Query 048325
Match_columns 137
No_of_seqs 118 out of 713
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 08:31:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048325.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048325hhsearch_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 2.2E-36 4.7E-41 235.6 7.5 102 34-137 1-109 (183)
2 cd00684 Terpene_cyclase_plant_ 100.0 1.2E-34 2.7E-39 254.8 11.5 112 24-137 1-117 (542)
3 PLN02279 ent-kaur-16-ene synth 99.8 4.8E-19 1E-23 162.3 6.8 65 73-137 268-334 (784)
4 PLN02592 ent-copalyl diphospha 99.7 1.1E-18 2.3E-23 160.1 6.2 65 73-137 308-379 (800)
5 PF02084 Bindin: Bindin; Inte 61.3 7.3 0.00016 31.9 2.5 18 114-131 123-140 (238)
6 cd07604 BAR_ASAPs The Bin/Amph 61.3 36 0.00078 27.2 6.4 54 50-105 13-68 (215)
7 COG4738 Predicted transcriptio 50.0 25 0.00054 26.1 3.5 51 79-133 14-70 (124)
8 PF11000 DUF2840: Protein of u 44.1 14 0.00031 28.3 1.5 14 78-91 97-110 (149)
9 PF08373 RAP: RAP domain; Int 43.4 15 0.00033 22.4 1.3 18 118-135 17-34 (58)
10 PLN02863 UDP-glucoronosyl/UDP- 42.6 41 0.00089 29.8 4.4 41 49-91 435-475 (477)
11 cd07603 BAR_ACAPs The Bin/Amph 33.8 1E+02 0.0022 24.3 4.9 52 52-105 15-66 (200)
12 COG1400 SEC65 Signal recogniti 33.3 28 0.00061 24.6 1.5 13 80-92 36-48 (93)
13 PF14164 YqzH: YqzH-like prote 31.4 29 0.00062 23.0 1.2 12 126-137 12-23 (64)
14 PF00601 Flu_NS2: Influenza no 31.0 81 0.0018 22.4 3.5 43 53-101 47-89 (94)
15 smart00027 EH Eps15 homology d 30.2 1.7E+02 0.0037 19.5 8.4 59 73-137 24-84 (96)
16 PHA00438 hypothetical protein 29.8 26 0.00057 24.2 0.9 11 124-134 40-50 (81)
17 cd07641 BAR_ASAP1 The Bin/Amph 29.5 1.1E+02 0.0023 24.9 4.4 53 51-105 14-68 (215)
18 PF02005 TRM: N2,N2-dimethylgu 29.0 81 0.0018 27.2 3.9 43 94-136 301-354 (377)
19 PF09633 DUF2023: Protein of u 27.5 16 0.00034 26.4 -0.6 39 54-95 6-44 (101)
20 cd03569 VHS_Hrs_Vps27p VHS dom 26.4 1.1E+02 0.0024 22.6 3.8 22 116-137 120-141 (142)
21 PF00233 PDEase_I: 3'5'-cyclic 26.2 36 0.00078 27.1 1.2 45 87-135 46-90 (237)
22 PF11848 DUF3368: Domain of un 25.7 51 0.0011 20.0 1.6 12 125-136 25-36 (48)
23 PF03578 HGWP: HGWP repeat; I 25.6 28 0.00061 19.4 0.4 12 126-137 7-18 (28)
24 TIGR03279 cyano_FeS_chp putati 24.9 2.4E+02 0.0051 25.2 6.1 90 9-107 89-205 (433)
25 PF08784 RPA_C: Replication pr 24.8 1.5E+02 0.0033 20.0 4.1 48 55-108 45-92 (102)
26 PF07499 RuvA_C: RuvA, C-termi 24.8 1.3E+02 0.0028 18.0 3.3 24 81-107 6-29 (47)
27 PF15469 Sec5: Exocyst complex 23.7 2E+02 0.0043 21.6 4.9 36 54-91 136-171 (182)
28 PF09278 MerR-DNA-bind: MerR, 23.4 1.3E+02 0.0028 18.5 3.2 23 77-102 2-24 (65)
29 PF01963 TraB: TraB family; I 23.2 36 0.00078 26.5 0.7 12 126-137 247-258 (259)
30 PF09124 Endonuc-dimeris: T4 r 21.7 67 0.0015 20.6 1.6 31 76-107 16-46 (54)
31 PF06248 Zw10: Centromere/kine 21.0 2.6E+02 0.0057 25.2 5.8 69 50-130 18-90 (593)
32 KOG3906 Tryptophan 2,3-dioxyge 20.6 2.3E+02 0.005 24.3 5.0 28 60-89 87-114 (399)
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=2.2e-36 Score=235.64 Aligned_cols=102 Identities=50% Similarity=0.839 Sum_probs=83.6
Q ss_pred CCcCccccCCCCC------ChhHHHHHHHHHHHHHHHHhhhccCCCCchhhHHHHHHHHhcCcccchHHHHHHHHHHHHh
Q 048325 34 WDHDFLHSLSCNF------TSESYKKQGEHLKGKVKTMTNEVSVTNKPLDQLELIDNLQRLRLAYHFETEIESILHNIYN 107 (137)
Q Consensus 34 W~~~fl~s~~~~~------~~e~~~~~~e~LKeeVr~mL~~~~~~~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~ 107 (137)
|||+|++++.+.+ ..+++.+++++||++||.||.... .++.++|+|||+||||||+|||++||+++|+++|.
