Query 041361
Match_columns 127
No_of_seqs 105 out of 714
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 06:21:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041361.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041361hhsearch_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 1E-38 2.2E-43 243.7 9.0 104 22-127 1-111 (183)
2 cd00684 Terpene_cyclase_plant_ 100.0 2.5E-36 5.5E-41 260.2 11.4 115 12-127 1-119 (542)
3 PLN02279 ent-kaur-16-ene synth 99.8 1.3E-21 2.8E-26 175.4 7.0 90 37-127 245-336 (784)
4 PLN02592 ent-copalyl diphospha 99.8 4.7E-21 1E-25 171.8 6.1 91 37-127 285-381 (800)
5 cd07604 BAR_ASAPs The Bin/Amph 74.7 21 0.00047 27.9 7.6 55 37-91 12-69 (215)
6 PF02084 Bindin: Bindin; Inte 54.0 15 0.00034 29.4 3.1 35 81-120 107-141 (238)
7 PF00601 Flu_NS2: Influenza no 54.0 34 0.00074 23.7 4.4 43 40-85 46-88 (94)
8 cd07603 BAR_ACAPs The Bin/Amph 51.2 78 0.0017 24.4 6.6 52 39-90 14-66 (200)
9 PF14164 YqzH: YqzH-like prote 51.0 10 0.00022 24.6 1.4 13 114-126 12-24 (64)
10 PF08373 RAP: RAP domain; Int 47.3 14 0.00031 22.1 1.7 18 106-123 17-34 (58)
11 PF11000 DUF2840: Protein of u 45.5 14 0.0003 27.7 1.6 15 63-77 97-111 (149)
12 PF11848 DUF3368: Domain of un 42.2 13 0.00028 22.2 0.8 19 108-126 20-38 (48)
13 PF07499 RuvA_C: RuvA, C-termi 40.1 52 0.0011 19.3 3.3 23 66-91 6-28 (47)
14 smart00027 EH Eps15 homology d 38.4 1.1E+02 0.0025 19.9 7.2 61 59-126 25-85 (96)
15 cd03569 VHS_Hrs_Vps27p VHS dom 36.9 1.1E+02 0.0024 22.2 5.2 22 104-125 120-141 (142)
16 PF03578 HGWP: HGWP repeat; I 36.7 14 0.0003 20.2 0.3 11 115-125 8-18 (28)
17 cd07641 BAR_ASAP1 The Bin/Amph 36.6 1.5E+02 0.0033 23.5 6.2 52 39-90 14-68 (215)
18 PLN02863 UDP-glucoronosyl/UDP- 35.9 71 0.0015 27.7 4.7 40 37-76 435-475 (477)
19 PF02847 MA3: MA3 domain; Int 35.7 1.2E+02 0.0026 20.1 5.0 35 47-82 2-36 (113)
20 COG1400 SEC65 Signal recogniti 31.5 29 0.00062 24.0 1.3 13 65-77 36-48 (93)
21 PF15469 Sec5: Exocyst complex 29.4 1.3E+02 0.0029 22.1 4.8 33 44-76 138-171 (182)
22 PF07582 AP_endonuc_2_N: AP en 29.0 32 0.0007 21.4 1.1 11 112-122 5-15 (55)
23 cd07639 BAR_ACAP1 The Bin/Amph 28.9 2.3E+02 0.005 22.0 6.1 53 39-91 14-67 (200)
24 PHA00438 hypothetical protein 28.5 30 0.00065 23.4 0.9 11 112-122 40-50 (81)
25 PF06248 Zw10: Centromere/kine 28.0 3.2E+02 0.0069 24.2 7.5 69 37-118 17-90 (593)
26 PF01963 TraB: TraB family; I 26.5 30 0.00065 26.4 0.8 13 113-125 246-258 (259)
27 PF09124 Endonuc-dimeris: T4 r 25.7 49 0.0011 20.7 1.5 31 61-92 16-46 (54)
28 PF09278 MerR-DNA-bind: MerR, 25.6 1.2E+02 0.0026 18.2 3.3 27 61-91 1-27 (65)
29 PF07862 Nif11: Nitrogen fixat 25.4 33 0.00072 20.1 0.7 11 115-125 35-45 (49)
30 PF00233 PDEase_I: 3'5'-cyclic 24.8 48 0.001 25.9 1.7 46 72-124 46-91 (237)
31 PF11576 DUF3236: Protein of u 23.4 53 0.0012 24.7 1.6 13 63-75 141-153 (154)
32 PRK10941 hypothetical protein; 23.1 2E+02 0.0042 23.2 4.9 35 35-69 30-64 (269)
33 PF15508 NAAA-beta: beta subun 22.7 2.4E+02 0.0052 18.7 6.2 23 64-86 50-75 (95)
34 PF15460 SAS4: Something about 21.3 2.9E+02 0.0064 19.2 5.7 35 58-92 38-88 (101)
35 cd07642 BAR_ASAP2 The Bin/Amph 21.3 3.1E+02 0.0068 21.7 5.6 48 43-90 18-68 (215)
36 PF08784 RPA_C: Replication pr 21.1 1.5E+02 0.0033 19.6 3.4 46 43-91 45-90 (102)
37 PF05384 DegS: Sensor protein 21.0 3.7E+02 0.0079 20.2 6.9 18 74-91 66-87 (159)
38 cd07640 BAR_ASAP3 The Bin/Amph 20.8 1.9E+02 0.0041 23.0 4.2 37 43-79 18-55 (213)
39 PF10390 ELL: RNA polymerase I 20.3 1.8E+02 0.0039 23.6 4.2 45 45-91 198-242 (284)
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=1e-38 Score=243.74 Aligned_cols=104 Identities=47% Similarity=0.808 Sum_probs=85.2
