Query 038162
Match_columns 127
No_of_seqs 118 out of 700
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:13:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038162.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038162hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01397 Terpene_synth: Terpen 100.0 5E-52 1.1E-56 320.9 13.0 123 2-127 22-145 (183)
2 cd00684 Terpene_cyclase_plant_ 100.0 1.1E-45 2.5E-50 320.9 12.3 123 3-127 28-153 (542)
3 PLN02279 ent-kaur-16-ene synth 100.0 9.9E-33 2.1E-37 249.4 9.3 100 23-127 268-371 (784)
4 PLN02592 ent-copalyl diphospha 100.0 5.5E-32 1.2E-36 244.8 9.4 103 23-127 308-417 (800)
5 PF11848 DUF3368: Domain of un 66.2 4.3 9.4E-05 24.7 1.6 25 73-97 20-44 (48)
6 cd07604 BAR_ASAPs The Bin/Amph 62.2 26 0.00057 27.8 5.8 85 3-99 13-100 (215)
7 PF00601 Flu_NS2: Influenza no 46.4 28 0.00061 24.6 3.2 41 6-49 47-87 (94)
8 PF08373 RAP: RAP domain; Int 45.5 19 0.00041 21.8 2.0 26 72-97 18-43 (58)
9 COG4738 Predicted transcriptio 45.3 50 0.0011 24.5 4.4 81 29-120 14-102 (124)
10 PF14164 YqzH: YqzH-like prote 43.4 11 0.00023 25.0 0.7 17 79-95 12-28 (64)
11 PF11000 DUF2840: Protein of u 41.3 17 0.00037 27.8 1.5 16 27-42 96-111 (149)
12 PF00233 PDEase_I: 3'5'-cyclic 39.7 17 0.00038 28.7 1.5 47 35-88 44-90 (237)
13 cd03569 VHS_Hrs_Vps27p VHS dom 38.0 78 0.0017 23.2 4.6 22 69-90 120-141 (142)
14 PF15508 NAAA-beta: beta subun 34.7 1.5E+02 0.0032 20.1 6.0 46 6-51 27-75 (95)
15 PLN02863 UDP-glucoronosyl/UDP- 34.5 67 0.0014 28.2 4.4 40 2-41 435-475 (477)
16 cd07603 BAR_ACAPs The Bin/Amph 33.7 1.7E+02 0.0037 22.8 6.1 50 6-55 16-66 (200)
17 PF02847 MA3: MA3 domain; Int 32.8 1.5E+02 0.0033 19.8 5.3 72 11-91 1-73 (113)
18 cd07641 BAR_ASAP1 The Bin/Amph 32.4 1.6E+02 0.0034 23.8 5.8 51 5-55 15-68 (215)
19 PF09278 MerR-DNA-bind: MerR, 32.0 86 0.0019 19.2 3.5 27 26-56 1-27 (65)
20 PF07862 Nif11: Nitrogen fixat 30.9 29 0.00063 20.7 1.1 14 80-93 35-48 (49)
21 PF13369 Transglut_core2: Tran 29.6 1E+02 0.0022 22.5 4.1 90 2-98 1-100 (152)
22 PF02084 Bindin: Bindin; Inte 29.1 65 0.0014 26.3 3.1 40 41-85 102-141 (238)
23 PF10390 ELL: RNA polymerase I 28.0 1.1E+02 0.0023 25.3 4.3 44 11-56 199-242 (284)
24 smart00027 EH Eps15 homology d 27.9 1.8E+02 0.004 19.2 6.8 62 23-91 24-85 (96)
25 PF07582 AP_endonuc_2_N: AP en 27.6 34 0.00073 21.7 1.0 12 77-88 5-16 (55)
26 PF08513 LisH: LisH; InterPro 27.5 37 0.0008 18.2 1.1 21 75-95 5-25 (27)
27 PF12017 Tnp_P_element: Transp 26.5 3.1E+02 0.0066 22.2 6.6 15 77-91 90-104 (236)
28 PF01963 TraB: TraB family; I 26.3 34 0.00073 26.3 1.0 13 78-90 246-258 (259)
29 PRK10941 hypothetical protein; 25.3 1.4E+02 0.003 24.5 4.5 40 3-42 33-74 (269)
30 PF09494 Slx4: Slx4 endonuclea 24.2 30 0.00065 22.1 0.3 24 81-104 34-61 (64)
31 PHA00438 hypothetical protein 23.2 41 0.00089 23.2 0.9 11 77-87 40-50 (81)
32 PF05384 DegS: Sensor protein 22.2 3.6E+02 0.0078 20.5 6.3 18 39-56 66-87 (159)
33 KOG2587 RNA polymerase III (C) 21.9 63 0.0014 29.4 2.0 31 77-116 402-432 (551)
34 PF03578 HGWP: HGWP repeat; I 21.7 27 0.00059 19.5 -0.2 15 79-93 7-21 (28)
35 PF14090 HTH_39: Helix-turn-he 21.0 44 0.00095 21.5 0.6 27 74-101 30-56 (70)
36 PF06248 Zw10: Centromere/kine 20.4 4.7E+02 0.01 23.3 7.2 18 4-21 19-36 (593)
37 COG1400 SEC65 Signal recogniti 20.2 62 0.0013 22.8 1.3 14 30-43 36-49 (93)
No 1
>PF01397 Terpene_synth: Terpene synthase, N-terminal domain; InterPro: IPR001906 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 2ONH_A 2ONG_B 3P5R_A 3P5P_A 3N0F_A 3N0G_B 3PYB_A 3PYA_A 3G4F_A 3G4D_B ....