T Consensus 1 W~d~fl~s~s~~~~~~~~~~~~~~~~~~~~Lk~~v~~~l~~~~--~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~ 78 (183)
T PF01397_consen 1 WGDDFLQSLSPSYTACMQSEDEKCKERAEELKEEVRNMLPASY--PDPLEKLELIDTLQRLGISYHFEDEIKEILDSIYR 78 (183)
T ss_dssp TTHHHHHHTBHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHSSS--SHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHH
T ss_pred CCCceecCCCCcchhccchhHHHHHHHHHHHHHHHHHHHhhcC--CCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhh
Confidence 9999996433322 247889999999999999999873 48999999999999999999999999999999998
Q ss_pred cCCCCC-CCCChHHHHHHHHHhhhCCCCCCC
Q 048325 108 NKDDKW-KNENLYATSLEFRLLRQHGYNVSQ 137 (137)
Q Consensus 108 ~~~~~~-~~~dL~~~AL~FRLLRQhGy~VS~ 137 (137)
.+.... ...|||+|||+|||||||||+|||
T Consensus 79 ~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~ 109 (183)
T PF01397_consen 79 SWDEDNEEIDDLYTTALRFRLLRQHGYYVSS 109 (183)
T ss_dssp TTTTTSHTSSCHHHHHHHHHHHHHTT----G
T ss_pred hccccccccCchhHHHHHHHHHHHcCCcccH
Confidence 755421 125999999999999999999996
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=1.2e-34 Score=254.83 Aligned_cols=112 Identities=46% Similarity=0.748 Sum_probs=94.8
Q ss_pred CCCCCCCCCCCCcCccccCCCCCChh-HHHHHHHHHHHHHHHHhhhc--cCCCCchhhHHHHHHHHhcCcccchHHHHHH
Q 048325 24 RRSANNQPSIWDHDFLHSLSCNFTSE-SYKKQGEHLKGKVKTMTNEV--SVTNKPLDQLELIDNLQRLRLAYHFETEIES 100 (137)
Q Consensus 24 r~~a~~~PsiW~~~fl~s~~~~~~~e-~~~~~~e~LKeeVr~mL~~~--~~~~~~~~~L~lID~lqRLGi~yhFe~EI~~ 100 (137)
|++++|+||+||++++.++.....+. .+.+++++||++||+||... . .|+.++|+|||+||||||+|||++||++
T Consensus 1 r~~~~~~~~~w~~~~~~s~~~~~~~~~~~~~~~~~lk~~v~~~~~~~~~~--~~~~~~l~liD~lqrLGi~~hF~~EI~~ 78 (542)
T cd00684 1 RPSANFPPSLWGDDHFLSLSSDYSEEDELEEEIEELKEEVRKMLEDSEYP--VDLFERLWLIDRLQRLGISYHFEDEIKE 78 (542)
T ss_pred CCCCCCCCCcCCCcceeecCCCcchhHHHHHHHHHHHHHHHHHHHhcccC--CCHHHHHHHHHHHHHcCchhhhHHHHHH
Confidence 68899999999995555444444333 78899999999999999873 3 7899999999999999999999999999
Q ss_pred HHHHHHhcCCCC--CCCCChHHHHHHHHHhhhCCCCCCC
Q 048325 101 ILHNIYNNKDDK--WKNENLYATSLEFRLLRQHGYNVSQ 137 (137)
Q Consensus 101 ~L~~i~~~~~~~--~~~~dL~~~AL~FRLLRQhGy~VS~ 137 (137)
+|+.||+.+... ....|||+|||+|||||||||+|||
T Consensus 79 ~L~~i~~~~~~~~~~~~~dl~~~al~FRlLR~~Gy~vs~ 117 (542)
T cd00684 79 ILDYIYRYWTERGESNEDDLYTTALGFRLLRQHGYNVSS 117 (542)
T ss_pred HHHHHHHhhcccccccCCCHHHHHHHHHHHHHcCCCcCH
Confidence 999999865321 1236999999999999999999996
No 3
>PLN02279 ent-kaur-16-ene synthase
Probab=99.77 E-value=4.8e-19 Score=162.29 Aligned_cols=65 Identities=34% Similarity=0.520 Sum_probs=57.0
