--SS-EEEEE-SS----EE
T ss_pred CeeEEEEEcCcEEEEECCCCCCCCCeecccCCCCCceeeeEEEEEEcCCeeEEEEEecCCCCcceEEECcccCC--CceE
Confidence 599999999999999999999999999999999999999999999999999 999999999999999999975 7999
Q ss_pred EcccccceeEEEEEeCCCCceeeEEEeeeeccCcccchhHHHHhHHHHhhhhhhhHHHHHhhhcCCCCCCCcCCCCceEE
Q 047538 105 PVIDSSRYFVLRIEENIGGRLRHAFIGIGFRERTEAYDFQAALHDHMKYLDKKKTAEEMEQQFQSTSAVDYSLKEGETLH 184 (293)
Q Consensus 105 ~ViDSSRYFVLRV~D~~~G~gR~AfIGiGF~ERsdAFDFnVALQD~~K~l~~~k~aee~~~~~~~~p~~DySLKEGETI~ 184 (293)
+|+||||||||||+|+ +| |||||||||+||+||||||||||||+||++++++.+++..+.+..|++||||||||||+
T Consensus 79 ~v~DSSRYFvlRv~d~-~G--r~AfiGiGF~eRsdAFDF~vaLqd~~k~~~~~~~~~~~~~~~~~~p~~D~sLKeGetI~ 155 (160)
T PF07933_consen 79 PVIDSSRYFVLRVQDP-SG--RHAFIGIGFRERSDAFDFNVALQDHRKYLKREKEAEEQSQAAESQPKKDYSLKEGETIK 155 (160)
T ss_dssp E-TT--S-EEEEEEET-TT--EEEEEEEE-S-HHHHHHHHHHHHHHHS-SS-----------------------------
T ss_pred EeecccceEEEEEEcC-CC--cEEEEEEeeccccccccHHHHHHHHHHHhhchhhhhhhhcccCCCCccCCcCCCCCEEE
Confidence 9999999999999997 45 89999999999999999999999999999998887777666778899999999999999
Q ss_pred EecCC
Q 047538 185 LHLKN 189 (293)
Q Consensus 185 Ini~~ 189 (293)
|||++
T Consensus 156 ini~g 160 (160)
T PF07933_consen 156 INIGG 160 (160)
T ss_dssp -----
T ss_pred EecCC
Confidence 99974
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=93.29 E-value=2.5 Score=34.68 Aligned_cols=110 Identities=18% Similarity=0.255 Sum_probs=78.4
Q ss_pred eeEEEeecceEEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEeCC--eeEEEEeeCCcccceeeeeccCCCCCCeeEc
Q 047538 29 EFVLFQVSECYVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSKGE--ECIIKLEDKSTGELYARAFLRKGELHPVEPV 106 (293)
Q Consensus 29 E~VL~v~~eV~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvekG~--~~~IkLED~~TGeLFA~cP~~~~~~~aVE~V 106 (293)
|.+||.++ |-+|+.=+- ..+|.. -=.|-|+|....+ .+.|.+-...+|.|...+++.. ...+.+.
T Consensus 10 E~~if~~r-~KLy~~~~~-------~~~Wke---rG~G~lki~~~k~~~~~RivmR~d~~~kv~lN~~i~~--~~~~~~~ 76 (122)
T cd00835 10 EEVIFSVR-AKLYRFDDE-------TKEWKE---RGVGELKILKHKDTGKYRLLMRRDQVLKLCLNHKLVP--GMKLQPM 76 (122)
T ss_pred cEEEEEEE-eEEEEEcCC-------CCCCee---ceEEEEEEEEcCCCCcEEEEEEeCCccEEEEeeEecC--CcEEeec
Confidence 55667665 666664211 457852 3389999988754 5667777778999999999984 3556777
Q ss_pred ccccceeEEEEEeCCCCceeeEEEeeeeccCcccchhHHHHhHHH
Q 047538 107 IDSSRYFVLRIEENIGGRLRHAFIGIGFRERTEAYDFQAALHDHM 151 (293)
Q Consensus 107 iDSSRYFVLRV~D~~~G~gR~AfIGiGF~ERsdAFDFnVALQD~~ 151 (293)
--|.+++++-..|..++.+......|-|..=.+|=.|.-+++++.