Q ss_pred CcccccccCcccch------HHHHHHHHHHHHHHHHHHHHhh-hhhhhHHHHHHHHHHhCcchhhHHHHHHHHHHHHHhh
Q 041361 22 WKYDFIQSLHSKYK------EEGCRSRAEKLTNDVKQMFLEA-ADLLAKLELIDRICKLGLSYLFEEQIREILVDTVAFL 94 (127)
Q Consensus 22 W~~~fl~s~~~~~~------~~~~~~~~e~Lk~~vr~~l~~~-~~~~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~~~~ 94 (127)
||++|++++.+.+. .+++.+++++||++||.||... .++.++|+|||+||||||+|||++||+++|+++|+.+
T Consensus 1 W~d~fl~s~s~~~~~~~~~~~~~~~~~~~~Lk~~v~~~l~~~~~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~ 80 (183)
T PF01397_consen 1 WGDDFLQSLSPSYTACMQSEDEKCKERAEELKEEVRNMLPASYPDPLEKLELIDTLQRLGISYHFEDEIKEILDSIYRSW 80 (183)
T ss_dssp TTHHHHHHTBHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHSSSSHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHHTT
T ss_pred CCCceecCCCCcchhccchhHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhhhc
Confidence 99999976555443 3789999999999999999876 4899999999999999999999999999999999643
Q ss_pred cccCCCCCCCCHHHHHHHHHHHhhCCCCCCCCC
Q 041361 95 KNDTGCLEVKDLYATALCFKLLRQHGYEISQGI 127 (127)
Q Consensus 95 ~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~DV 127 (127)
.. ......|||+|||+|||||||||+|||||
T Consensus 81 ~~--~~~~~~dL~~~AL~FRLLRqhGy~VS~Dv 111 (183)
T PF01397_consen 81 DE--DNEEIDDLYTTALRFRLLRQHGYYVSSDV 111 (183)
T ss_dssp TT--TSHTSSCHHHHHHHHHHHHHTT----GGG
T ss_pred cc--cccccCchhHHHHHHHHHHHcCCcccHHH
Confidence 32 11122599999999999999999999997
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=2.5e-36 Score=260.25 Aligned_cols=115 Identities=43% Similarity=0.745 Sum_probs=96.5
Q ss_pred CCCCCCCCCCCcccccccCcccchHH-HHHHHHHHHHHHHHHHHHh---hhhhhhHHHHHHHHHHhCcchhhHHHHHHHH
Q 041361 12 RQSANYKPNIWKYDFIQSLHSKYKEE-GCRSRAEKLTNDVKQMFLE---AADLLAKLELIDRICKLGLSYLFEEQIREIL 87 (127)
Q Consensus 12 r~~a~~~ps~W~~~fl~s~~~~~~~~-~~~~~~e~Lk~~vr~~l~~---~~~~~~~L~lID~lqRLGI~yhFe~EI~~~L 87 (127)
|++++|+||+||++++.+..+.+... .+.+++++||++||+||.. +.|+.++|+|||+||||||+|||++||+++|
T Consensus 1 r~~~~~~~~~w~~~~~~s~~~~~~~~~~~~~~~~~lk~~v~~~~~~~~~~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L 80 (542)
T cd00684 1 RPSANFPPSLWGDDHFLSLSSDYSEEDELEEEIEELKEEVRKMLEDSEYPVDLFERLWLIDRLQRLGISYHFEDEIKEIL 80 (542)
T ss_pred CCCCCCCCCcCCCcceeecCCCcchhHHHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHcCchhhhHHHHHHHH
Confidence 68999999999995555454444333 6889999999999999986 5799999999999999999999999999999
Q ss_pred HHHHHhhcccCCCCCCCCHHHHHHHHHHHhhCCCCCCCCC
Q 041361 88 VDTVAFLKNDTGCLEVKDLYATALCFKLLRQHGYEISQGI 127 (127)
Q Consensus 88 ~~i~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~DV 127 (127)
++||+.+... ......|||+|||+|||||||||+|||||
T Consensus 81 ~~i~~~~~~~-~~~~~~dl~~~al~FRlLR~~Gy~vs~dv 119 (542)
T cd00684 81 DYIYRYWTER-GESNEDDLYTTALGFRLLRQHGYNVSSDV 119 (542)
T ss_pred HHHHHhhccc-ccccCCCHHHHHHHHHHHHHcCCCcCHHH
Confidence 9999754320 10122699999999999999999999997
No 3
>PLN02279 ent-kaur-16-ene synthase
Probab=99.85 E-value=1.3e-21 Score=175.38 Aligned_cols=90 Identities=26% Similarity=0.444 Sum_probs=70.0
Q ss_pred HHHHHHHHHHHHHHHHHHHh--hhhhhhHHHHHHHHHHhCcchhhHHHHHHHHHHHHHhhcccCCCCCCCCHHHHHHHHH
Q 041361 37 EGCRSRAEKLTNDVKQMFLE--AADLLAKLELIDRICKLGLSYLFEEQIREILVDTVAFLKNDTGCLEVKDLYATALCFK 114 (127)
Q Consensus 37 ~~~~~~~e~Lk~~vr~~l~~--~~~~~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FR 114 (127)
+++.++++.+..+....+.. +.+.++++++||+||||||+|||++||+++|+.+|+.+... ......|||+|||+||
T Consensus 245 ~~~~~yL~~~~~~~~g~vP~~yp~~~fe~l~lvd~L~rlGi~~hF~~EI~~~L~~~~~~~~~~-~~~~~~Dl~~tAl~FR 323 (784)