Q ss_pred CCchhhHHHHHHHHhcCcccchHHHHHHHHHHHHhcCCCCC--CCCChHHHHHHHHHhhhCCCCCCC
Q 048325 73 NKPLDQLELIDNLQRLRLAYHFETEIESILHNIYNNKDDKW--KNENLYATSLEFRLLRQHGYNVSQ 137 (137)
Q Consensus 73 ~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~--~~~dL~~~AL~FRLLRQhGy~VS~ 137 (137)
.+..+++.+||+||||||+|||++||+++|+.+|+.+.... ...|||+|||+|||||||||+|||
T Consensus 268 ~~~fe~l~lvd~L~rlGi~~hF~~EI~~~L~~~~~~~~~~~~~~~~Dl~~tAl~FRLLR~hGy~VS~ 334 (784)
T PLN02279 268 LDQYARLSMVDTLERLGIDRHFRKEIKSVLDETYRYWLQGEEEIFLDLATCALAFRILRLNGYDVSS 334 (784)
T ss_pred ccHHHHhHHHHHHHHhCCccccHHHHHHHHHHHHHhhcccccCCCCCHHHHHHHHHHHHHcCCCCCh
Confidence 46899999999999999999999999999999998543211 126999999999999999999996
No 4
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.75 E-value=1.1e-18 Score=160.11 Aligned_cols=65 Identities=31% Similarity=0.504 Sum_probs=56.2
Q ss_pred CCchhhHHHHHHHHhcCcccchHHHHHHHHHHHHhcCCC---CC--C--CCChHHHHHHHHHhhhCCCCCCC
Q 048325 73 NKPLDQLELIDNLQRLRLAYHFETEIESILHNIYNNKDD---KW--K--NENLYATSLEFRLLRQHGYNVSQ 137 (137)
Q Consensus 73 ~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~---~~--~--~~dL~~~AL~FRLLRQhGy~VS~ 137 (137)
.++.++|+|||+||||||+|||++||+++|+.+|..+.. .+ . ..|||+|||+|||||||||+|||
T Consensus 308 ~d~fE~LwlVDtLqRLGIs~hF~~EI~~iLd~iy~~w~~~g~~~a~~~~~~Dld~TALaFRLLRqhGy~VS~ 379 (800)
T PLN02592 308 VDLFEHIWAVDRLQRLGISRYFEPEIKECIDYVHRYWTENGICWARNSHVHDIDDTAMGFRLLRLHGHQVSA 379 (800)
T ss_pred CcHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhcCcccccCCCcCCHHHHHHHHHHHHHcCCCCCh
Confidence 478999999999999999999999999999999973211 01 1 26999999999999999999996
No 5
>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=61.34 E-value=7.3 Score=31.91 Aligned_cols=18 Identities=33% Similarity=0.501 Sum_probs=15.8
Q ss_pred CCCChHHHHHHHHHhhhC
Q 048325 114 KNENLYATSLEFRLLRQH 131 (137)
Q Consensus 114 ~~~dL~~~AL~FRLLRQh 131 (137)
+.+|-|+.-|..|-||+|
T Consensus 123 DINDPYDlGLLLRhLRHH 140 (238)
T PF02084_consen 123 DINDPYDLGLLLRHLRHH 140 (238)
T ss_pred ccCChhhHHHHHHHHHHH
Confidence 357899999999999998
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=61.27 E-value=36 Score=27.22 Aligned_cols=54 Identities=17% Similarity=0.183 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCchhhHHHHHHHHhcCcccc--hHHHHHHHHHHH
Q 048325 50 SYKKQGEHLKGKVKTMTNEVSVTNKPLDQLELIDNLQRLRLAYH--FETEIESILHNI 105 (137)
Q Consensus 50 ~~~~~~e~LKeeVr~mL~~~~~~~~~~~~L~lID~lqRLGi~yh--Fe~EI~~~L~~i 105 (137)
....+.+++++.++.|..+.. .=......++++|+.||=..- .+.+|..+|.+.