Probab=100.00 E-value=5e-52 Score=320.86 Aligned_cols=123 Identities=46% Similarity=0.726 Sum_probs=107.1
Q ss_pred hhHHHHHHHHHHHHHHHHHhhh-cHhhhHHHHHHHHHhCcchhhHHHHHHHHHHHHHhhcccCCCCCCCChHHHHHHHHH
Q 038162 2 EGYRSRAEKLKNDVKQMFLEAA-DLLAKLELIDRICKLGLSYLFEEKIREVLVDTVAFLKNDTGCLQVKDLYATALCFKL 80 (127)
Q Consensus 2 ~~~~~~~~~LkeeVk~~l~~~~-~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FRL 80 (127)
+++.+++++||++||.||.... +++++|+|||+||||||+|||++||+++|++||+.|.. ......|||+|||+|||
T Consensus 22 ~~~~~~~~~Lk~~v~~~l~~~~~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~--~~~~~~dL~~~AL~FRL 99 (183)
T PF01397_consen 22 EKCKERAEELKEEVRNMLPASYPDPLEKLELIDTLQRLGISYHFEDEIKEILDSIYRSWDE--DNEEIDDLYTTALRFRL 99 (183)
T ss_dssp HHHHHHHHHHHHHHHHHHHSSSSHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHHTTTT--TSHTSSCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhhhccc--cccccCchhHHHHHHHH
Confidence 5678999999999999998754 89999999999999999999999999999999976654 22222599999999999
Q ss_pred HHhcCcceehhhhhccccccccccccccccchHHHHHHhHhhccCCC
Q 038162 81 LRQHGYEISQDVFLDFMDETGTTFSTSKCTDIKGPIELCEASQLALE 127 (127)
Q Consensus 81 LRqhGy~VS~DvF~~F~d~~G~~F~~~l~~DvkglL~LYeAS~L~~~ 127 (127)
||||||+||||||++|+|++| +|+.++.+||+|||+|||||||+++
T Consensus 100 LRqhGy~VS~DvF~~F~d~~g-~F~~~l~~Dv~glLsLYeAS~l~~~ 145 (183)
T PF01397_consen 100 LRQHGYYVSSDVFNKFKDEKG-NFKESLSNDVKGLLSLYEASHLRFH 145 (183)
T ss_dssp HHHTT----GGGGGGGBETTS-SBSGGGGGHHHHHHHHHHHHTT--T
T ss_pred HHHcCCcccHHHHhCcccCCC-ccchhhhHhHHHHHHHHHHHHccCC
Confidence 999999999999999999999 9999999999999999999999986
No 2
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=100.00 E-value=1.1e-45 Score=320.94 Aligned_cols=123 Identities=44% Similarity=0.727 Sum_probs=112.0
Q ss_pred hHHHHHHHHHHHHHHHHHh---hhcHhhhHHHHHHHHHhCcchhhHHHHHHHHHHHHHhhcccCCCCCCCChHHHHHHHH
Q 038162 3 GYRSRAEKLKNDVKQMFLE---AADLLAKLELIDRICKLGLSYLFEEKIREVLVDTVAFLKNDTGCLQVKDLYATALCFK 79 (127)
Q Consensus 3 ~~~~~~~~LkeeVk~~l~~---~~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FR 79 (127)
.+.+++++||++||+||.. ..|++++|++||+||||||+|||++||+++|++||++|... ......|||+|||+||
T Consensus 28 ~~~~~~~~lk~~v~~~~~~~~~~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L~~i~~~~~~~-~~~~~~dl~~~al~FR 106 (542)
T cd00684 28 ELEEEIEELKEEVRKMLEDSEYPVDLFERLWLIDRLQRLGISYHFEDEIKEILDYIYRYWTER-GESNEDDLYTTALGFR 106 (542)
T ss_pred HHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHcCchhhhHHHHHHHHHHHHHhhccc-ccccCCCHHHHHHHHH
Confidence 4678999999999999986 56999999999999999999999999999999999877531 1111269999999999
Q ss_pred HHHhcCcceehhhhhccccccccccccccccchHHHHHHhHhhccCCC
Q 038162 80 LLRQHGYEISQDVFLDFMDETGTTFSTSKCTDIKGPIELCEASQLALE 127 (127)
Q Consensus 80 LLRqhGy~VS~DvF~~F~d~~G~~F~~~l~~DvkglL~LYeAS~L~~~ 127 (127)
|||||||+||||||++|+|++| +|++++.+||+|||||||||||+++
T Consensus 107 lLR~~Gy~vs~dvf~~F~~~~g-~f~~~~~~d~~g~l~Ly~As~l~~~ 153 (542)
T cd00684 107 LLRQHGYNVSSDVFKKFKDEDG-KFKESLTQDVKGMLSLYEASHLSFP 153 (542)
T ss_pred HHHHcCCCcCHHHHhhhcCCCC-CcCchhhhhhHHHHHHHHHhhcCCC
Confidence 9999999999999999999999 9999999999999999999999986
No 3
>PLN02279 ent-kaur-16-ene synthase
Probab=99.98 E-value=9.9e-33 Score=249.42 Aligned_cols=100 Identities=33% Similarity=0.550 Sum_probs=89.6
Q ss_pred hcHhhhHHHHHHHHHhCcchhhHHHHHHHHHHHHHhhcccCCCCC-CCChHHHHHHHHHHHhcCcceehhhhhccccccc
Q 038162 23 ADLLAKLELIDRICKLGLSYLFEEKIREVLVDTVAFLKNDTGCLQ-VKDLYATALCFKLLRQHGYEISQDVFLDFMDETG 101 (127)
Q Consensus 23 ~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~-~~dL~~~AL~FRLLRqhGy~VS~DvF~~F~d~~G 101 (127)
.++++++++||+||||||+|||++||+++|+.+|++|.. +..+ ..|+++|||+|||||||||+||||||++|+|++
T Consensus 268 ~~~fe~l~lvd~L~rlGi~~hF~~EI~~~L~~~~~~~~~--~~~~~~~Dl~~tAl~FRLLR~hGy~VS~dvf~~F~~~~- 344 (784)
T PLN02279 268 LDQYARLSMVDTLERLGIDRHFRKEIKSVLDETYRYWLQ--GEEEIFLDLATCALAFRILRLNGYDVSSDPLKQFAEDH- 344 (784)
T ss_pred ccHHHHhHHHHHHHHhCCccccHHHHHHHHHHHHHhhcc--cccCCCCCHHHHHHHHHHHHHcCCCCChhHHhhcCCCc-
Confidence 578999999999999999999999999999999987754 2221 269999999999999999999999999998653
Q ss_pred ccccccc---ccchHHHHHHhHhhccCCC
Q 038162 102 TTFSTSK---CTDIKGPIELCEASQLALE 127 (127)
Q Consensus 102 ~~F~~~l---~~DvkglL~LYeAS~L~~~ 127 (127)
|++++ .+||+|||+||||||++++
T Consensus 345 --F~~~l~~~~~dv~gmL~LY~AS~l~~~ 371 (784)
T PLN02279 345 --FSDSLGGYLKDTGAVLELFRASQISYP 371 (784)
T ss_pred --ccchhcccchhhHHHHHHHHHHhcCCC
Confidence 99887 5899999999999999985
No 4
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.97 E-value=5.5e-32 Score=244.81 Aligned_cols=103 Identities=33% Similarity=0.533 Sum_probs=90.7
Q ss_pred hcHhhhHHHHHHHHHhCcchhhHHHHHHHHHHHHHhhcccCCC---C-CCCChHHHHHHHHHHHhcCcceehhhhhcccc
Q 038162 23 ADLLAKLELIDRICKLGLSYLFEEKIREVLVDTVAFLKNDTGC---L-QVKDLYATALCFKLLRQHGYEISQDVFLDFMD 98 (127)
Q Consensus 23 ~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~---~-~~~dL~~~AL~FRLLRqhGy~VS~DvF~~F~d 98 (127)
.+++++|++||+||||||+|||++||+++|+.+|++|...... . ...|+++|||+|||||||||+||||||++|++
T Consensus 308 ~d~fE~LwlVDtLqRLGIs~hF~~EI~~iLd~iy~~w~~~g~~~a~~~~~~Dld~TALaFRLLRqhGy~VS~DvF~~F~~ 387 (800)