T Consensus 77 ~~~~k~~~~~~~d~~~~~~~~~~~~lrfk~~~~a~~f~~~~~~~~ 121 (122)
T cd00835 77 GNSDKSIVWAAMDFSDDEPKPETFAIRFKTEEIADEFKEAIEEAK 121 (122)
T ss_pred CCCCcEEEEEeeecCCCCCcEEEEEEEECCHHHHHHHHHHHHHhh
Confidence 656778877777765433467888999988788888888888764
No 4
>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=85.89 E-value=17 Score=29.39 Aligned_cols=111 Identities=19% Similarity=0.293 Sum_probs=74.7
Q ss_pred eeeEEEeecceEEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEeC--CeeEEEEeeCCcccceeeeeccCCCCCCeeE
Q 047538 28 IEFVLFQVSECYVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSKG--EECIIKLEDKSTGELYARAFLRKGELHPVEP 105 (293)
Q Consensus 28 iE~VL~v~~eV~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvekG--~~~~IkLED~~TGeLFA~cP~~~~~~~aVE~ 105 (293)
=|.+||..+ |-+|+.=.-. ..|. -.=+|.|||.... ..+.|.+-...+|.|...+++... ..+.+
T Consensus 8 ~E~~l~~~r-~Kl~~~~~~~-------~~W~---erG~G~l~i~~~k~~~~~RlvmR~d~~~kv~lN~~i~~~--m~~~~ 74 (122)
T PF00638_consen 8 DEEILFEVR-AKLYRFDKED-------KEWK---ERGVGTLKILKHKETGKYRLVMRRDGTGKVLLNHPIFKG--MKLKP 74 (122)
T ss_dssp SEEEEEEEE-EEEEEEETTT-------TEEE---EEEEEEEEEEEETTSCEEEEEEEETTTTEEEEEEE--TT--C-EEE
T ss_pred CcEEEEEEE-EEEEEEeCCC-------CCcc---ccceeEEEEEEccCCcceEEEEEEcccCceeEEEEecCC--ceecc
Confidence 366888877 8888873211 4663 2448999999875 467788887789999999998843 45777
Q ss_pred cccccceeEEEEEeCCCCceeeEEEeeeeccCcccchhHHHHhHHH
Q 047538 106 VIDSSRYFVLRIEENIGGRLRHAFIGIGFRERTEAYDFQAALHDHM 151 (293)
Q Consensus 106 ViDSSRYFVLRV~D~~~G~gR~AfIGiGF~ERsdAFDFnVALQD~~ 151 (293)
.-.|.+.++.-..|-.++.+....+=|=|..=.+|=.|.-+++++.
T Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~irf~~~e~a~~f~~~i~e~~ 120 (122)
T PF00638_consen 75 MKGSEKSLVWTAIDYADEEGKPETYLIRFKSAEDADEFKKKIEEAK 120 (122)
T ss_dssp STTTTTEEEEEEEECTTSSSEEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred cccCCcEEEEEeccccCCCCceEEEEEEECCHHHHHHHHHHHHHHh
Confidence 7777666555434433333467888888888777888888877764
No 5
>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=81.36 E-value=16 Score=29.51 Aligned_cols=92 Identities=15% Similarity=0.233 Sum_probs=65.0
Q ss_pred eEEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEe--CCeeEEEEeeCCcccceeeeeccCCCCCCeeEcccccceeEE
Q 047538 38 CYVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSK--GEECIIKLEDKSTGELYARAFLRKGELHPVEPVIDSSRYFVL 115 (293)
Q Consensus 38 V~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvek--G~~~~IkLED~~TGeLFA~cP~~~~~~~aVE~ViDSSRYFVL 115 (293)
+.||..-|.+ ..|.... -..|.|.++.. +....|++.|..++.+-=.|.+.. -++---++.-|+.-
T Consensus 9 a~v~~~~~~~-------~~W~~~~-~~~g~v~~~~d~~~~~y~i~~~~~~~~~vv~~~~l~~----~~~y~~~~~~Fh~w 76 (104)
T cd00837 9 AQVYTADPST-------GKWVPAS-GGTGAVSLVKDSTRNTYRIRGVDIQDQKVIWNQEIYK----GLKYTQATPFFHQW 76 (104)
T ss_pred EEEEEECCCC-------CceEECC-CCeEEEEEEEECCCCEEEEEEEecCCCeEEEEEEecC----CcEEeecCCeEEEE
Confidence 6677775543 2575322 36799999974 445779999988777766666654 25556677777777
Q ss_pred EEEeCCCCceeeEEEeeeeccCcccchhHHHHhH
Q 047538 116 RIEENIGGRLRHAFIGIGFRERTEAYDFQAALHD 149 (293)
Q Consensus 116 RV~D~~~G~gR~AfIGiGF~ERsdAFDFnVALQD 149 (293)
+.. ...+||.|.+-.||-.|.-++++
T Consensus 77 ~~~--------~~~~GL~F~se~eA~~F~~~v~~ 102 (104)
T cd00837 77 EDD--------NCVYGLNFASEEEAAQFRKKVLE 102 (104)
T ss_pred EcC--------CcEEEEeeCCHHHHHHHHHHHHh
Confidence 655 24799999999999999877654
No 6
>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=79.92 E-value=35 Score=28.69 Aligned_cols=108 Identities=19% Similarity=0.276 Sum_probs=70.6
Q ss_pred eeEEEeecceEEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEeC---CeeEEEEeeCCcccceeeeeccCCCCCCeeE
Q 047538 29 EFVLFQVSECYVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSKG---EECIIKLEDKSTGELYARAFLRKGELHPVEP 105 (293)