T PLN02279 245 AGCLRYLRSLLQKFGNAVPTVYPLDQYARLSMVDTLERLGIDRHFRKEIKSVLDETYRYWLQG-EEEIFLDLATCALAFR 323 (784)
T ss_pred hHHHHHHHHHHHhcCCCCCCCCcccHHHHhHHHHHHHHhCCccccHHHHHHHHHHHHHhhccc-ccCCCCCHHHHHHHHH
Confidence 45556666655444333443 36899999999999999999999999999999999654320 1111269999999999
Q ss_pred HHhhCCCCCCCCC
Q 041361 115 LLRQHGYEISQGI 127 (127)
Q Consensus 115 LLRqhGy~VS~DV 127 (127)
|||||||+|||||
T Consensus 324 LLR~hGy~VS~dv 336 (784)
T PLN02279 324 ILRLNGYDVSSDP 336 (784)
T ss_pred HHHHcCCCCChhH
Confidence 9999999999997
No 4
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.83 E-value=4.7e-21 Score=171.82 Aligned_cols=91 Identities=29% Similarity=0.473 Sum_probs=68.9
Q ss_pred HHHHHHHHHHHHHHHHHHHh--hhhhhhHHHHHHHHHHhCcchhhHHHHHHHHHHHHHhhcccCCC---C-CCCCHHHHH
Q 041361 37 EGCRSRAEKLTNDVKQMFLE--AADLLAKLELIDRICKLGLSYLFEEQIREILVDTVAFLKNDTGC---L-EVKDLYATA 110 (127)
Q Consensus 37 ~~~~~~~e~Lk~~vr~~l~~--~~~~~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~---~-~~~dL~~~A 110 (127)
+++.++++.+..+....+.. +.+++++|+|||+||||||+|||++||+++|+.+|+.+...... . ...|||+||
T Consensus 285 ~~cl~YL~~~~~k~~GgVP~vyP~d~fE~LwlVDtLqRLGIs~hF~~EI~~iLd~iy~~w~~~g~~~a~~~~~~Dld~TA 364 (800)
T PLN02592 285 ENCLEYLNKAVQRFNGGVPNVYPVDLFEHIWAVDRLQRLGISRYFEPEIKECIDYVHRYWTENGICWARNSHVHDIDDTA 364 (800)
T ss_pred hHHHHHHHHHHHHcCCCCCCCCCCcHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhcCcccccCCCcCCHHHHH
Confidence 44555555544443333333 36899999999999999999999999999999999744321000 1 126999999
Q ss_pred HHHHHHhhCCCCCCCCC
Q 041361 111 LCFKLLRQHGYEISQGI 127 (127)
Q Consensus 111 L~FRLLRqhGy~VS~DV 127 (127)
|+|||||||||+|||||
T Consensus 365 LaFRLLRqhGy~VS~Dv 381 (800)
T PLN02592 365 MGFRLLRLHGHQVSADV 381 (800)
T ss_pred HHHHHHHHcCCCCChHH
Confidence 99999999999999986
No 5
>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=74.71 E-value=21 Score=27.90 Aligned_cols=55 Identities=25% Similarity=0.314 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhh-hhhHHHHHHHHHHhCcchh--hHHHHHHHHHHHH
Q 041361 37 EGCRSRAEKLTNDVKQMFLEAAD-LLAKLELIDRICKLGLSYL--FEEQIREILVDTV 91 (127)
Q Consensus 37 ~~~~~~~e~Lk~~vr~~l~~~~~-~~~~L~lID~lqRLGI~yh--Fe~EI~~~L~~i~ 91 (127)
+....+++++++.++.|..+..+ ......++++|+.||=.+- .+.+|..+|.+.-
T Consensus 12 ~~~~~~l~Kl~K~~k~~~~~g~~~~~~~~~F~~aL~~~g~~~~~~~~~~i~~~l~kF~ 69 (215)
T cd07604 12 EGDRVGLQKLKKAVKAIHNSGLAHVENELQFAEALEKLGSKALSREEEDLGAAFLKFS 69 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHHH
Confidence 34556778888888888865433 4667889999999993322 3346888887653
No 6
>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=54.04 E-value=15 Score=29.37 Aligned_cols=35 Identities=29% Similarity=0.450 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhhcccCCCCCCCCHHHHHHHHHHHhhCC
Q 041361 81 EQIREILVDTVAFLKNDTGCLEVKDLYATALCFKLLRQHG 120 (127)
Q Consensus 81 ~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FRLLRqhG 120 (127)
+.|+++|.-.- .+ --.+..|-|+.-|..|-||+|-
T Consensus 107 ~~ikavLgaTK---iD--LPVDINDPYDlGLLLRhLRHHS 141 (238)
T PF02084_consen 107 EDIKAVLGATK---ID--LPVDINDPYDLGLLLRHLRHHS 141 (238)
T ss_pred HHHHHHhcccc---cc--cccccCChhhHHHHHHHHHHHH
Confidence 56777776542 21 1124468999999999999984
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=53.99 E-value=34 Score=23.69 Aligned_cols=43 Identities=12% Similarity=0.194 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhCcchhhHHHHHH
Q 041361 40 RSRAEKLTNDVKQMFLEAADLLAKLELIDRICKLGLSYLFEEQIRE 85 (127)
Q Consensus 40 ~~~~e~Lk~~vr~~l~~~~~~~~~L~lID~lqRLGI~yhFe~EI~~ 85 (127)
.+++.-|.+++|..|..++++++++-+.-+||-| |--+.||+.