T PLN02592 308 VDLFEHIWAVDRLQRLGISRYFEPEIKECIDYVHRYWTENGICWARNSHVHDIDDTAMGFRLLRLHGHQVSADVFKHFEK 387 (800)
T ss_pred CcHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhcCcccccCCCcCCHHHHHHHHHHHHHcCCCCChHHHHhhcC
Confidence 5899999999999999999999999999999999877541011 1 12699999999999999999999999999997
Q ss_pred cccccccccc---ccchHHHHHHhHhhccCCC
Q 038162 99 ETGTTFSTSK---CTDIKGPIELCEASQLALE 127 (127)
Q Consensus 99 ~~G~~F~~~l---~~DvkglL~LYeAS~L~~~ 127 (127)
+| +|+..+ .+|++|||+|||||||+++
T Consensus 388 -~g-~F~~~~ge~~~Dv~glL~LYeAS~l~~~ 417 (800)
T PLN02592 388 -GG-EFFCFAGQSTQAVTGMFNLYRASQVLFP 417 (800)
T ss_pred -CC-CccccccccccchHHHHHHHHHHhcCCC
Confidence 88 998655 7999999999999999975
No 5
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=66.17 E-value=4.3 Score=24.69 Aligned_cols=25 Identities=20% Similarity=0.383 Sum_probs=18.6
Q ss_pred HHHHHHHHHHhcCcceehhhhhccc
Q 038162 73 ATALCFKLLRQHGYEISQDVFLDFM 97 (127)
Q Consensus 73 ~~AL~FRLLRqhGy~VS~DvF~~F~ 97 (127)
.+.=.+.-|+++||++|++++..+.
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L 44 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEIL 44 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHH
Confidence 3444456669999999999888764
No 6
>cd07604 BAR_ASAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ASAPs (ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) with similarity to ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins) in that they contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and ankyrin (ANK) repeats. However, ASAPs contain an additional C-terminal SH3 domain. ASAPs function in regulating cell growth, migration, and invasion. Vertebrates contain at least three members, ASAP1, ASAP2, and ASAP3. ASAP1 and ASAP2 shows GTPase activating protein (GAP) activity towards Arf1 and Arf5. They do not show GAP activity towards Arf6, but is able to mediate
Probab=62.21 E-value=26 Score=27.77 Aligned_cols=85 Identities=24% Similarity=0.187 Sum_probs=53.4
Q ss_pred hHHHHHHHHHHHHHHHHHhhhc-HhhhHHHHHHHHHhCcchh--hHHHHHHHHHHHHHhhcccCCCCCCCChHHHHHHHH
Q 038162 3 GYRSRAEKLKNDVKQMFLEAAD-LLAKLELIDRICKLGLSYL--FEEKIREVLVDTVAFLKNDTGCLQVKDLYATALCFK 79 (127)
Q Consensus 3 ~~~~~~~~LkeeVk~~l~~~~~-~~~~L~lID~lqRLGi~yh--Fe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FR 79 (127)
.+..++++++.-+|.|.....+ .-....++++|+.||=..- -+++|..+|...- . -+..++=.+.
T Consensus 13 ~~~~~l~Kl~K~~k~~~~~g~~~~~~~~~F~~aL~~~g~~~~~~~~~~i~~~l~kF~---~---------~l~El~~~~~ 80 (215)
T cd07604 13 GDRVGLQKLKKAVKAIHNSGLAHVENELQFAEALEKLGSKALSREEEDLGAAFLKFS---V---------FTKELAALFK 80 (215)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHH---H---------HHHHHHHHHH
Confidence 3456778888888888865444 5567889999999994322 3335777775542 1 1333444455
Q ss_pred HHHhcCcceehhhhhccccc
Q 038162 80 LLRQHGYEISQDVFLDFMDE 99 (127)
Q Consensus 80 LLRqhGy~VS~DvF~~F~d~ 99 (127)
.|++|=-++-...+.+|..+
T Consensus 81 ~L~~~~~~~i~~pL~~f~k~ 100 (215)
T cd07604 81 NLMQNLNNIIMFPLDSLLKG 100 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 56666555555566666554
No 7
>PF00601 Flu_NS2: Influenza non-structural protein (NS2); InterPro: IPR000968 The Influenza A virus belongs to the class of ssRNA negative-strand viruses. Nonstructural protein 2 (NS2) may play a role in promoting normal replication of the genomic RNAs by preventing the replication of short-length RNA species []. NS1 and NS2 proteins are produced from the same gene by alternative splicing.; GO: 0006405 RNA export from nucleus, 0042025 host cell nucleus; PDB: 1PD3_B.
Probab=46.42 E-value=28 Score=24.61 Aligned_cols=41 Identities=12% Similarity=0.214 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHhhhcHhhhHHHHHHHHHhCcchhhHHHHH
Q 038162 6 SRAEKLKNDVKQMFLEAADLLAKLELIDRICKLGLSYLFEEKIR 49 (127)
Q Consensus 6 ~~~~~LkeeVk~~l~~~~~~~~~L~lID~lqRLGi~yhFe~EI~ 49 (127)
+++.-|.+++|..|..+.+.++++-+.-+||-| +--++||+
T Consensus 47 e~IrwlI~e~r~~l~~tensf~qItfmqaLqlL---lEve~eir 87 (94)
T PF00601_consen 47 EEIRWLIEEHRHRLKITENSFEQITFMQALQLL---LEVEQEIR 87 (94)
T ss_dssp HHHHHHHHHHHHC----TTSHHHHHHHHHHHHH---HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH---HHHHHHHH
Confidence 566777888888887777777776666555544 55555554
No 8
>PF08373 RAP: RAP domain; InterPro: IPR013584 The ~60-residue RAP (an acronym for RNA-binding domain abundant in Apicomplexans) domain is found in various proteins in eukaryotes. It is particularly abundant in apicomplexans and might mediate a range of cellular functions through its potential interactions with RNA []. The RAP domain consists of multiple blocks of charged and aromatics residues and is predicted to be composed of alpha helical and beta strand structures. Two predicted loop regions that are dominated by glycine and tryptophan residues are found before and after the central beta sheet []. Some proteins known to contain a RAP domain are listed below: Human hypothetical protein MGC5297, Mammalian FAST kinase domain-containing proteins (FASTKDs), Chlamydomonas reinhardtii chloroplastic trans-splicing factor Raa3.