Q Consensus 29 E~VL~v~~eV~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvekG---~~~~IkLED~~TGeLFA~cP~~~~~~~aVE~ 105 (293)
|.+||.++ |-+|+.-. ....|.. -=.|.|||.... ....|.+-...+|.+.+.|++.. ...+++
T Consensus 19 E~~lf~~r-~KL~~~~~-------~~~~Wke---rG~G~lki~~~~~~~~~~RivmR~~~~~kv~lN~~i~~--~~~~~~ 85 (130)
T smart00160 19 EEVIFSAR-AKLYRFAN-------DKKEWKE---RGVGDLKILKSKDNGGKVRIVMRRDGVLKVCANHPIFK--SMTLKP 85 (130)
T ss_pred eEEEEEEE-eEEEEEcC-------CCCCCee---ccEEEEEEEEcCCCCCeEEEEEEECCCceEEeccEecC--CcEEee
Confidence 45666543 55666532 1347863 237999997753 45778888888999999999984 345666
Q ss_pred cccccceeEEEEEeCCCCceeeEEEeeeeccCcccchhHHHHhH
Q 047538 106 VIDSSRYFVLRIEENIGGRLRHAFIGIGFRERTEAYDFQAALHD 149 (293)
Q Consensus 106 ViDSSRYFVLRV~D~~~G~gR~AfIGiGF~ERsdAFDFnVALQD 149 (293)
+--|-+.++.-..|..++.+.-....|-|..=.+|=-|.-++++
T Consensus 86 ~~~~~~~~~~~~~d~~d~~~~~~~~~irfk~~e~a~~f~~~~~e 129 (130)
T smart00160 86 LAGSNRALKWTPEDFADDIPKLVLYAVRFKTKEEADSFKNIFEE 129 (130)
T ss_pred cCCCcceEEEeeeecCCCCCceEEEEEEeCCHHHHHHHHHHHHh
Confidence 65555665443444333333566778888877777777777664
No 7
>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=75.97 E-value=20 Score=29.09 Aligned_cols=93 Identities=18% Similarity=0.302 Sum_probs=61.8
Q ss_pred ceEEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEe--CCeeEEEEeeCCcccceeeeeccCCCCCCeeEcccccceeE
Q 047538 37 ECYVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSK--GEECIIKLEDKSTGELYARAFLRKGELHPVEPVIDSSRYFV 114 (293)
Q Consensus 37 eV~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvek--G~~~~IkLED~~TGeLFA~cP~~~~~~~aVE~ViDSSRYFV 114 (293)
.++||.+=|.+. ..|... .-+|.|.++.. .....|++.|-.++.+--.|-+..+ ++=.-++.-|..
T Consensus 15 vA~v~~~~p~~~------~~W~~~--~~~g~v~~v~d~~~~~y~I~~~~~~~~~~v~e~~l~~~----~~Y~~~~~~Fh~ 82 (111)
T PF00568_consen 15 VAQVYQADPDTK------RQWSPV--KGTGVVCFVKDNSRRSYFIRLYDLQDGKVVWEQELYPG----FVYTKARPFFHQ 82 (111)
T ss_dssp EEEEEEEETTTS------ESEEES--SSEEEEEEEEETTTTEEEEEEEETTTTEEEEEEEESTT-----EEEEESSSEEE
T ss_pred EEEEEEEEcCCC------CcEeeC--CeEEEEEEEEECCCCEEEEEEEEccccEEEEEeEecCC----CEEEeCCCcEEE
Confidence 356676633321 137532 66899999975 3557799999888888777777642 333334454555
Q ss_pred EEEEeCCCCceeeEEEeeeeccCcccchhHHHHhH
Q 047538 115 LRIEENIGGRLRHAFIGIGFRERTEAYDFQAALHD 149 (293)
Q Consensus 115 LRV~D~~~G~gR~AfIGiGF~ERsdAFDFnVALQD 149 (293)
-+ ++ ...+||+|.+-.||-.|.-.+++
T Consensus 83 f~--~~------~~~~GLnF~se~eA~~F~~~v~~ 109 (111)
T PF00568_consen 83 FE--DD------DCVYGLNFASEEEADQFYKKVQE 109 (111)
T ss_dssp EE--ET------TCEEEEEESSHHHHHHHHHHHHH
T ss_pred EE--eC------CeEEEEecCCHHHHHHHHHHHhc
Confidence 54 32 23999999999999999877765
No 8
>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=72.31 E-value=11 Score=30.58 Aligned_cols=78 Identities=14% Similarity=0.218 Sum_probs=47.7
Q ss_pred CCCCCceeeE-EEEEEE--eCCeeEEEEeeCCcc-cceeeeeccCCCCCCeeEcccccceeEEEEEeCCCCceeeEEEee
Q 047538 57 WNVNKWAWEG-MLKVVS--KGEECIIKLEDKSTG-ELYARAFLRKGELHPVEPVIDSSRYFVLRIEENIGGRLRHAFIGI 132 (293)
Q Consensus 57 W~~~~piWTG-RLRVve--kG~~~~IkLED~~TG-eLFA~cP~~~~~~~aVE~ViDSSRYFVLRV~D~~~G~gR~AfIGi 132 (293)
|. |...| -+.|+- ....+.+||.|-..+ .+-=.|.+..+ .+---++.=|..-+ +. ..++||
T Consensus 23 W~---~~~~gg~~~~~~~~~~~~~~~ri~~~~~~~~vv~e~ely~~----~~y~~~~~~Fh~f~--~~------~~~~GL 87 (106)
T smart00461 23 WV---PTGEGGAANLVIDKNQRSYFFRIVGIKGQDKVIWNQELYKN----FKYNQATPTFHQWA--DD------KCVYGL 87 (106)
T ss_pred eE---ECCCCCEEEEEEEecCCeEEEEEEEecCCCeEEEEEeccCC----CEEeecCCceEEEE--eC------CeEEEe
Confidence 85 34456 444444 356788999997665 44444555432 22222333333333 21 468999
Q ss_pred eeccCcccchhHHHHhH
Q 047538 133 GFRERTEAYDFQAALHD 149 (293)
Q Consensus 133 GF~ERsdAFDFnVALQD 149 (293)
.|.+-.||-.|.-++++
T Consensus 88 nF~se~EA~~F~~~v~~ 104 (106)
T smart00461 88 NFASEEEAKKFRKKVLK 104 (106)