T Consensus 46 fe~IrwlI~e~r~~l~~tensf~qItfmqaLqlL---lEve~eirt 88 (94)
T PF00601_consen 46 FEEIRWLIEEHRHRLKITENSFEQITFMQALQLL---LEVEQEIRT 88 (94)
T ss_dssp HHHHHHHHHHHHHC----TTSHHHHHHHHHHHHH---HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH---HHHHHHHHH
Confidence 3566666788888777777888887777666644 566666664
No 8
>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=51.18 E-value=78 Score=24.37 Aligned_cols=52 Identities=15% Similarity=0.113 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhhh-hhHHHHHHHHHHhCcchhhHHHHHHHHHHH
Q 041361 39 CRSRAEKLTNDVKQMFLEAADL-LAKLELIDRICKLGLSYLFEEQIREILVDT 90 (127)
Q Consensus 39 ~~~~~e~Lk~~vr~~l~~~~~~-~~~L~lID~lqRLGI~yhFe~EI~~~L~~i 90 (127)
...++++|...++.|+....+. .....++++|+.||-.+-=+..|..+|.+.
T Consensus 14 l~~~l~kl~K~~~~~~~ag~~~~~a~~~F~~~L~~~~~~~~~d~~i~~~l~kF 66 (200)
T cd07603 14 LETRLEKLLKLCNGMVDSGKTYVNANSLFVNSLNDLSDYFRDDSLVQNCLNKF 66 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH
Confidence 4456666667777777543333 457889999999997543456677777665
No 9
>PF14164 YqzH: YqzH-like protein
Probab=50.97 E-value=10 Score=24.59 Aligned_cols=13 Identities=38% Similarity=0.590 Sum_probs=10.5
Q ss_pred HHHhhCCCCCCCC
Q 041361 114 KLLRQHGYEISQG 126 (127)
Q Consensus 114 RLLRqhGy~VS~D 126 (127)
+-|||+||++.++
T Consensus 12 ~~l~QYg~d~~~~ 24 (64)
T PF14164_consen 12 NCLRQYGYDVECM 24 (64)
T ss_pred HHHHHhCCcccCC
Confidence 5789999998764
No 10
>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=47.31 E-value=14 Score=22.07 Aligned_cols=18 Identities=28% Similarity=0.429 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHhhCCCCC
Q 041361 106 LYATALCFKLLRQHGYEI 123 (127)
Q Consensus 106 L~~~AL~FRLLRqhGy~V 123 (127)
+-.++|+=|+|+..||+|
T Consensus 17 ~g~t~lk~r~L~~~G~~V 34 (58)
T PF08373_consen 17 TGSTKLKHRHLKALGYKV 34 (58)
T ss_pred chHHHHHHHHHHHCCCEE
Confidence 357999999999999987
No 11
>PF11000 DUF2840: Protein of unknown function (DUF2840); InterPro: IPR021263 This bacterial family of proteins have no known function.
Probab=45.51 E-value=14 Score=27.72 Aligned_cols=15 Identities=40% Similarity=0.496 Sum_probs=12.6
Q ss_pred HHHHHHHHHHhCcch
Q 041361 63 KLELIDRICKLGLSY 77 (127)
Q Consensus 63 ~L~lID~lqRLGI~y 77 (127)
-|..||+|+.|||+-
T Consensus 97 VL~~IDaiEalGidp 111 (149)
T PF11000_consen 97 VLQAIDAIEALGIDP 111 (149)
T ss_pred HHHHHhHHHHcCCCh
Confidence 467899999999873
No 12
>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=42.15 E-value=13 Score=22.17 Aligned_cols=19 Identities=26% Similarity=0.361 Sum_probs=11.7
Q ss_pred HHHHHHHHHhhCCCCCCCC
Q 041361 108 ATALCFKLLRQHGYEISQG 126 (127)
Q Consensus 108 ~~AL~FRLLRqhGy~VS~D 126 (127)
++.-.+.-|+++||++|++
T Consensus 20 ~~~~~l~~l~~~g~~is~~ 38 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPK 38 (48)
T ss_pred hHHHHHHHHHHcCcccCHH
Confidence 3333445558888888765
No 13
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=40.15 E-value=52 Score=19.26 Aligned_cols=23 Identities=9% Similarity=0.278 Sum_probs=19.2
Q ss_pred HHHHHHHhCcchhhHHHHHHHHHHHH
Q 041361 66 LIDRICKLGLSYLFEEQIREILVDTV 91 (127)
Q Consensus 66 lID~lqRLGI~yhFe~EI~~~L~~i~ 91 (127)
.+.+|.-|| +-+.||..++.++.
T Consensus 6 ~~~AL~~LG---y~~~e~~~av~~~~ 28 (47)
T PF07499_consen 6 ALEALISLG---YSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHTT---S-HHHHHHHHHHHH
T ss_pred HHHHHHHcC---CCHHHHHHHHHHhh
Confidence 577899999 55789999999996
No 14
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=38.39 E-value=1.1e+02 Score=19.95 Aligned_cols=61 Identities=21% Similarity=0.280 Sum_probs=34.6
Q ss_pred hhhhHHHHHHHHHHhCcchhhHHHHHHHHHHHHHhhcccCCCCCCCCHHHHHHHHHHHhhCCCCCCCC
Q 041361 59 DLLAKLELIDRICKLGLSYLFEEQIREILVDTVAFLKNDTGCLEVKDLYATALCFKLLRQHGYEISQG 126 (127)
Q Consensus 59 ~~~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~D 126 (127)
..+..-++...+.++|++ ++|++.++..+ ..+.....+ .+=+-.++..---.+.|+++++.