Probab=45.45 E-value=19 Score=21.83 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhcCcceehhhhhccc
Q 038162 72 YATALCFKLLRQHGYEISQDVFLDFM 97 (127)
Q Consensus 72 ~~~AL~FRLLRqhGy~VS~DvF~~F~ 97 (127)
-.++|.=|+|+..||.|-+=.|-.+.
T Consensus 18 g~t~lk~r~L~~~G~~Vi~Ip~~eW~ 43 (58)
T PF08373_consen 18 GSTKLKHRHLKALGYKVISIPYYEWN 43 (58)
T ss_pred hHHHHHHHHHHHCCCEEEEecHHHHH
Confidence 57999999999999999776555544
No 9
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=45.26 E-value=50 Score=24.45 Aligned_cols=81 Identities=12% Similarity=0.204 Sum_probs=44.3
Q ss_pred HHHHHHHHHhCcchhhHHHHHHHHHHHHHhhccc--CCCCCC---CC--hHHHHHHHHHHHhcCcceehhhhhccccccc
Q 038162 29 LELIDRICKLGLSYLFEEKIREVLVDTVAFLKND--TGCLQV---KD--LYATALCFKLLRQHGYEISQDVFLDFMDETG 101 (127)
Q Consensus 29 L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~--~~~~~~---~d--L~~~AL~FRLLRqhGy~VS~DvF~~F~d~~G 101 (127)
-++|+.|++|||++.-. +.-+| .... ..+... .. =..+|++.|.||.+|. |.----.+ -.+|
T Consensus 14 ~~~ie~L~~lgi~R~vA------~tlv~--L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gW-V~~R~eKK--kGKG 82 (124)
T COG4738 14 YEIIELLRILGIPRNVA------TTLVC--LAKGDEASSREIERVSGLRQPEVSIAMRYLRENGW-VDEREEKK--KGKG 82 (124)
T ss_pred HHHHHHHHHcCCCchHH------HHHHH--HhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccc-cchHHhcc--cCCC
Confidence 46899999999998752 22233 2220 011111 12 2479999999999994 42222222 3344
Q ss_pred ccccc-ccccchHHHHHHhH
Q 038162 102 TTFST-SKCTDIKGPIELCE 120 (127)
Q Consensus 102 ~~F~~-~l~~DvkglL~LYe 120 (127)
.-.+. .|+.+...+++-++
T Consensus 83 RPik~Y~Lt~~~~eIvs~ie 102 (124)
T COG4738 83 RPIKLYRLTVPFDEIVSEIE 102 (124)
T ss_pred CCceEEEecCcHHHHHHHHH
Confidence 11221 35667777766554
No 10
>PF14164 YqzH: YqzH-like protein
Probab=43.45 E-value=11 Score=24.97 Aligned_cols=17 Identities=35% Similarity=0.516 Sum_probs=14.2
Q ss_pred HHHHhcCcceehhhhhc
Q 038162 79 KLLRQHGYEISQDVFLD 95 (127)
Q Consensus 79 RLLRqhGy~VS~DvF~~ 95 (127)
+-|||.||++.++.+..
T Consensus 12 ~~l~QYg~d~~~~pls~ 28 (64)
T PF14164_consen 12 NCLRQYGYDVECMPLSD 28 (64)
T ss_pred HHHHHhCCcccCCCCCH
Confidence 56899999999887665
No 11
>PF11000 DUF2840: Protein of unknown function (DUF2840); InterPro: IPR021263 This bacterial family of proteins have no known function.
Probab=41.32 E-value=17 Score=27.77 Aligned_cols=16 Identities=38% Similarity=0.453 Sum_probs=13.6
Q ss_pred hhHHHHHHHHHhCcch
Q 038162 27 AKLELIDRICKLGLSY 42 (127)
Q Consensus 27 ~~L~lID~lqRLGi~y 42 (127)
.-|+.||+++.|||+-
T Consensus 96 ~VL~~IDaiEalGidp 111 (149)
T PF11000_consen 96 RVLQAIDAIEALGIDP 111 (149)
T ss_pred HHHHHHhHHHHcCCCh
Confidence 3488999999999974
No 12
>PF00233 PDEase_I: 3'5'-cyclic nucleotide phosphodiesterase; InterPro: IPR002073 The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction. PDE enzymes are often targets for pharmacological inhibition due to their unique tissue distribution, structural properties, and functional properties. Inhibitors include: Roflumilast for chronic obstructive pulmonary disease and asthma [], Sildenafil for erectile dysfunction [] and Cilostazol for peripheral arterial occlusive disease [], amongst others. Retinal 3',5'-cGMP phosphodiesterase is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion. This entry represents the catalytic domain of PDE which is multihelical and can be divided into three subdomains.; GO: 0004114 3',5'-cyclic-nucleotide phosphodiesterase activity, 0007165 signal transduction; PDB: 3I8V_A 3TVX_A 2QYK_A 1ZKL_A 3G3N_A 4DFF_B 2OUS_B 3SNL_A 2OUY_A 2OUP_B ....