T ss_pred ecCCHHHHHHHHHHHHh
Confidence 99999999999877764
No 9
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=53.09 E-value=75 Score=33.65 Aligned_cols=84 Identities=21% Similarity=0.348 Sum_probs=55.5
Q ss_pred CCCCCCCceeeEEEEEEEe--CCeeEEEEeeCCcccce-eeeeccCCCCCCeeEcccccceeEEEEEeCCCCceeeEEEe
Q 047538 55 DEWNVNKWAWEGMLKVVSK--GEECIIKLEDKSTGELY-ARAFLRKGELHPVEPVIDSSRYFVLRIEENIGGRLRHAFIG 131 (293)
Q Consensus 55 adW~~~~piWTGRLRVvek--G~~~~IkLED~~TGeLF-A~cP~~~~~~~aVE~ViDSSRYFVLRV~D~~~G~gR~AfIG 131 (293)
+.|+.. .-.|-|-+|-. +..|++||.|-..+.|- -+==| ...|-+- .|-|-+..+. -.-++|
T Consensus 55 ~~W~~~--~~~Gal~lVkD~~~rsyFlrl~di~~~rliWdqELY-----~nf~y~q--~r~ffhtFeg------ddc~aG 119 (569)
T KOG3671|consen 55 NHWNKT--GLCGALCLVKDNAQRSYFLRLVDIVNNRLIWDQELY-----QNFEYRQ--PRTFFHTFEG------DDCQAG 119 (569)
T ss_pred hhhccc--cCceeEEEeeccccceeeeEEeeecCceeeehHHhh-----hhceecc--Cccceeeecc------ccceee
Confidence 478744 22366666653 67799999998888763 22222 2344443 6677788883 255999
Q ss_pred eeeccCcccchhHHHHhHHHHh
Q 047538 132 IGFRERTEAYDFQAALHDHMKY 153 (293)
Q Consensus 132 iGF~ERsdAFDFnVALQD~~K~ 153 (293)
|-|.+-.||=-|.-.+||-..+
T Consensus 120 LnF~~E~EA~~F~k~V~~r~~~ 141 (569)
T KOG3671|consen 120 LNFASEEEAQKFRKKVQDRICH 141 (569)
T ss_pred ecccCHHHHHHHHHHHHHHhhh
Confidence 9999999998887777764443
No 10
>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=50.84 E-value=13 Score=28.70 Aligned_cols=46 Identities=15% Similarity=0.127 Sum_probs=32.8
Q ss_pred eeeEEEeecceEEEEcCCCCCCCc--cccCCCCCCCceeeEEEEEEEeCC
Q 047538 28 IEFVLFQVSECYVYLIPPRKSAAS--YRADEWNVNKWAWEGMLKVVSKGE 75 (293)
Q Consensus 28 iE~VL~v~~eV~VYkIPPr~S~~G--YrAadW~~~~piWTGRLRVvekG~ 75 (293)
|..|++++.-=.+|.+ +++... ++-+=|....|+|||.-+++..+.
T Consensus 9 y~~v~~~~s~g~~f~~--~ST~~~~~i~vdi~s~~HPfyTG~~~~~~~~G 56 (68)
T TIGR00105 9 YHEITVTCTCGNVFTT--RSTWGKETLNLDICSKCHPFYTGKQKIVDTGG 56 (68)
T ss_pred CEEEEEEECCCCEEEE--eeecCCceEEEEECCCCcccCCCceEEeccCC
Confidence 7777777654455666 333333 888889988999999988886544
No 11
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=48.55 E-value=9 Score=29.91 Aligned_cols=24 Identities=38% Similarity=0.396 Sum_probs=21.9
Q ss_pred eCCeeEEEEeeCCcccceeeeecc
Q 047538 73 KGEECIIKLEDKSTGELYARAFLR 96 (293)
Q Consensus 73 kG~~~~IkLED~~TGeLFA~cP~~ 96 (293)
.|+...|.|||-..||.-|.||--
T Consensus 27 CGDRFeIsLeDl~~GE~VArCPSC 50 (67)
T COG5216 27 CGDRFEISLEDLRNGEVVARCPSC 50 (67)
T ss_pred CCCEeEEEHHHhhCCceEEEcCCc
Confidence 589999999999999999999854
No 12
>PF07935 SSV1_ORF_D-335: ORF D-335-like protein; InterPro: IPR012922 The sequences featured in this family are similar to a probable integrase (P20214 from SWISSPROT) expressed by the SSV1 virus of the archaeon Sulfolobus shibatae. This protein may be necessary for the integration of the virus into the host genome by a process of site-specific recombination [].
Probab=42.98 E-value=26 Score=28.01 Aligned_cols=23 Identities=35% Similarity=0.872 Sum_probs=19.9
Q ss_pred cceeEEEEEeCCCCceeeEEEee
Q 047538 110 SRYFVLRIEENIGGRLRHAFIGI 132 (293)
Q Consensus 110 SRYFVLRV~D~~~G~gR~AfIGi 132 (293)
-||+|-.|+..++|+.|+-|||-
T Consensus 15 GkYYVY~iE~~~~G~~re~YVGp 37 (72)
T PF07935_consen 15 GKYYVYKIEKDINGERRETYVGP 37 (72)
T ss_pred CeEEEEEEEeccCCceeeeeecc
Confidence 48999999987778889999983
No 13
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=41.08 E-value=26 Score=27.54 Aligned_cols=49 Identities=18% Similarity=0.108 Sum_probs=35.1
Q ss_pred eeeEEEeecceEEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEeCCe
Q 047538 28 IEFVLFQVSECYVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSKGEE 76 (293)
Q Consensus 28 iE~VL~v~~eV~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvekG~~ 76 (293)
|..|++++.-=.+|.+-......-++.+=|....|+|||.-|++..+..