T Consensus 25 G~Is~~el~~~l~~~~~~---~~ev~~i~~~~---d~~~~g~I~-~~eF~~~~~~~~~~~~g~~~~~~ 85 (96)
T smart00027 25 GTVTGAQAKPILLKSGLP---QTLLAKIWNLA---DIDNDGELD-KDEFALAMHLIYRKLNGYPIPAS 85 (96)
T ss_pred CeEeHHHHHHHHHHcCCC---HHHHHHHHHHh---cCCCCCCcC-HHHHHHHHHHHHHHHcCCCCCcc
Confidence 345555566777788875 46777776654 221001011 12334555556667789999864
No 15
>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=36.87 E-value=1.1e+02 Score=22.16 Aligned_cols=22 Identities=14% Similarity=0.314 Sum_probs=18.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCCC
Q 041361 104 KDLYATALCFKLLRQHGYEISQ 125 (127)
Q Consensus 104 ~dL~~~AL~FRLLRqhGy~VS~ 125 (127)
.+|-.+.=.|..||..||..++
T Consensus 120 ~~l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 120 PQLKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred cccHHHHHHHHHHHHcCCCCCC
Confidence 4677777889999999998875
No 16
>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=36.70 E-value=14 Score=20.19 Aligned_cols=11 Identities=45% Similarity=0.733 Sum_probs=9.2
Q ss_pred HHhhCCCCCCC
Q 041361 115 LLRQHGYEISQ 125 (127)
Q Consensus 115 LLRqhGy~VS~ 125 (127)
-||.||..|.|
T Consensus 8 c~rLhGW~i~p 18 (28)
T PF03578_consen 8 CLRLHGWPIMP 18 (28)
T ss_pred heeeccCcccC
Confidence 47999999876
No 17
>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=36.56 E-value=1.5e+02 Score=23.50 Aligned_cols=52 Identities=13% Similarity=0.222 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHHHhh-hhhhhHHHHHHHHHHhCcch--hhHHHHHHHHHHH
Q 041361 39 CRSRAEKLTNDVKQMFLEA-ADLLAKLELIDRICKLGLSY--LFEEQIREILVDT 90 (127)
Q Consensus 39 ~~~~~e~Lk~~vr~~l~~~-~~~~~~L~lID~lqRLGI~y--hFe~EI~~~L~~i 90 (127)
....++++|+-|+.|+.+. .-.-...-+|+.|.+||=.. -=+.+|.++|.+.
T Consensus 14 ~e~~L~Kl~K~~kam~~SG~~yv~n~~~f~~~l~~Lg~~~~~~dd~~i~~a~~kf 68 (215)
T cd07641 14 DRTALQKVKKSVKAIYNSGQDHVQNEENYAQALDKFGSNFLSRDNPDLGTAFVKF 68 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchhHHHHHHHH
Confidence 3457788888888888664 33345677999999999433 2246777776654
No 18
>PLN02863 UDP-glucoronosyl/UDP-glucosyl transferase family protein
Probab=35.87 E-value=71 Score=27.69 Aligned_cols=40 Identities=20% Similarity=0.278 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhh-hhhhhHHHHHHHHHHhCcc
Q 041361 37 EGCRSRAEKLTNDVKQMFLEA-ADLLAKLELIDRICKLGLS 76 (127)
Q Consensus 37 ~~~~~~~e~Lk~~vr~~l~~~-~~~~~~L~lID~lqRLGI~ 76 (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 456677778888777776542 1222334579999999975
No 19
>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=35.67 E-value=1.2e+02 Score=20.14 Aligned_cols=35 Identities=11% Similarity=0.077 Sum_probs=16.3
Q ss_pred HHHHHHHHHhhhhhhhHHHHHHHHHHhCcchhhHHH
Q 041361 47 TNDVKQMFLEAADLLAKLELIDRICKLGLSYLFEEQ 82 (127)
Q Consensus 47 k~~vr~~l~~~~~~~~~L~lID~lqRLGI~yhFe~E 82 (127)
|++++..|.+.-+.-..-+.+..|+.|++. .|..|
T Consensus 2 rk~i~~~l~ey~~~~d~~ea~~~l~el~~~-~~~~~ 36 (113)
T PF02847_consen 2 RKKIFSILMEYFSSGDVDEAVECLKELKLP-SQHHE 36 (113)
T ss_dssp HHHHHHHHHHHHHHT-HHHHHHHHHHTT-G-GGHHH
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHhCCC-ccHHH
Confidence 445555555432222334455566667777 44433
No 20
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=31.46 E-value=29 Score=24.03 Aligned_cols=13 Identities=31% Similarity=0.542 Sum_probs=11.5
Q ss_pred HHHHHHHHhCcch
Q 041361 65 ELIDRICKLGLSY 77 (127)
Q Consensus 65 ~lID~lqRLGI~y 77 (127)
++.++++.||+.+
T Consensus 36 ei~~a~~~LGl~~ 48 (93)
T COG1400 36 EIAEALRELGLKP 48 (93)
T ss_pred HHHHHHHHcCCCe
Confidence 4788999999999
No 21
>PF15469 Sec5: Exocyst complex component Sec5
Probab=29.44 E-value=1.3e+02 Score=22.06 Aligned_cols=33 Identities=18% Similarity=0.320 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHhh-hhhhhHHHHHHHHHHhCcc
Q 041361 44 EKLTNDVKQMFLEA-ADLLAKLELIDRICKLGLS 76 (127)
Q Consensus 44 e~Lk~~vr~~l~~~-~~~~~~L~lID~lqRLGI~ 76 (127)
+.+++.+..-|.++ .+.-+.+.+|+.|..||+.