Probab=39.71 E-value=17 Score=28.69 Aligned_cols=47 Identities=26% Similarity=0.234 Sum_probs=35.1
Q ss_pred HHHhCcchhhHHHHHHHHHHHHHhhcccCCCCCCCChHHHHHHHHHHHhcCcce
Q 038162 35 ICKLGLSYLFEEKIREVLVDTVAFLKNDTGCLQVKDLYATALCFKLLRQHGYEI 88 (127)
Q Consensus 35 lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~V 88 (127)
+..=|+..-|.-..+..|..+| ++.+.-.-|.+|+.|++|+..|+++
T Consensus 44 v~HpG~~N~flv~~~~~LA~~Y-------~d~SvLE~~H~~~~~~lL~~~~~ni 90 (237)
T PF00233_consen 44 VDHPGVNNAFLVKTNSPLAILY-------NDRSVLENHHCALAFQLLRKEECNI 90 (237)
T ss_dssp TT-SSSCHHHHHHTTSHHHHHT-------TTSSHHHHHHHHHHHHHHTSTTTTT
T ss_pred CCCCccccchhhccccchhhhc-------CccCCccccHHHHHHHHHHhhhhhh
Confidence 4456888889888888888888 2223334678999999999888854
No 13
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=37.99 E-value=78 Score=23.24 Aligned_cols=22 Identities=14% Similarity=0.314 Sum_probs=17.3
Q ss_pred CChHHHHHHHHHHHhcCcceeh
Q 038162 69 KDLYATALCFKLLRQHGYEISQ 90 (127)
Q Consensus 69 ~dL~~~AL~FRLLRqhGy~VS~ 90 (127)
.++..+.=.+..||..||..++
T Consensus 120 ~~l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 120 PQLKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred cccHHHHHHHHHHHHcCCCCCC
Confidence 3666677788999999998764
No 14
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=34.74 E-value=1.5e+02 Score=20.13 Aligned_cols=46 Identities=17% Similarity=0.253 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHhhhcHhhhHHHHHHHHHh---CcchhhHHHHHHH
Q 038162 6 SRAEKLKNDVKQMFLEAADLLAKLELIDRICKL---GLSYLFEEKIREV 51 (127)
Q Consensus 6 ~~~~~LkeeVk~~l~~~~~~~~~L~lID~lqRL---Gi~yhFe~EI~~~ 51 (127)
.++..+.+.++.++......-.-+.+|+.+-+. -++.-|.+||+-+
T Consensus 27 ~~i~~l~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~~~~~~~~EirGI 75 (95)
T PF15508_consen 27 DEIRELIEVLKDLLQSFVPSGKVLDFVDKLLPHLLRYLPQPYAEEIRGI 75 (95)
T ss_pred HHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 344445555555554311111234444444332 3355667777655
No 15
>PLN02863 UDP-glucoronosyl/UDP-glucosyl transferase family protein
Probab=34.46 E-value=67 Score=28.18 Aligned_cols=40 Identities=20% Similarity=0.299 Sum_probs=28.6
Q ss_pred hhHHHHHHHHHHHHHHHHHhhh-cHhhhHHHHHHHHHhCcc
Q 038162 2 EGYRSRAEKLKNDVKQMFLEAA-DLLAKLELIDRICKLGLS 41 (127)
Q Consensus 2 ~~~~~~~~~LkeeVk~~l~~~~-~~~~~L~lID~lqRLGi~ 41 (127)
+.+.+++.++++.++.-+.... +.-.--++|+.|+++|+.
T Consensus 435 ~~~r~~a~~l~e~a~~Av~~gGSS~~~l~~~v~~i~~~~~~ 475 (477)
T PLN02863 435 QVERERAKELRRAALDAIKERGSSVKDLDGFVKHVVELGLE 475 (477)
T ss_pred HHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHhccC
Confidence 4567888889988888876432 222335689999999985
No 16
>cd07603 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=33.66 E-value=1.7e+02 Score=22.80 Aligned_cols=50 Identities=16% Similarity=0.135 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHhhhc-HhhhHHHHHHHHHhCcchhhHHHHHHHHHHH
Q 038162 6 SRAEKLKNDVKQMFLEAAD-LLAKLELIDRICKLGLSYLFEEKIREVLVDT 55 (127)
Q Consensus 6 ~~~~~LkeeVk~~l~~~~~-~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i 55 (127)
.++++|+..++.|+....+ ....-.++++|+.||-.+-=.+.|..+|...
T Consensus 16 ~~l~kl~K~~~~~~~ag~~~~~a~~~F~~~L~~~~~~~~~d~~i~~~l~kF 66 (200)
T cd07603 16 TRLEKLLKLCNGMVDSGKTYVNANSLFVNSLNDLSDYFRDDSLVQNCLNKF 66 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH
Confidence 4556666666666654333 3347889999999997543344555555544
No 17
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=32.83 E-value=1.5e+02 Score=19.81 Aligned_cols=72 Identities=10% Similarity=0.024 Sum_probs=40.0
Q ss_pred HHHHHHHHHHhhhcHhhhHHHHHHHHHhCcchhhHHHHH-HHHHHHHHhhcccCCCCCCCChHHHHHHHHHHHhcCccee
Q 038162 11 LKNDVKQMFLEAADLLAKLELIDRICKLGLSYLFEEKIR-EVLVDTVAFLKNDTGCLQVKDLYATALCFKLLRQHGYEIS 89 (127)
Q Consensus 11 LkeeVk~~l~~~~~~~~~L~lID~lqRLGi~yhFe~EI~-~~L~~i~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS 89 (127)
+|..|+..|.+.-+.-..-+.+..|+.|+++ .+..|+= .++.... + . +..+-..++.-+.-|-+.|.--+
T Consensus 1 ~rk~i~~~l~ey~~~~d~~ea~~~l~el~~~-~~~~~vv~~~l~~~l----e--~--~~~~r~~~~~Ll~~L~~~~~~~~ 71 (113)
T PF02847_consen 1 LRKKIFSILMEYFSSGDVDEAVECLKELKLP-SQHHEVVKVILECAL----E--E--KKSYREYYSKLLSHLCKRKLISK 71 (113)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHHHHTT-G-GGHHHHHHHHHHHHH----T--S--SHHHHHHHHHHHHHHHHTTSS-H
T ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHhCCC-ccHHHHHHHHHHHHh----h--c--cHHHHHHHHHHHHHHHhcCCCCH
Confidence 4667777777654334557788889999999 6666654 4444443 1 1 11233345555666666665333
Q ss_pred hh
Q 038162 90 QD 91 (127)
Q Consensus 90 ~D 91 (127)
.+
T Consensus 72 ~~ 73 (113)
T PF02847_consen 72 EQ 73 (113)
T ss_dssp HH
T ss_pred HH
Confidence 33
No 18
>cd07641 BAR_ASAP1 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP1 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 1) is also known as DDEF1 (Development and Differentiation Enhancing Factor 1), AMAP1, centaurin beta-4, or PAG2. ASAP1 is an Arf GTPase activating protein (GAP) with activity towards Arf1 and Arf5 but not Arf6 However, it has been shown to bind GTP-Arf6 stably without GAP activity. It has been implicated in cell growth, migration, and survival, as well as in tumor invasion and malignancy. It binds paxillin and cortactin, two components of invadopodia which are essential for tumor invasiveness. It also binds focal adhesion kinase (FAK) and the SH2/SH3 adaptor CrkL. ASAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Ar
Probab=32.40 E-value=1.6e+02 Score=23.82 Aligned_cols=51 Identities=16% Similarity=0.271 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHhhh-cHhhhHHHHHHHHHhCcch--hhHHHHHHHHHHH
Q 038162 5 RSRAEKLKNDVKQMFLEAA-DLLAKLELIDRICKLGLSY--LFEEKIREVLVDT 55 (127)
Q Consensus 5 ~~~~~~LkeeVk~~l~~~~-~~~~~L~lID~lqRLGi~y--hFe~EI~~~L~~i 55 (127)
..++++++.-|+.|..+.. =.-..-.+|+.|++||=.. -=+.+|..+|...