T Consensus 9 y~~v~~~c~~g~~f~~~ST~~~~~i~vdi~s~~HPFyTG~q~~~dt~GR 57 (72)
T PRK00019 9 YEEVTVTCSCGNVFETRSTLGKDEINVDVCSKCHPFYTGKQKIVDTGGR 57 (72)
T ss_pred CEEEEEEECCCCEEEEeecCCCCcEEEEeCCCCCCcCcCCEeEeccCCc
Confidence 6677777653345555444333448999999999999999999887654
No 14
>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=38.30 E-value=1.8e+02 Score=24.35 Aligned_cols=79 Identities=22% Similarity=0.425 Sum_probs=53.5
Q ss_pred CCCCCCCceeeEEEEEEEe--CCeeEEEEeeCCcc-cceeeeeccCCCCCCeeEcccccceeEEEEEeCCCCceeeEEEe
Q 047538 55 DEWNVNKWAWEGMLKVVSK--GEECIIKLEDKSTG-ELYARAFLRKGELHPVEPVIDSSRYFVLRIEENIGGRLRHAFIG 131 (293)
Q Consensus 55 adW~~~~piWTGRLRVvek--G~~~~IkLED~~TG-eLFA~cP~~~~~~~aVE~ViDSSRYFVLRV~D~~~G~gR~AfIG 131 (293)
+.|.- . ++|-|-++.. +....|||.|-.++ -||-+==|.. .+---|- .|| .-.+ | ...++|
T Consensus 22 ~~W~~--~-~~Gvl~~vkD~~~~sy~lrl~D~~~~~v~weqElY~~-----f~y~~~r-~fF-htFe----~--d~c~~G 85 (105)
T cd01205 22 GRWTK--T-LTGAVCLVKDNVQKSYFIRLFDIKANRIIWEQELYDN-----FEYQQPR-PFF-HTFE----G--DDCVVG 85 (105)
T ss_pred CeeEE--E-eEEEEEEEEECCCCEEEEEEEEccCCcEEEEEEcccC-----cEEccCC-CcE-EEEe----c--cCcEEE
Confidence 47863 2 7899999885 67788999997764 5566644442 2222222 333 3445 2 368999
Q ss_pred eeeccCcccchhHHHHhH
Q 047538 132 IGFRERTEAYDFQAALHD 149 (293)
Q Consensus 132 iGF~ERsdAFDFnVALQD 149 (293)
+-|.+-.||-.|.-.+++
T Consensus 86 L~Fade~EA~~F~k~v~~ 103 (105)
T cd01205 86 LNFADETEAAEFRKKVLD 103 (105)
T ss_pred EEECCHHHHHHHHHHHHh
Confidence 999999999999877654
No 15
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=35.37 E-value=36 Score=27.16 Aligned_cols=50 Identities=18% Similarity=0.197 Sum_probs=33.4
Q ss_pred ceeeEEEeecce-EEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEeCCe
Q 047538 27 AIEFVLFQVSEC-YVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSKGEE 76 (293)
Q Consensus 27 ~iE~VL~v~~eV-~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvekG~~ 76 (293)
-|+.|+|++.-| .+|.|=......--+-+=|....|+|||+.|++..+..
T Consensus 9 y~~~v~~~~~s~g~~f~~~ST~~~~~i~vdV~s~~HPFyTG~qk~~d~~Gr 59 (75)
T COG0254 9 YYRPVVFVCSSCGNEFTTRSTKGTDEINLDVCSKCHPFYTGKQKIVDTEGR 59 (75)
T ss_pred ccceEEEEeCCCCCEEEEEeccCCceEEEEeCCCCCCcCcCceeEeecccc
Confidence 357788887643 34555333222235666677779999999999998754
No 16
>PRK14948 DNA polymerase III subunits gamma and tau; Provisional
Probab=31.20 E-value=1.8e+02 Score=30.73 Aligned_cols=11 Identities=27% Similarity=0.748 Sum_probs=7.6
Q ss_pred CceEEEecCCC
Q 047538 180 GETLHLHLKNK 190 (293)
Q Consensus 180 GETI~Ini~~k 190 (293)
|..|+|+|..+
T Consensus 503 ~~~~~~~~~~~ 513 (620)
T PRK14948 503 GRSIKLNLESQ 513 (620)
T ss_pred CCCeEEEEEec
Confidence 56688888643
No 17
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=30.62 E-value=43 Score=34.72 Aligned_cols=20 Identities=15% Similarity=0.281 Sum_probs=14.6
Q ss_pred CCCCeeEcccccceeEEEEE
Q 047538 99 ELHPVEPVIDSSRYFVLRIE 118 (293)
Q Consensus 99 ~~~aVE~ViDSSRYFVLRV~ 118 (293)
|...|....|.+-||.=||-
T Consensus 156 P~p~vke~~daa~FY~NrvL 175 (480)
T KOG2675|consen 156 PAPYVKEFKDAAQFYTNRVL 175 (480)
T ss_pred CchHHHHHHHHHHHHHHHHH
Confidence 33457778888888877775
No 18
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=30.15 E-value=37 Score=23.21 Aligned_cols=17 Identities=18% Similarity=0.411 Sum_probs=13.1
Q ss_pred CCCCCCcCCCCceEEEe
Q 047538 170 TSAVDYSLKEGETLHLH 186 (293)
Q Consensus 170 ~p~~DySLKEGETI~In 186 (293)
....+++|++|+.|.|-
T Consensus 9 ~~~~eLs~~~Gd~i~v~ 25 (48)
T PF00018_consen 9 EDPDELSFKKGDIIEVL 25 (48)
T ss_dssp SSTTBSEB-TTEEEEEE
T ss_pred CCCCEEeEECCCEEEEE
Confidence 34668999999999984
No 19
>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=29.17 E-value=56 Score=27.66 Aligned_cols=31 Identities=19% Similarity=0.443 Sum_probs=23.4
Q ss_pred eeEEEeeeeccCcc-----cchhHHHHhHHHHhhhh
Q 047538 126 RHAFIGIGFRERTE-----AYDFQAALHDHMKYLDK 156 (293)
Q Consensus 126 R~AfIGiGF~ERsd-----AFDFnVALQD~~K~l~~ 156 (293)
..-||||-|..-.. ..|+..++++|...++.