T Consensus 138 ~~~r~~l~~~L~~~~~s~~~~~~~i~~Ll~L~~~ 171 (182)
T PF15469_consen 138 EEFREKLWEKLLSPPSSQEEFLKLIRKLLELNVE 171 (182)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhCCCC
Confidence 33334343333333 3556778888888888764
No 22
>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=28.96 E-value=32 Score=21.41 Aligned_cols=11 Identities=45% Similarity=0.912 Sum_probs=7.9
Q ss_pred HHHHHhhCCCC
Q 041361 112 CFKLLRQHGYE 122 (127)
Q Consensus 112 ~FRLLRqhGy~ 122 (127)
-|+.||+.||+
T Consensus 5 i~~~L~~~GYd 15 (55)
T PF07582_consen 5 IFSALREIGYD 15 (55)
T ss_dssp HHHHHHHTT--
T ss_pred HHHHHHHcCCC
Confidence 48899999996
No 23
>cd07639 BAR_ACAP1 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, 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. ACAP1 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 1), also called centaurin beta-1, is an Arf6-specific GTPase activating protein (GAP) which mediates Arf6 signaling. Arf6 is involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration. ACAP1 also participates in the cargo sorting and recycling of the transferrin receptor and integrin beta1. It may also play a role in innate immune responses. ACAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=28.93 E-value=2.3e+02 Score=22.02 Aligned_cols=53 Identities=21% Similarity=0.165 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHhh-hhhhhHHHHHHHHHHhCcchhhHHHHHHHHHHHH
Q 041361 39 CRSRAEKLTNDVKQMFLEA-ADLLAKLELIDRICKLGLSYLFEEQIREILVDTV 91 (127)
Q Consensus 39 ~~~~~e~Lk~~vr~~l~~~-~~~~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~ 91 (127)
...++++|...++.|+.+. .=....-.+++.|+-||-.+.=+..|..+|.+.-
T Consensus 14 le~~l~kl~K~~k~~~~agk~~~~a~~~F~~~L~~f~~~~~~D~~i~~~l~kFs 67 (200)
T cd07639 14 LETRLEKLVKLGSGMLEGGRHYCAASRAFVDGLCDLAHHGPKDPMMAECLEKFS 67 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCchhHHHHHHHH
Confidence 4456667777777777653 3335567789999999853333344777776653
No 24
>PHA00438 hypothetical protein
Probab=28.54 E-value=30 Score=23.36 Aligned_cols=11 Identities=55% Similarity=0.905 Sum_probs=8.8
Q ss_pred HHHHHhhCCCC
Q 041361 112 CFKLLRQHGYE 122 (127)
Q Consensus 112 ~FRLLRqhGy~ 122 (127)
..|+|||+||-
T Consensus 40 ~i~~lR~~G~S 50 (81)
T PHA00438 40 EIRLLRQAGYS 50 (81)
T ss_pred hHHHHHHcCCc
Confidence 45899999983
No 25
>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=27.99 E-value=3.2e+02 Score=24.16 Aligned_cols=69 Identities=22% Similarity=0.304 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhh-h----hhhhHHHHHHHHHHhCcchhhHHHHHHHHHHHHHhhcccCCCCCCCCHHHHHH
Q 041361 37 EGCRSRAEKLTNDVKQMFLEA-A----DLLAKLELIDRICKLGLSYLFEEQIREILVDTVAFLKNDTGCLEVKDLYATAL 111 (127)
Q Consensus 37 ~~~~~~~e~Lk~~vr~~l~~~-~----~~~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL 111 (127)
....++++++|.+|+.++... . .....-.+|+.+..|+ +||+++++... ... ...+|...+=
T Consensus 17 ~~L~~~i~~~k~eV~~~I~~~y~df~~~~~~~~~L~~~~~~l~------~eI~d~l~~~~--~~~-----i~~~l~~a~~ 83 (593)
T PF06248_consen 17 SRLSRRIEELKEEVHSMINKKYSDFSPSLQSAKDLIERSKSLA------REINDLLQSEI--ENE-----IQPQLRDAAE 83 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH------HHHHHHHHhhc--cch-----hHHHHHHHHH
Confidence 445688899999999988753 1 1222334455555443 77777766632 110 1135666666
Q ss_pred HHHHHhh
Q 041361 112 CFKLLRQ 118 (127)
Q Consensus 112 ~FRLLRq 118 (127)
.+..|++
T Consensus 84 e~~~L~~ 90 (593)
T PF06248_consen 84 ELQELKR 90 (593)
T ss_pred HHHHHHH
Confidence 6666654
No 26
>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=26.47 E-value=30 Score=26.44 Aligned_cols=13 Identities=38% Similarity=0.889 Sum_probs=11.2
Q ss_pred HHHHhhCCCCCCC
Q 041361 113 FKLLRQHGYEISQ 125 (127)
Q Consensus 113 FRLLRqhGy~VS~ 125 (127)
-.+||+.||.|++
T Consensus 246 l~lLr~~Gy~V~~ 258 (259)
T PF01963_consen 246 LDLLRKKGYTVEP 258 (259)
T ss_pred HHHHHhCCceeec
Confidence 3899999999975
No 27
>PF09124 Endonuc-dimeris: T4 recombination endonuclease VII, dimerisation; InterPro: IPR015208 This entry represents a dimerisation domain predominantly found in Bacteriophage T4 recombination endonuclease VII. It adopts a helical secondary structure, with three alpha helices oriented parallel to each other. As well as mediating dimerisation of the protein, this domain is also involved in binding to the DNA major groove []. ; PDB: 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=25.65 E-value=49 Score=20.71 Aligned_cols=31 Identities=29% Similarity=0.452 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHHhCcchhhHHHHHHHHHHHHH