T Consensus 15 e~~L~Kl~K~~kam~~SG~~yv~n~~~f~~~l~~Lg~~~~~~dd~~i~~a~~kf 68 (215)
T cd07641 15 RTALQKVKKSVKAIYNSGQDHVQNEENYAQALDKFGSNFLSRDNPDLGTAFVKF 68 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchhHHHHHHHH
Confidence 4577889999999987643 3445677999999999544 3356676666554
No 19
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=32.02 E-value=86 Score=19.16 Aligned_cols=27 Identities=41% Similarity=0.746 Sum_probs=20.2
Q ss_pred hhhHHHHHHHHHhCcchhhHHHHHHHHHHHH
Q 038162 26 LAKLELIDRICKLGLSYLFEEKIREVLVDTV 56 (127)
Q Consensus 26 ~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~ 56 (127)
+++|.+|=.++.||++- +||++.| .++
T Consensus 1 v~rL~~I~~~r~lGfsL---~eI~~~l-~l~ 27 (65)
T PF09278_consen 1 VERLQFIRRLRELGFSL---EEIRELL-ELY 27 (65)
T ss_dssp HHHHHHHHHHHHTT--H---HHHHHHH-HHC
T ss_pred ChHHHHHHHHHHcCCCH---HHHHHHH-hcc
Confidence 46799999999999984 7888888 443
No 20
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=30.85 E-value=29 Score=20.68 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=10.9
Q ss_pred HHHhcCcceehhhh
Q 038162 80 LLRQHGYEISQDVF 93 (127)
Q Consensus 80 LLRqhGy~VS~DvF 93 (127)
+-|.+||.+|++-+
T Consensus 35 lA~~~Gy~ft~~el 48 (49)
T PF07862_consen 35 LAREAGYDFTEEEL 48 (49)
T ss_pred HHHHcCCCCCHHHh
Confidence 45999999997643
No 21
>PF13369 Transglut_core2: Transglutaminase-like superfamily
Probab=29.58 E-value=1e+02 Score=22.47 Aligned_cols=90 Identities=18% Similarity=0.199 Sum_probs=55.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhcHhhhHHHHHHH--HHhCcchhh---HHHHHHHHHHHHHhhcccCCCCCCCChHHHHH
Q 038162 2 EGYRSRAEKLKNDVKQMFLEAADLLAKLELIDRI--CKLGLSYLF---EEKIREVLVDTVAFLKNDTGCLQVKDLYATAL 76 (127)
Q Consensus 2 ~~~~~~~~~LkeeVk~~l~~~~~~~~~L~lID~l--qRLGi~yhF---e~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL 76 (127)
+.+..+++++-.+||..+....++.++++.|..+ +.+|....- .+--...|..+. ... . + .-+--+++
T Consensus 1 ~~~~~~Ld~la~~v~~~~~~~~~~~~~l~al~~~l~~~~gF~~~~~~y~~~~n~~l~~vL--~~r--~--G-~Pi~L~il 73 (152)
T PF13369_consen 1 EAVLQRLDALAAQVRQRLPARASPREKLEALNDVLYQELGFSGNSENYYDPENSFLHKVL--ERR--R--G-IPISLAIL 73 (152)
T ss_pred ChHHHHHHHHHHHHHHHccccCCHHHHHHHHHHHHHHHcCCCCCccccCChHhhhHHHHH--hcC--C--C-CcHHHHHH
Confidence 4577899999999999987666777788777654 788876422 121244455554 111 1 1 12444555
Q ss_pred HHHHHHhcCcceeh-----hhhhcccc
Q 038162 77 CFKLLRQHGYEISQ-----DVFLDFMD 98 (127)
Q Consensus 77 ~FRLLRqhGy~VS~-----DvF~~F~d 98 (127)
.=-+.|.-|.++.+ -++-++.+
T Consensus 74 y~~va~rlGl~~~~v~~Pgh~l~r~~~ 100 (152)
T PF13369_consen 74 YLEVARRLGLPAEPVNFPGHFLVRVRS 100 (152)
T ss_pred HHHHHHHcCCeEEEEecCCEEEEEEec
Confidence 55677888888765 34555554
No 22
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=29.08 E-value=65 Score=26.35 Aligned_cols=40 Identities=30% Similarity=0.346 Sum_probs=26.6
Q ss_pred chhhHHHHHHHHHHHHHhhcccCCCCCCCChHHHHHHHHHHHhcC
Q 038162 41 SYLFEEKIREVLVDTVAFLKNDTGCLQVKDLYATALCFKLLRQHG 85 (127)
Q Consensus 41 ~yhFe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FRLLRqhG 85 (127)
|----+.|+.+|-.+- -+ --.++.|.|+.-|..|-||.|-
T Consensus 102 SAKvm~~ikavLgaTK---iD--LPVDINDPYDlGLLLRhLRHHS 141 (238)
T PF02084_consen 102 SAKVMEDIKAVLGATK---ID--LPVDINDPYDLGLLLRHLRHHS 141 (238)
T ss_pred cHHHHHHHHHHhcccc---cc--cccccCChhhHHHHHHHHHHHH
Confidence 3344567777776552 11 1134479999999999999983
No 23
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=27.98 E-value=1.1e+02 Score=25.26 Aligned_cols=44 Identities=25% Similarity=0.311 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhhhcHhhhHHHHHHHHHhCcchhhHHHHHHHHHHHH
Q 038162 11 LKNDVKQMFLEAADLLAKLELIDRICKLGLSYLFEEKIREVLVDTV 56 (127)
Q Consensus 11 LkeeVk~~l~~~~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~ 56 (127)
+++.|=.+|. -.|+.+-||+..|+|-||.--=.++|..+|+.|-
T Consensus 199 lReRvIHLLA--LkpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va 242 (284)
T PF10390_consen 199 LRERVIHLLA--LKPYKKPELLLRLQKDGLSPKDKDELDSILQEVA 242 (284)
T ss_dssp HHHHHHHHHH--HS-EEHHHHHHHHHHH---HHHHHHHHHHHHHCC
T ss_pred ccccchhhhh--cCccccHHHHHHHHhcCCChHHHHHHHHHHHHHh
Confidence 5666766664 4667778999999999999988899999999995
No 24
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=27.94 E-value=1.8e+02 Score=19.16 Aligned_cols=62 Identities=19% Similarity=0.258 Sum_probs=35.7
Q ss_pred hcHhhhHHHHHHHHHhCcchhhHHHHHHHHHHHHHhhcccCCCCCCCChHHHHHHHHHHHhcCcceehh
Q 038162 23 ADLLAKLELIDRICKLGLSYLFEEKIREVLVDTVAFLKNDTGCLQVKDLYATALCFKLLRQHGYEISQD 91 (127)
Q Consensus 23 ~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~D 91 (127)
+..+..-++...+.++|++ ++|++.++..+ ..+..+..+ .+=+-.++..---.+.|++||+.