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 47899999998765 49999999999998864
No 20
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=28.35 E-value=38 Score=23.83 Aligned_cols=17 Identities=18% Similarity=0.423 Sum_probs=12.3
Q ss_pred CCCCCCcCCCCceEEEe
Q 047538 170 TSAVDYSLKEGETLHLH 186 (293)
Q Consensus 170 ~p~~DySLKEGETI~In 186 (293)
.....+||+.||.|.|-
T Consensus 11 ~~~~~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 11 EDPDELSFKKGDVIEVL 27 (55)
T ss_dssp SSTTB-EB-TTEEEEEE
T ss_pred CCCCceEEecCCEEEEE
Confidence 34567999999999996
No 21
>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=28.24 E-value=1.1e+02 Score=23.22 Aligned_cols=12 Identities=25% Similarity=0.481 Sum_probs=9.7
Q ss_pred cCCCCceEEEec
Q 047538 176 SLKEGETLHLHL 187 (293)
Q Consensus 176 SLKEGETI~Ini 187 (293)
.|++|.+|.|.-
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 489999998863
No 22
>COG5443 FlbT Flagellar biosynthesis regulator FlbT [Cell motility and secretion]
Probab=27.53 E-value=32 Score=30.60 Aligned_cols=15 Identities=33% Similarity=0.607 Sum_probs=13.1
Q ss_pred CCCCcCCCCceEEEe
Q 047538 172 AVDYSLKEGETLHLH 186 (293)
Q Consensus 172 ~~DySLKEGETI~In 186 (293)
.+-+|||.||+|-||
T Consensus 4 tlriSLk~gEki~iN 18 (148)
T COG5443 4 TLRISLKPGEKIFIN 18 (148)
T ss_pred ceEEeecCCCEEEEe
Confidence 455899999999999
No 23
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=24.81 E-value=73 Score=24.79 Aligned_cols=35 Identities=17% Similarity=0.320 Sum_probs=26.4
Q ss_pred EEEcCCCCCCCccccCCCCCCCceeeEEEEEEEeCCe
Q 047538 40 VYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSKGEE 76 (293)
Q Consensus 40 VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvekG~~ 76 (293)
+|.+ +++..-++-+=|....|+|||..+++..+..
T Consensus 23 ~~~~--~ST~~~i~vdv~s~~HPfyTG~~~~~~~~Gr 57 (68)
T CHL00136 23 VMTV--GSTKPELNVDIWSGNHPFYTGSQKIIDTEGR 57 (68)
T ss_pred EEEE--eecCCCEEEEeCCCCCccCcCCeeEeccccc
Confidence 3444 4444568888888889999999999887654
No 24
>PF06863 DUF1254: Protein of unknown function (DUF1254); InterPro: IPR010679 This entry represents an immunoglobulin-like beta-sandwich domain found in a group of hypothetical proteins of unknown function.; PDB: 3VB9_D 2P3Y_A 3U07_A.
Probab=23.72 E-value=1.5e+02 Score=24.50 Aligned_cols=38 Identities=24% Similarity=0.375 Sum_probs=23.5
Q ss_pred CCcccceeeeeccCCCCCCeeEccc--ccceeEEEEEeCC
Q 047538 84 KSTGELYARAFLRKGELHPVEPVID--SSRYFVLRIEENI 121 (293)
Q Consensus 84 ~~TGeLFA~cP~~~~~~~aVE~ViD--SSRYFVLRV~D~~ 121 (293)
+|.-.|++.|-++-..+..|=.+=| ..|||.+-|.|..