T Consensus 13 ~~~~~l~Kl~K~~k~~~~~g~--~~~~~~~~F~~aL~~~g~~~~~~~~~~i~~~l~kF 68 (215)
T cd07604 13 GDRVGLQKLKKAVKAIHNSGL--AHVENELQFAEALEKLGSKALSREEEDLGAAFLKF 68 (215)
T ss_pred HHHHHHHHHHHHHHHHHHhHH--HHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHH
Confidence 345677888888888886541 224567889999999994322 233688888776
No 7
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=49.99 E-value=25 Score=26.11 Aligned_cols=51 Identities=22% Similarity=0.384 Sum_probs=30.4
Q ss_pred HHHHHHHHhcCcccchHHHHHHHHHHHHhcCCCC-CC---CCChH--HHHHHHHHhhhCCC
Q 048325 79 LELIDNLQRLRLAYHFETEIESILHNIYNNKDDK-WK---NENLY--ATSLEFRLLRQHGY 133 (137)
Q Consensus 79 L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~-~~---~~dL~--~~AL~FRLLRQhGy 133 (137)
-.+|+.|+.|||..-- ..+|-.+-+..... .+ ...|- +||++-|.||.+|+
T Consensus 14 ~~~ie~L~~lgi~R~v----A~tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gW 70 (124)
T COG4738 14 YEIIELLRILGIPRNV----ATTLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENGW 70 (124)
T ss_pred HHHHHHHHHcCCCchH----HHHHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccc
Confidence 4689999999998753 23333332221100 00 02232 59999999999996
No 8
>PF11000 DUF2840: Protein of unknown function (DUF2840); InterPro: IPR021263 This bacterial family of proteins have no known function.
Probab=44.11 E-value=14 Score=28.27 Aligned_cols=14 Identities=29% Similarity=0.496 Sum_probs=12.3
Q ss_pred hHHHHHHHHhcCcc
Q 048325 78 QLELIDNLQRLRLA 91 (137)
Q Consensus 78 ~L~lID~lqRLGi~ 91 (137)
-|..||+|+.|||+
T Consensus 97 VL~~IDaiEalGid 110 (149)
T PF11000_consen 97 VLQAIDAIEALGID 110 (149)
T ss_pred HHHHHhHHHHcCCC
Confidence 47789999999987
No 9
>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=43.44 E-value=15 Score=22.45 Aligned_cols=18 Identities=39% Similarity=0.547 Sum_probs=15.9
Q ss_pred hHHHHHHHHHhhhCCCCC
Q 048325 118 LYATSLEFRLLRQHGYNV 135 (137)
Q Consensus 118 L~~~AL~FRLLRQhGy~V 135 (137)
+-.++|+=|+|+..||+|
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 10
>PLN02863 UDP-glucoronosyl/UDP-glucosyl transferase family protein
Probab=42.63 E-value=41 Score=29.76 Aligned_cols=41 Identities=12% Similarity=0.166 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHHHHHHHhhhccCCCCchhhHHHHHHHHhcCcc
Q 048325 49 ESYKKQGEHLKGKVKTMTNEVSVTNKPLDQLELIDNLQRLRLA 91 (137)
Q Consensus 49 e~~~~~~e~LKeeVr~mL~~~~~~~~~~~~L~lID~lqRLGi~ 91 (137)
+.+++++.++++.+++.+...+ +....--+||+.|+++|+.
T Consensus 435 ~~~r~~a~~l~e~a~~Av~~gG--SS~~~l~~~v~~i~~~~~~ 475 (477)
T PLN02863 435 QVERERAKELRRAALDAIKERG--SSVKDLDGFVKHVVELGLE 475 (477)
T ss_pred HHHHHHHHHHHHHHHHHhccCC--cHHHHHHHHHHHHHHhccC
Confidence 4566777888888888776542 3333445689999999975
No 11
>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=33.81 E-value=1e+02 Score=24.27 Aligned_cols=52 Identities=12% Similarity=0.118 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHhhhccCCCCchhhHHHHHHHHhcCcccchHHHHHHHHHHH
Q 048325 52 KKQGEHLKGKVKTMTNEVSVTNKPLDQLELIDNLQRLRLAYHFETEIESILHNI 105 (137)
Q Consensus 52 ~~~~e~LKeeVr~mL~~~~~~~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i 105 (137)
..++++|.+.++.|+.... .=......++++|..||-.+-=+..|..+|.+.