Q 041361 61 LAKLELIDRICKLGLSYLFEEQIREILVDTVA 92 (127)
Q Consensus 61 ~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~~ 92 (127)
+.+-+||..++..|++|- +..-++.|-.+|+
T Consensus 16 l~k~eMiaem~~~G~~y~-~~~tK~~Lvk~fk 46 (54)
T PF09124_consen 16 LTKPEMIAEMDSYGFEYN-EKDTKAQLVKIFK 46 (54)
T ss_dssp S-HHHHHHHHHHTT-----TTS-HHHHHHHHH
T ss_pred cCHHHHHHHHHHhCCcCC-ccccHHHHHHHHH
Confidence 345679999999999997 4555556666663
No 28
>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=25.58 E-value=1.2e+02 Score=18.21 Aligned_cols=27 Identities=41% Similarity=0.764 Sum_probs=20.0
Q ss_pred hhHHHHHHHHHHhCcchhhHHHHHHHHHHHH
Q 041361 61 LAKLELIDRICKLGLSYLFEEQIREILVDTV 91 (127)
Q Consensus 61 ~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~ 91 (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 36789999999999764 6999998 443
No 29
>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=25.39 E-value=33 Score=20.09 Aligned_cols=11 Identities=36% Similarity=0.900 Sum_probs=9.2
Q ss_pred HHhhCCCCCCC
Q 041361 115 LLRQHGYEISQ 125 (127)
Q Consensus 115 LLRqhGy~VS~ 125 (127)
+-|.+||.+++
T Consensus 35 lA~~~Gy~ft~ 45 (49)
T PF07862_consen 35 LAREAGYDFTE 45 (49)
T ss_pred HHHHcCCCCCH
Confidence 46999999985
No 30
>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=24.75 E-value=48 Score=25.88 Aligned_cols=46 Identities=24% Similarity=0.208 Sum_probs=33.8
Q ss_pred HhCcchhhHHHHHHHHHHHHHhhcccCCCCCCCCHHHHHHHHHHHhhCCCCCC
Q 041361 72 KLGLSYLFEEQIREILVDTVAFLKNDTGCLEVKDLYATALCFKLLRQHGYEIS 124 (127)
Q Consensus 72 RLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS 124 (127)
.=|+.--|....+..|-.+| .. .+.-.=|.+|+.|++|+..|+++=
T Consensus 46 HpG~~N~flv~~~~~LA~~Y--~d-----~SvLE~~H~~~~~~lL~~~~~nil 91 (237)
T PF00233_consen 46 HPGVNNAFLVKTNSPLAILY--ND-----RSVLENHHCALAFQLLRKEECNIL 91 (237)
T ss_dssp -SSSCHHHHHHTTSHHHHHT--TT-----SSHHHHHHHHHHHHHHTSTTTTTT
T ss_pred CCccccchhhccccchhhhc--Cc-----cCCccccHHHHHHHHHHhhhhhhh
Confidence 44888888888888888887 21 111246889999999999998863
No 31
>PF11576 DUF3236: Protein of unknown function (DUF3236); InterPro: IPR012019 This family of proteins with unknown function appears to be restricted to Methanobacteria. ; PDB: 3BRC_B.
Probab=23.35 E-value=53 Score=24.68 Aligned_cols=13 Identities=31% Similarity=0.731 Sum_probs=10.0
Q ss_pred HHHHHHHHHHhCc
Q 041361 63 KLELIDRICKLGL 75 (127)
Q Consensus 63 ~L~lID~lqRLGI 75 (127)
..+|+++|+|+|+
T Consensus 141 ~~E~~~AL~RiG~ 153 (154)
T PF11576_consen 141 KKEMIEALKRIGI 153 (154)
T ss_dssp HHHHHHHHHTTT-
T ss_pred HHHHHHHHHHhCC
Confidence 3578899999996
No 32
>PRK10941 hypothetical protein; Provisional
Probab=23.10 E-value=2e+02 Score=23.24 Aligned_cols=35 Identities=11% Similarity=0.062 Sum_probs=24.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHH
Q 041361 35 KEEGCRSRAEKLTNDVKQMFLEAADLLAKLELIDR 69 (127)
Q Consensus 35 ~~~~~~~~~e~Lk~~vr~~l~~~~~~~~~L~lID~ 69 (127)
..+.+..+++.|..+|+..+....++.+++..+..
T Consensus 30 ~~~~~~~~L~~l~~~~~~~l~~~~~~~~~l~~L~~ 64 (269)
T PRK10941 30 PSQDVYDELERLVSLAREEISQLLPQDEQLEKLIA 64 (269)
T ss_pred CHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHH
Confidence 34567788899999999988765566666554433
No 33
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=22.73 E-value=2.4e+02 Score=18.74 Aligned_cols=23 Identities=30% Similarity=0.533 Sum_probs=12.0
Q ss_pred HHHHHHHHHh---CcchhhHHHHHHH
Q 041361 64 LELIDRICKL---GLSYLFEEQIREI 86 (127)
Q Consensus 64 L~lID~lqRL---GI~yhFe~EI~~~ 86 (127)
+.+|+.+-+. -+...|.+||+-+
T Consensus 50 ~~~v~~~~~~l~~~~~~~~~~EirGI 75 (95)
T PF15508_consen 50 LDFVDKLLPHLLRYLPQPYAEEIRGI 75 (95)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 4445444432 2355566777665
No 34
>PF15460 SAS4: Something about silencing, SAS, complex subunit 4
Probab=21.29 E-value=2.9e+02 Score=19.16 Aligned_cols=35 Identities=29% Similarity=0.299 Sum_probs=28.2
Q ss_pred hhhhhHHHHHHHHHHh-Ccc---------------hhhHHHHHHHHHHHHH
Q 041361 58 ADLLAKLELIDRICKL-GLS---------------YLFEEQIREILVDTVA 92 (127)
Q Consensus 58 ~~~~~~L~lID~lqRL-GI~---------------yhFe~EI~~~L~~i~~ 92 (127)
...+++|...|.+.-| ||. -||.+||...|++...