T Consensus 21 pN~DtlYs~a~~DL~~gPvvi~vP~~~~~ry~sv~~~D~~ 60 (128)
T PF06863_consen 21 PNNDTLYSSAWLDLSNGPVVIEVPDTTGDRYYSVQVYDAW 60 (128)
T ss_dssp --SSCEEEEEEEEHCCSSEEEEE-SS-TT--EEEEEEETT
T ss_pred CCCCceeEEEEEEcCCCCEEEEeCCCCCCceEEEEEEeCC
Confidence 5667899999988533333444444 6799999999874
No 25
>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=23.24 E-value=1.6e+02 Score=24.77 Aligned_cols=98 Identities=24% Similarity=0.360 Sum_probs=62.2
Q ss_pred ceeeEEEeecceEEEEcCCCCCCCccccCCCCCCCceeeEEEEEEEeC---CeeEEEEeeCCcccceeeeeccCCCCCCe
Q 047538 27 AIEFVLFQVSECYVYLIPPRKSAASYRADEWNVNKWAWEGMLKVVSKG---EECIIKLEDKSTGELYARAFLRKGELHPV 103 (293)
Q Consensus 27 ~iE~VL~v~~eV~VYkIPPr~S~~GYrAadW~~~~piWTGRLRVvekG---~~~~IkLED~~TGeLFA~cP~~~~~~~aV 103 (293)
.|++||.+++.|.||+.=+. ...|. +.--.|.|=|+++. .-|.|.|--.++.. |-. |++. ..-+
T Consensus 18 ~I~~Il~~a~~v~vY~f~~~-------~~~W~--K~~iEG~LFv~~r~~~p~~~~~vlNR~~~~n-~~~-~i~~--~~~~ 84 (122)
T PF06058_consen 18 SIESILDTASHVVVYKFDHE-------TNEWE--KTDIEGTLFVYKRSSSPRYGLIVLNRRSTEN-FVE-PITP--DLDF 84 (122)
T ss_dssp TEEEEEEEEEEEEEEEEETT-------TTEEE--EEEEEEEEEEEEEETTS-ECEEEEESSSS---EEE-EE-S--GGGE
T ss_pred hHHHHHhhCCeEEEEeecCC-------CCcEe--ecCcEeeEEEEEeecccceEEEEecCCCCCc-eee-ecCC--CcEE
Confidence 59999999999999997554 45897 55669999999863 23556665554432 322 3332 1234
Q ss_pred eEcccccceeEEEEEeCCCCceeeEEEeeeeccCcccchhHHHH
Q 047538 104 EPVIDSSRYFVLRIEENIGGRLRHAFIGIGFRERTEAYDFQAAL 147 (293)
Q Consensus 104 E~ViDSSRYFVLRV~D~~~G~gR~AfIGiGF~ERsdAFDFnVAL 147 (293)
| + .-.|..+| + + ++-..||.|-+-.|.=+..-.|
T Consensus 85 e-~--~~~~l~~r--~---~--~~~I~GiWf~~~~d~~ri~~~l 118 (122)
T PF06058_consen 85 E-L--QDPYLIYR--N---D--NQEIYGIWFYDDEDRQRIYNLL 118 (122)
T ss_dssp E-E--ETTEEEEE--E---T--TTEEEEEEESSHHHHHHHHHHH
T ss_pred E-E--eCCEEEEE--c---C--CceEEEEEEEeHHHHHHHHHHH
Confidence 4 1 23477777 2 1 2578999998877665554444
No 26
>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=23.21 E-value=1.4e+02 Score=30.45 Aligned_cols=48 Identities=27% Similarity=0.272 Sum_probs=27.0
Q ss_pred Ccccceeeee-ccCC-----CCCCeeE--------cccccceeEEEEEeCCCCceeeEEEeeee
Q 047538 85 STGELYARAF-LRKG-----ELHPVEP--------VIDSSRYFVLRIEENIGGRLRHAFIGIGF 134 (293)
Q Consensus 85 ~TGeLFA~cP-~~~~-----~~~aVE~--------ViDSSRYFVLRV~D~~~G~gR~AfIGiGF 134 (293)
-||+.|+-|| |+.. ...+-|- ..=||-||.+--.|..+| -++|||.|=
T Consensus 312 ltgkff~l~pp~ritnnyfad~~v~e~tvt~gn~~~~~~~~y~~vy~tdg~g~--a~~fi~~gg 373 (560)
T PF09214_consen 312 LTGKFFALCPPYRITNNYFADEEVNEFTVTRGNWRGAMSSVYWQVYQTDGYGM--AKCFIGFGG 373 (560)
T ss_dssp EEEEEEEE---EEEEEEEEETTCEE--EEEES---SEEEE-SEEEEEE-SSSE--EEEEEESSS
T ss_pred eecceeeeCCceEeccccccccccccceEEecceechhhheeeeeEeccCCCc--eeEEEecCC
Confidence 3799999995 3310 0112222 224788999988886654 799999873
No 27
>cd01268 Numb Numb Phosphotyrosine-binding (PTB) domain. Numb Phosphotyrosine-binding (PTB) domain. Numb is a membrane associated adaptor protein, which is a determinant of asymmetric cell division. Numb has an N-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=22.40 E-value=3.3e+02 Score=23.74 Aligned_cols=78 Identities=19% Similarity=0.227 Sum_probs=50.5
Q ss_pred eEEEEEEEeCCeeEEEEeeCCcccceeeeeccCCCCCCeeEcccccceeEEEEEeCCCCc-eeeEEEeeeeccCcccchh
Q 047538 65 EGMLKVVSKGEECIIKLEDKSTGELYARAFLRKGELHPVEPVIDSSRYFVLRIEENIGGR-LRHAFIGIGFRERTEAYDF 143 (293)
Q Consensus 65 TGRLRVvekG~~~~IkLED~~TGeLFA~cP~~~~~~~aVE~ViDSSRYFVLRV~D~~~G~-gR~AfIGiGF~ERsdAFDF 143 (293)
+.-|.|...| |+|.|+.|++|....|+..- ..+=.--+.-|||.-=-.|+.+.+ -=|+|+.... + |...