T Consensus 15 ~~~l~kl~K~~~~~~~ag~--~~~~a~~~F~~~L~~~~~~~~~d~~i~~~l~kF 66 (200)
T cd07603 15 ETRLEKLLKLCNGMVDSGK--TYVNANSLFVNSLNDLSDYFRDDSLVQNCLNKF 66 (200)
T ss_pred HHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH
Confidence 4455666667766665431 123447889999999997543345677777665
No 12
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=33.31 E-value=28 Score=24.62 Aligned_cols=13 Identities=31% Similarity=0.447 Sum_probs=11.8
Q ss_pred HHHHHHHhcCccc
Q 048325 80 ELIDNLQRLRLAY 92 (137)
Q Consensus 80 ~lID~lqRLGi~y 92 (137)
++.++++.||+.+
T Consensus 36 ei~~a~~~LGl~~ 48 (93)
T COG1400 36 EIAEALRELGLKP 48 (93)
T ss_pred HHHHHHHHcCCCe
Confidence 5789999999999
No 13
>PF14164 YqzH: YqzH-like protein
Probab=31.39 E-value=29 Score=23.03 Aligned_cols=12 Identities=50% Similarity=0.717 Sum_probs=9.4
Q ss_pred HHhhhCCCCCCC
Q 048325 126 RLLRQHGYNVSQ 137 (137)
Q Consensus 126 RLLRQhGy~VS~ 137 (137)
+-|||.||++.+
T Consensus 12 ~~l~QYg~d~~~ 23 (64)
T PF14164_consen 12 NCLRQYGYDVEC 23 (64)
T ss_pred HHHHHhCCcccC
Confidence 578999998754
No 14
>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=31.05 E-value=81 Score=22.37 Aligned_cols=43 Identities=19% Similarity=0.282 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHhhhccCCCCchhhHHHHHHHHhcCcccchHHHHHHH
Q 048325 53 KQGEHLKGKVKTMTNEVSVTNKPLDQLELIDNLQRLRLAYHFETEIESI 101 (137)
Q Consensus 53 ~~~e~LKeeVr~mL~~~~~~~~~~~~L~lID~lqRLGi~yhFe~EI~~~ 101 (137)
+++.-|.+++|..|..+ ++.++++-+.-+||-| |--++||...
T Consensus 47 e~IrwlI~e~r~~l~~t---ensf~qItfmqaLqlL---lEve~eirtf 89 (94)
T PF00601_consen 47 EEIRWLIEEHRHRLKIT---ENSFEQITFMQALQLL---LEVEQEIRTF 89 (94)
T ss_dssp HHHHHHHHHHHHC-------TTSHHHHHHHHHHHHH---HHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHh---hhhHHHHHHHHHHHHH---HHHHHHHHHH
Confidence 44555667777777777 7788887777666644 5666776653
No 15
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=30.17 E-value=1.7e+02 Score=19.49 Aligned_cols=59 Identities=14% Similarity=0.193 Sum_probs=36.2
Q ss_pred CCchhhHHHHHHHHhcCcccchHHHHHHHHHHHHhcCCCCCCCCC--hHHHHHHHHHhhhCCCCCCC
Q 048325 73 NKPLDQLELIDNLQRLRLAYHFETEIESILHNIYNNKDDKWKNEN--LYATSLEFRLLRQHGYNVSQ 137 (137)
Q Consensus 73 ~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~d--L~~~AL~FRLLRQhGy~VS~ 137 (137)
+..+..-++...+.++|++ ++|++.++..+-.. .+ +.-+ =+...+..--..+.|+.|++
T Consensus 24 ~G~Is~~el~~~l~~~~~~---~~ev~~i~~~~d~~-~~--g~I~~~eF~~~~~~~~~~~~g~~~~~ 84 (96)