T Consensus 38 ~~lle~L~~~dW~r~l~~iT~I~d~~d~~e~e~KR~lti~ei~~~L~Kf~~ 88 (101)
T PF15460_consen 38 QRLLEKLQGHDWLRVLPGITGINDPSDKKELEPKRELTIKEIQAMLDKFEN 88 (101)
T ss_pred HHHHHHHcCCCHHHHHhccccccCcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4668899999999999 654 3788999999998753
No 35
>cd07642 BAR_ASAP2 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP2 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2) is also known as DDEF2 (Development and Differentiation Enhancing Factor 2), AMAP2, centaurin beta-3, or PAG3. ASAP2 mediates the functions of Arf GTPases vial dual mechanisms: it exhibits GTPase activating protein (GAP) activity towards class I (Arf1) and II (Arf5) Arfs; and binds class III Arfs (GTP-Arf6) stably without GAP activity. It binds paxillin and is implicated in Fcgamma receptor-mediated phagocytosis in macrophages and in cell migration. ASAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, i
Probab=21.28 E-value=3.1e+02 Score=21.70 Aligned_cols=48 Identities=13% Similarity=0.159 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHhh-hhhhhHHHHHHHHHHhCcc--hhhHHHHHHHHHHH
Q 041361 43 AEKLTNDVKQMFLEA-ADLLAKLELIDRICKLGLS--YLFEEQIREILVDT 90 (127)
Q Consensus 43 ~e~Lk~~vr~~l~~~-~~~~~~L~lID~lqRLGI~--yhFe~EI~~~L~~i 90 (127)
+.++|..||.+..+. .-.-...-+++.|++||=. .+=+++|..+|..+
T Consensus 18 l~~~kk~~k~~~~sG~~yv~~~~~f~~~L~~LG~~~l~~dd~~~~~~l~kf 68 (215)
T cd07642 18 LYKMKKSVKAIHTSGLAHVENEEQYTQALEKFGSNCVCRDDPDLGSAFLKF 68 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHH
Confidence 356667776666543 2334567799999999965 33467888877765
No 36
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=21.10 E-value=1.5e+02 Score=19.61 Aligned_cols=46 Identities=17% Similarity=0.210 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhCcchhhHHHHHHHHHHHH
Q 041361 43 AEKLTNDVKQMFLEAADLLAKLELIDRICKLGLSYLFEEQIREILVDTV 91 (127)
Q Consensus 43 ~e~Lk~~vr~~l~~~~~~~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~ 91 (127)
...++++|=..|......-+.+.+=+..++||+. +++|+.+|+.+-
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~---~~~v~~al~~L~ 90 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMS---ENEVRKALDFLS 90 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS----HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcC---HHHHHHHHHHHH
Confidence 3455566666666522333344444556888776 789999999885
No 37
>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=20.99 E-value=3.7e+02 Score=20.16 Aligned_cols=18 Identities=33% Similarity=0.416 Sum_probs=12.9
Q ss_pred Ccchhh----HHHHHHHHHHHH
Q 041361 74 GLSYLF----EEQIREILVDTV 91 (127)
Q Consensus 74 GI~yhF----e~EI~~~L~~i~ 91 (127)
-|+-+| +++|+++-+..+
T Consensus 66 eVS~~f~~ysE~dik~AYe~A~ 87 (159)
T PF05384_consen 66 EVSRNFDRYSEEDIKEAYEEAH 87 (159)
T ss_pred HHHhhhcccCHHHHHHHHHHHH
Confidence 456677 899999966554
No 38
>cd07640 BAR_ASAP3 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP3 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 3) is also known as ACAP4 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 4), DDEFL1 (Development and Differentiation Enhancing Factor-Like 1), or centaurin beta-6. It is an Arf6-specific GTPase activating protein (GAP) and is co-localized with Arf6 in ruffling membranes upon EGF stimulation. ASAP3 is implicated in the pathogenesis of hepatocellular carcinoma and plays a role in regulating cell migration and invasion. ASAP3 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membran
Probab=20.75 E-value=1.9e+02 Score=22.95 Aligned_cols=37 Identities=16% Similarity=0.169 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHhhh-hhhhHHHHHHHHHHhCcchhh
Q 041361 43 AEKLTNDVKQMFLEAA-DLLAKLELIDRICKLGLSYLF 79 (127)
Q Consensus 43 ~e~Lk~~vr~~l~~~~-~~~~~L~lID~lqRLGI~yhF 79 (127)
+.++|..||.+..+.. -.-....++++|++||=.+--
T Consensus 18 L~k~kk~vkai~~sg~~hv~ne~~~~~~le~lg~~~l~ 55 (213)
T cd07640 18 LQRIKKIVKAIHNSGLNHVENEEQYTEALENLGNSHLS 55 (213)
T ss_pred HHHHHHHHHHHHHhhHHHHhHHHHHHHHHHHHhhhhhc
Confidence 3566677766655432 334467789999999965543
No 39
>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=20.33 E-value=1.8e+02 Score=23.57 Aligned_cols=45 Identities=27% Similarity=0.289 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhhhhhhhHHHHHHHHHHhCcchhhHHHHHHHHHHHH
Q 041361 45 KLTNDVKQMFLEAADLLAKLELIDRICKLGLSYLFEEQIREILVDTV 91 (127)
Q Consensus 45 ~Lk~~vr~~l~~~~~~~~~L~lID~lqRLGI~yhFe~EI~~~L~~i~ 91 (127)
-+++.|=++|. ..|..+=+|+..|+|-||.--=.++|..+|+++-
T Consensus 198 plReRvIHLLA--LkpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va 242 (284)
T PF10390_consen 198 PLRERVIHLLA--LKPYKKPELLLRLQKDGLSPKDKDELDSILQEVA 242 (284)
T ss_dssp -HHHHHHHHHH--HS-EEHHHHHHHHHHH---HHHHHHHHHHHHHCC
T ss_pred cccccchhhhh--cCccccHHHHHHHHhcCCChHHHHHHHHHHHHHh
Confidence 34455545442 4566777899999999999888899999999985
Done!