T Consensus 51 kv~L~VS~~G----i~vvd~~Tk~~i~~~~i~~I--Sfca~D~~d~r~FayIakd~~~~r~~CHvF~~~k~---s-a~~i 120 (138)
T cd01268 51 KAVLWVSGDG----LRVVDEKTKGLIVDQTIEKV--SFCAPDRNFDRGFSYICRDGTTRRWMCHGFLAVKD---T-GERL 120 (138)
T ss_pred EEEEEEecCc----EEEEecCCCcEEEEEeEEEE--EEEecCCCCCcEEEEEecCCCcccEEEEEEEeecc---c-hhHH
Confidence 3445554444 68889999999999988741 112223456799999888876542 1289998843 2 5555
Q ss_pred HHHHhHHHH
Q 047538 144 QAALHDHMK 152 (293)
Q Consensus 144 nVALQD~~K 152 (293)
..|+-+.++
T Consensus 121 ~~avG~AF~ 129 (138)
T cd01268 121 SHAVGCAFA 129 (138)
T ss_pred HHHHHHHHH
Confidence 566655554
No 28
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=22.11 E-value=71 Score=23.95 Aligned_cols=19 Identities=37% Similarity=0.735 Sum_probs=16.2
Q ss_pred CCcCCCCceEEEecCCCCC
Q 047538 174 DYSLKEGETLHLHLKNKSS 192 (293)
Q Consensus 174 DySLKEGETI~Ini~~k~g 192 (293)
+|.+++|.+|++.+....|
T Consensus 55 ~~~i~~g~~l~v~~~~~gg 73 (76)
T cd01800 55 YYNLANGTIIHLQLKERGG 73 (76)
T ss_pred HcCCCCCCEEEEEEecCCC
Confidence 7999999999999875544
No 29
>PF03664 Glyco_hydro_62: Glycosyl hydrolase family 62 ; InterPro: IPR005193 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is a family of alpha -L-arabinofuranosidases (3.2.1.55 from EC) which are all members of glycoside hydrolase family 62 (GH62 from CAZY). This enzyme hydrolyzed aryl alpha-L-arabinofuranosides and cleaves arabinosyl side chains from arabinoxylan and arabinan.; GO: 0046556 alpha-N-arabinofuranosidase activity, 0046373 L-arabinose metabolic process
Probab=22.10 E-value=2.7e+02 Score=27.22 Aligned_cols=62 Identities=13% Similarity=0.277 Sum_probs=37.4
Q ss_pred eEEEEcCCC-----CCCCccccCCCCCCCceeeEEEE----------EEEeCCeeEEEEeeCCcccce-eeeeccCCCC
Q 047538 38 CYVYLIPPR-----KSAASYRADEWNVNKWAWEGMLK----------VVSKGEECIIKLEDKSTGELY-ARAFLRKGEL 100 (293)
Q Consensus 38 V~VYkIPPr-----~S~~GYrAadW~~~~piWTGRLR----------VvekG~~~~IkLED~~TGeLF-A~cP~~~~~~ 100 (293)
|.||+=.+. ++..=-....|...+++++|.+. |+-.+..|.+-+-+.+ |.|| ++-|+...|.
T Consensus 91 ~L~yQwg~~~fsY~Ts~DptnpngWSapq~lf~g~i~~~~~g~iD~~vI~D~~n~yLFfa~Dn-GkiYRs~~~i~nFP~ 168 (271)
T PF03664_consen 91 YLAYQWGPAAFSYSTSSDPTNPNGWSAPQPLFSGSISGSGTGPIDQWVICDDTNMYLFFAGDN-GKIYRSSMPIGNFPG 168 (271)
T ss_pred EEEEecCCCcceeecCCCCCCCccCCCCcccccccccCCCCCceeeEEEecCCceEEEEcCCC-CcEEEeccchhhCCC
Confidence 457776654 34444457789999999999753 1222334555554444 7877 5556665543
No 30
>COG5558 Transposase [DNA replication, recombination, and repair]
Probab=21.19 E-value=1.1e+02 Score=29.11 Aligned_cols=31 Identities=35% Similarity=0.736 Sum_probs=24.2
Q ss_pred eEEEEEeCCCCceeeEEEeeeeccCcccchhHHHH
Q 047538 113 FVLRIEENIGGRLRHAFIGIGFRERTEAYDFQAAL 147 (293)
Q Consensus 113 FVLRV~D~~~G~gR~AfIGiGF~ERsdAFDFnVAL 147 (293)
+|.||.|-.+| .|||.|+-+||+.=-|.-|+
T Consensus 117 y~f~iidl~t~----myvg~~~~~rse~da~eka~ 147 (261)
T COG5558 117 YVFRIIDIDTG----MYVGFGYSDRSEKDAFEKAL 147 (261)
T ss_pred EEEEEEEeccc----eEEEeeccccchhHHHHHHH
Confidence 47889987654 89999999999975555444
No 31
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=20.96 E-value=86 Score=35.14 Aligned_cols=14 Identities=43% Similarity=0.733 Sum_probs=5.5
Q ss_pred ccccCCCCCCCCCC
Q 047538 219 VICLKPLPPPPAPL 232 (293)
Q Consensus 219 ~~~~~lpppp~~~~ 232 (293)
|..=+.|||||+|.
T Consensus 550 lpggag~PPPPppl 563 (1102)
T KOG1924|consen 550 LPGGAGPPPPPPPL 563 (1102)
T ss_pred CCCCCCCCccCCCC
Confidence 33333344444333
Done!