T Consensus 24 ~G~Is~~el~~~l~~~~~~---~~ev~~i~~~~---d~~~~g~I~-~~eF~~~~~~~~~~~~g~~~~~~ 85 (96)
T smart00027 24 DGTVTGAQAKPILLKSGLP---QTLLAKIWNLA---DIDNDGELD-KDEFALAMHLIYRKLNGYPIPAS 85 (96)
T ss_pred CCeEeHHHHHHHHHHcCCC---HHHHHHHHHHh---cCCCCCCcC-HHHHHHHHHHHHHHHcCCCCCcc
Confidence 3456666777788888976 46777766554 222001111 12223455555566789999875
No 25
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=27.56 E-value=34 Score=21.75 Aligned_cols=12 Identities=42% Similarity=0.711 Sum_probs=8.4
Q ss_pred HHHHHHhcCcce
Q 038162 77 CFKLLRQHGYEI 88 (127)
Q Consensus 77 ~FRLLRqhGy~V 88 (127)
.|+.||+.||+=
T Consensus 5 i~~~L~~~GYdG 16 (55)
T PF07582_consen 5 IFSALREIGYDG 16 (55)
T ss_dssp HHHHHHHTT--S
T ss_pred HHHHHHHcCCCc
Confidence 489999999974
No 26
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=27.48 E-value=37 Score=18.17 Aligned_cols=21 Identities=24% Similarity=0.545 Sum_probs=13.5
Q ss_pred HHHHHHHHhcCcceehhhhhc
Q 038162 75 ALCFKLLRQHGYEISQDVFLD 95 (127)
Q Consensus 75 AL~FRLLRqhGy~VS~DvF~~ 95 (127)
.|-.+=|..+||.-+...|.+
T Consensus 5 ~lI~~YL~~~Gy~~tA~~f~~ 25 (27)
T PF08513_consen 5 QLIYDYLVENGYKETAKAFAK 25 (27)
T ss_dssp HHHHHHHHHCT-HHHHHHHHH
T ss_pred HHHHHHHHHCCcHHHHHHHHh
Confidence 455666777888777776653
No 27
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=26.48 E-value=3.1e+02 Score=22.15 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=12.0
Q ss_pred HHHHHHhcCcceehh
Q 038162 77 CFKLLRQHGYEISQD 91 (127)
Q Consensus 77 ~FRLLRqhGy~VS~D 91 (127)
+++-|+..||+.|+.
T Consensus 90 ~Y~yL~kk~~pLPs~ 104 (236)
T PF12017_consen 90 AYNYLRKKGYPLPSV 104 (236)
T ss_pred HHHHHHHcCCCCCCH
Confidence 477787779999886
No 28
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=26.29 E-value=34 Score=26.34 Aligned_cols=13 Identities=38% Similarity=0.889 Sum_probs=11.3
Q ss_pred HHHHHhcCcceeh
Q 038162 78 FKLLRQHGYEISQ 90 (127)
Q Consensus 78 FRLLRqhGy~VS~ 90 (127)
-.+||+.||.|++
T Consensus 246 l~lLr~~Gy~V~~ 258 (259)
T PF01963_consen 246 LDLLRKKGYTVEP 258 (259)
T ss_pred HHHHHhCCceeec
Confidence 3899999999976
No 29
>PRK10941 hypothetical protein; Provisional
Probab=25.33 E-value=1.4e+02 Score=24.47 Aligned_cols=40 Identities=13% Similarity=0.073 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHHHHHHHhhhcHhhhHHHHHHH--HHhCcch
Q 038162 3 GYRSRAEKLKNDVKQMFLEAADLLAKLELIDRI--CKLGLSY 42 (127)
Q Consensus 3 ~~~~~~~~LkeeVk~~l~~~~~~~~~L~lID~l--qRLGi~y 42 (127)
.+..+++.|..+|+..+....++.++++.+..+ +.+|.+-
T Consensus 33 ~~~~~L~~l~~~~~~~l~~~~~~~~~l~~L~~~fy~~lgF~G 74 (269)
T PRK10941 33 DVYDELERLVSLAREEISQLLPQDEQLEKLIALFYGEWGFGG 74 (269)
T ss_pred HHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHhCCCC
Confidence 355678888888888886666666666666554 5555443
No 30
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=24.25 E-value=30 Score=22.08 Aligned_cols=24 Identities=25% Similarity=0.625 Sum_probs=20.4
Q ss_pred HHhcCc----ceehhhhhcccccccccc
Q 038162 81 LRQHGY----EISQDVFLDFMDETGTTF 104 (127)
Q Consensus 81 LRqhGy----~VS~DvF~~F~d~~G~~F 104 (127)
|+++|. .|+++....|.|.+|=.|
T Consensus 34 L~~~g~~~~~~~~~~~l~~~lD~~gIt~ 61 (64)
T PF09494_consen 34 LKASGIGFDRKVDPSKLKEWLDSQGITF 61 (64)
T ss_pred HHHcCCCccceeCHHHHHHHHHHCCcee
Confidence 559999 999999999999998333
No 31
>PHA00438 hypothetical protein
Probab=23.22 E-value=41 Score=23.19 Aligned_cols=11 Identities=55% Similarity=0.905 Sum_probs=9.2
Q ss_pred HHHHHHhcCcc
Q 038162 77 CFKLLRQHGYE 87 (127)
Q Consensus 77 ~FRLLRqhGy~ 87 (127)
.-++||++||.