T smart00027 24 DGTVTGAQAKPILLKSGLP---QTLLAKIWNLADID-ND--GELDKDEFALAMHLIYRKLNGYPIPA 84 (96)
T ss_pred CCeEeHHHHHHHHHHcCCC---HHHHHHHHHHhcCC-CC--CCcCHHHHHHHHHHHHHHHcCCCCCc
Confidence 4556777788888888875 56788777655211 11 1112 23455555556678998874
No 16
>PHA00438 hypothetical protein
Probab=29.84 E-value=26 Score=24.18 Aligned_cols=11 Identities=73% Similarity=1.186 Sum_probs=8.9
Q ss_pred HHHHhhhCCCC
Q 048325 124 EFRLLRQHGYN 134 (137)
Q Consensus 124 ~FRLLRQhGy~ 134 (137)
.-|+|||+||-
T Consensus 40 ~i~~lR~~G~S 50 (81)
T PHA00438 40 EIRLLRQAGYS 50 (81)
T ss_pred hHHHHHHcCCc
Confidence 45899999984
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=29.52 E-value=1.1e+02 Score=24.90 Aligned_cols=53 Identities=9% Similarity=0.173 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCchhhHHHHHHHHhcCccc--chHHHHHHHHHHH
Q 048325 51 YKKQGEHLKGKVKTMTNEVSVTNKPLDQLELIDNLQRLRLAY--HFETEIESILHNI 105 (137)
Q Consensus 51 ~~~~~e~LKeeVr~mL~~~~~~~~~~~~L~lID~lqRLGi~y--hFe~EI~~~L~~i 105 (137)
.....+++++-|+.|..+.. .-.-..-.+|+.|.+||=.. -=+.+|.++|.++
T Consensus 14 ~e~~L~Kl~K~~kam~~SG~--~yv~n~~~f~~~l~~Lg~~~~~~dd~~i~~a~~kf 68 (215)
T cd07641 14 DRTALQKVKKSVKAIYNSGQ--DHVQNEENYAQALDKFGSNFLSRDNPDLGTAFVKF 68 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHhhccCCchhHHHHHHHH
Confidence 34567888888988887642 33455778999999999433 2246777777766
No 18
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=29.01 E-value=81 Score=27.23 Aligned_cols=43 Identities=26% Similarity=0.221 Sum_probs=23.2
Q ss_pred hHHHHHHHHHHHHhcCCCCCCCCChHHHHH-----------HHHHhhhCCCCCC
Q 048325 94 FETEIESILHNIYNNKDDKWKNENLYATSL-----------EFRLLRQHGYNVS 136 (137)
Q Consensus 94 Fe~EI~~~L~~i~~~~~~~~~~~dL~~~AL-----------~FRLLRQhGy~VS 136 (137)
+.++|...|..+..+.....--.+++.+|= -..-||+.||.+|
T Consensus 301 ~~~ri~~lL~~i~eE~~~~P~yY~l~~ias~lk~~~P~~~~ii~aL~~~Gy~aS 354 (377)
T PF02005_consen 301 TSKRIEKLLETIKEELIDPPFYYDLHEIASRLKCNPPPLDKIISALRNAGYRAS 354 (377)
T ss_dssp THHHHHHHHHHHHHCHS-SSS-EEHHHHHHHHT-SC--HHHHHHHHHHTTTTEE
T ss_pred hHHHHhhhcchhhhhcccceeEEeHHHHHHhcCCCCCCHHHHHHHHhhcceEEE
Confidence 356666666666544111001134555542 2345999999986
No 19
>PF09633 DUF2023: Protein of unknown function (DUF2023); InterPro: IPR018594 This protein of approx.120 residues consists of three beta strands and five alpha helices, thought to fold into a homo-dimer. ; PDB: 2GUK_B.