T Consensus 40 ~i~~lR~~G~S 50 (81)
T PHA00438 40 EIRLLRQAGYS 50 (81)
T ss_pred hHHHHHHcCCc
Confidence 45899999995
No 32
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=22.23 E-value=3.6e+02 Score=20.53 Aligned_cols=18 Identities=33% Similarity=0.425 Sum_probs=13.0
Q ss_pred Ccchhh----HHHHHHHHHHHH
Q 038162 39 GLSYLF----EEKIREVLVDTV 56 (127)
Q Consensus 39 Gi~yhF----e~EI~~~L~~i~ 56 (127)
-+|.+| +++|+++-+...
T Consensus 66 eVS~~f~~ysE~dik~AYe~A~ 87 (159)
T PF05384_consen 66 EVSRNFDRYSEEDIKEAYEEAH 87 (159)
T ss_pred HHHhhhcccCHHHHHHHHHHHH
Confidence 457777 899998855543
No 33
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=21.89 E-value=63 Score=29.45 Aligned_cols=31 Identities=23% Similarity=0.331 Sum_probs=24.9
Q ss_pred HHHHHHhcCcceehhhhhccccccccccccccccchHHHH
Q 038162 77 CFKLLRQHGYEISQDVFLDFMDETGTTFSTSKCTDIKGPI 116 (127)
Q Consensus 77 ~FRLLRqhGy~VS~DvF~~F~d~~G~~F~~~l~~DvkglL 116 (127)
-||+++|.| .|+.+.-++|-=-.+ +|++.||
T Consensus 402 l~R~l~~k~-~veekqv~~~Alm~~--------Kd~r~~L 432 (551)
T KOG2587|consen 402 LFRLLLQKK-HVEEKQVEDFALMPA--------KDARDML 432 (551)
T ss_pred HHHHHHhcc-cchHHHHHHhhcccc--------ccHHHHH
Confidence 489999999 899998888755554 6888875
No 34
>PF03578 HGWP: HGWP repeat; InterPro: IPR005213 This short (30 amino acids) repeat is found in a number of plant proteins. It contains a conserved HGWP motif, hence its name. The function of these proteins is unknown.
Probab=21.74 E-value=27 Score=19.52 Aligned_cols=15 Identities=33% Similarity=0.530 Sum_probs=11.6
Q ss_pred HHHHhcCcceehhhh
Q 038162 79 KLLRQHGYEISQDVF 93 (127)
Q Consensus 79 RLLRqhGy~VS~DvF 93 (127)
+-||.||..|+|-..
T Consensus 7 Wc~rLhGW~i~ppll 21 (28)
T PF03578_consen 7 WCLRLHGWPIMPPLL 21 (28)
T ss_pred hheeeccCcccCcce
Confidence 458999999988643
No 35
>PF14090 HTH_39: Helix-turn-helix domain
Probab=21.02 E-value=44 Score=21.51 Aligned_cols=27 Identities=30% Similarity=0.491 Sum_probs=16.5
Q ss_pred HHHHHHHHHhcCcceehhhhhccccccc
Q 038162 74 TALCFKLLRQHGYEISQDVFLDFMDETG 101 (127)
Q Consensus 74 ~AL~FRLLRqhGy~VS~DvF~~F~d~~G 101 (127)
.|=+=.=||++||+|.+. .....+.+|
T Consensus 30 ~~aRI~eLR~~G~~I~t~-~~~~~~~~g 56 (70)
T PF14090_consen 30 LAARISELRKKGYPIVTE-WVTVPTEDG 56 (70)
T ss_pred HHHHHHHHHHcCCeeeEE-EEEeeccCC
Confidence 344444589999999775 233344444
No 36
>PF06248 Zw10: Centromere/kinetochore Zw10; InterPro: IPR009361 Zeste white 10 (ZW10) was initially identified as a mitotic checkpoint protein involved in chromosome segregation, and then implicated in targeting cytoplasmic dynein and dynactin to mitotic kinetochores, but it is also important in non-dividing cells. These include cytoplasmic dynein targeting to Golgi and other membranes, and SNARE-mediated ER-Golgi trafficking [, ]. Dominant-negative ZW10, anti-ZW10 antibody, and ZW10 RNA interference (RNAi) cause Golgi dispersal. ZW10 RNAi also disperse endosomes and lysosomes []. Drosophila kinetochore components Rough deal (Rod) and Zw10 are required for the proper functioning of the metaphase checkpoint in flies []. The eukaryotic spindle assembly checkpoint (SAC) monitors microtubule attachment to kinetochores and prevents anaphase onset until all kinetochores are aligned on the metaphase plate. It is an essential surveillance mechanism that ensures high fidelity chromosome segregation during mitosis. In higher eukaryotes, cytoplasmic dynein is involved in silencing the SAC by removing the checkpoint proteins Mad2 and the Rod-Zw10-Zwilch complex (RZZ) from aligned kinetochores [, , ].; GO: 0007067 mitosis, 0000775 chromosome, centromeric region, 0005634 nucleus
Probab=20.35 E-value=4.7e+02 Score=23.31 Aligned_cols=18 Identities=33% Similarity=0.497 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 038162 4 YRSRAEKLKNDVKQMFLE 21 (127)
Q Consensus 4 ~~~~~~~LkeeVk~~l~~ 21 (127)
..++++++|.+|+.++..
T Consensus 19 L~~~i~~~k~eV~~~I~~ 36 (593)
T PF06248_consen 19 LSRRIEELKEEVHSMINK 36 (593)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 347888999999999875
No 37
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=20.22 E-value=62 Score=22.79 Aligned_cols=14 Identities=29% Similarity=0.453 Sum_probs=11.8
Q ss_pred HHHHHHHHhCcchh
Q 038162 30 ELIDRICKLGLSYL 43 (127)
Q Consensus 30 ~lID~lqRLGi~yh 43 (127)
+++++++.||+.+-
T Consensus 36 ei~~a~~~LGl~~~ 49 (93)
T COG1400 36 EIAEALRELGLKPK 49 (93)
T ss_pred HHHHHHHHcCCCee
Confidence 58899999999883
Done!