Probab=27.48 E-value=16 Score=26.36 Aligned_cols=39 Identities=15% Similarity=0.096 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHhhhccCCCCchhhHHHHHHHHhcCcccchH
Q 048325 54 QGEHLKGKVKTMTNEVSVTNKPLDQLELIDNLQRLRLAYHFE 95 (137)
Q Consensus 54 ~~e~LKeeVr~mL~~~~~~~~~~~~L~lID~lqRLGi~yhFe 95 (137)
.+-+.++-||.|+.-+ ...-..-..+..|++-||+|+.+
T Consensus 6 hIYEy~KGvR~LvL~T---~~~~~~~~~~~rL~~~~I~y~iq 44 (101)
T PF09633_consen 6 HIYEYKKGVRQLVLHT---LPKRYEEFAIARLERQGIDYFIQ 44 (101)
T ss_dssp HHHHHHCTS-SEEEEE---EEGGGHHHHHHHHHHTT--EEEE
T ss_pred HHHHhhhhhhhHhhhh---CCHhhHHHHHHHHHHCCCCEEEE
Confidence 3456778888887654 33344455788999999999964
No 20
>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=26.35 E-value=1.1e+02 Score=22.59 Aligned_cols=22 Identities=14% Similarity=0.282 Sum_probs=18.3
Q ss_pred CChHHHHHHHHHhhhCCCCCCC
Q 048325 116 ENLYATSLEFRLLRQHGYNVSQ 137 (137)
Q Consensus 116 ~dL~~~AL~FRLLRQhGy~VS~ 137 (137)
.+|-.+.=.|..||..||..++
T Consensus 120 ~~l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 120 PQLKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred cccHHHHHHHHHHHHcCCCCCC
Confidence 4677788889999999998764
No 21
>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=26.22 E-value=36 Score=27.15 Aligned_cols=45 Identities=24% Similarity=0.332 Sum_probs=32.8
Q ss_pred hcCcccchHHHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHhhhCCCCC
Q 048325 87 RLRLAYHFETEIESILHNIYNNKDDKWKNENLYATSLEFRLLRQHGYNV 135 (137)
Q Consensus 87 RLGi~yhFe~EI~~~L~~i~~~~~~~~~~~dL~~~AL~FRLLRQhGy~V 135 (137)
.=|+.--|.-..+..|..+|...+. -.-|-+|+.|+||+..|+++
T Consensus 46 HpG~~N~flv~~~~~LA~~Y~d~Sv----LE~~H~~~~~~lL~~~~~ni 90 (237)
T PF00233_consen 46 HPGVNNAFLVKTNSPLAILYNDRSV----LENHHCALAFQLLRKEECNI 90 (237)
T ss_dssp -SSSCHHHHHHTTSHHHHHTTTSSH----HHHHHHHHHHHHHTSTTTTT
T ss_pred CCccccchhhccccchhhhcCccCC----ccccHHHHHHHHHHhhhhhh
Confidence 3477777888888888888754211 24677899999999999876
No 22
>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=25.72 E-value=51 Score=19.96 Aligned_cols=12 Identities=33% Similarity=0.672 Sum_probs=7.2
Q ss_pred HHHhhhCCCCCC
Q 048325 125 FRLLRQHGYNVS 136 (137)
Q Consensus 125 FRLLRQhGy~VS 136 (137)
+.-|+++||++|
T Consensus 25 l~~l~~~g~~is 36 (48)
T PF11848_consen 25 LDRLQQAGFRIS 36 (48)
T ss_pred HHHHHHcCcccC
Confidence 444466666665
No 23
>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=25.59 E-value=28 Score=19.45 Aligned_cols=12 Identities=33% Similarity=0.592 Sum_probs=9.1
Q ss_pred HHhhhCCCCCCC
Q 048325 126 RLLRQHGYNVSQ 137 (137)
Q Consensus 126 RLLRQhGy~VS~ 137 (137)
+-||.||+.|.+
T Consensus 7 Wc~rLhGW~i~p 18 (28)
T PF03578_consen 7 WCLRLHGWPIMP 18 (28)
T ss_pred hheeeccCcccC
Confidence 357899998864
No 24
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=24.89 E-value=2.4e+02 Score=25.22 Aligned_cols=90 Identities=21% Similarity=0.244 Sum_probs=53.8
Q ss_pred ceeecCCCCCcccccCCCC-----CCCCCCCCcCccccCCCCCChhHHHHHHHHH------------HHHHHHHhhhccC
Q 048325 9 AQCFASAQPDTAAVVRRSA-----NNQPSIWDHDFLHSLSCNFTSESYKKQGEHL------------KGKVKTMTNEVSV 71 (137)
Q Consensus 9 ~~~~~~~~~~~~~~~r~~a-----~~~PsiW~~~fl~s~~~~~~~e~~~~~~e~L------------KeeVr~mL~~~~~ 71 (137)
+=|..-+.|+- .|.+- .|+-|.|--.|++ +.+- .+..-+|+.+. ..++|+.|+..
T Consensus 89 ~FCFidQlP~g---mR~sLY~KDDDyRLSFL~GnyiT-LTNl--~~~d~~RI~~~~lspl~iSVhat~p~lR~~ll~n-- 160 (433)
T TIGR03279 89 PFCFIDQQPPG---KRESLYLKDDDYRLSFLYGSYLT-LTNL--PPAEWQRIEQLRLSPLYVSVHATEPSLRARLLKN-- 160 (433)
T ss_pred ceEeccCCCCC---CcCcceeccCcchhhhhccceee-ecCC--CHHHHHHHHHcCCCCEEEEEecCCHHHHHHHhCC--
Confidence 56777776664 45553 3444433333443 2222 22223444443 37888887765
Q ss_pred CCCchhhHHHHHHHHhcCcccchH----------HHHHHHHHHHHh
Q 048325 72 TNKPLDQLELIDNLQRLRLAYHFE----------TEIESILHNIYN 107 (137)
Q Consensus 72 ~~~~~~~L~lID~lqRLGi~yhFe----------~EI~~~L~~i~~ 107 (137)
...-.-|+.+..|..=||+.|=+ +|++..+..+..
T Consensus 161 -~~a~~il~~l~~l~~~~I~~h~qiVlcPGiNDg~~L~~Ti~dL~~ 205 (433)
T TIGR03279 161 -PRAGLILEQLKWFQERRLQLHAQVVVCPGINDGKHLERTLRDLAQ 205 (433)
T ss_pred -CCHHHHHHHHHHHHHcCCeEEEEEEEcCCcCCHHHHHHHHHHHHh
Confidence 45566677777777779999864 788888887753
No 25
>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=24.79 E-value=1.5e+02 Score=20.05 Aligned_cols=48 Identities=19% Similarity=0.237 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhhhccCCCCchhhHHHHHHHHhcCcccchHHHHHHHHHHHHhc
Q 048325 55 GEHLKGKVKTMTNEVSVTNKPLDQLELIDNLQRLRLAYHFETEIESILHNIYNN 108 (137)
Q Consensus 55 ~e~LKeeVr~mL~~~~~~~~~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~ 108 (137)
...++++|-..|... ...-+-+.+=+..++||++ +++|..+|+.+-.+
T Consensus 45 ~~~~~~~Vl~~i~~~---~~~~~Gv~v~~I~~~l~~~---~~~v~~al~~L~~e 92 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQ---PNSEEGVHVDEIAQQLGMS---ENEVRKALDFLSNE 92 (102)
T ss_dssp S-HHHHHHHHHHHC-------TTTEEHHHHHHHSTS----HHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHhc---CCCCCcccHHHHHHHhCcC---HHHHHHHHHHHHhC
Confidence 355667777777762 2334455555667888776 78999999998654
No 26
>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=24.77 E-value=1.3e+02 Score=17.96 Aligned_cols=24 Identities=13% Similarity=0.218 Sum_probs=19.6
Q ss_pred HHHHHHhcCcccchHHHHHHHHHHHHh
Q 048325 81 LIDNLQRLRLAYHFETEIESILHNIYN 107 (137)
Q Consensus 81 lID~lqRLGi~yhFe~EI~~~L~~i~~ 107 (137)
.+.+|.-|| +-+.||+.++..+..
T Consensus 6 ~~~AL~~LG---y~~~e~~~av~~~~~ 29 (47)
T PF07499_consen 6 ALEALISLG---YSKAEAQKAVSKLLE 29 (47)
T ss_dssp HHHHHHHTT---S-HHHHHHHHHHHHH
T ss_pred HHHHHHHcC---CCHHHHHHHHHHhhc
Confidence 577888899 457999999999975
No 27
>PF15469 Sec5: Exocyst complex component Sec5
Probab=23.65 E-value=2e+02 Score=21.58 Aligned_cols=36 Identities=19% Similarity=0.157 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHhhhccCCCCchhhHHHHHHHHhcCcc
Q 048325 54 QGEHLKGKVKTMTNEVSVTNKPLDQLELIDNLQRLRLA 91 (137)
Q Consensus 54 ~~e~LKeeVr~mL~~~~~~~~~~~~L~lID~lqRLGi~ 91 (137)
.++.+++.+..-|.+.. .+.-+.+.+|+.|..||+.
T Consensus 136 ii~~~r~~l~~~L~~~~--~s~~~~~~~i~~Ll~L~~~ 171 (182)
T PF15469_consen 136 IIEEFREKLWEKLLSPP--SSQEEFLKLIRKLLELNVE 171 (182)
T ss_pred HHHHHHHHHHHHHhCCC--CCHHHHHHHHHHHHhCCCC
Confidence 34455555555555542 4667888899999999874
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=23.36 E-value=1.3e+02 Score=18.47 Aligned_cols=23 Identities=30% Similarity=0.621 Sum_probs=18.5
Q ss_pred hhHHHHHHHHhcCcccchHHHHHHHH
Q 048325 77 DQLELIDNLQRLRLAYHFETEIESIL 102 (137)
Q Consensus 77 ~~L~lID~lqRLGi~yhFe~EI~~~L 102 (137)
+.|.+|=.++.||++- +||.+.|
T Consensus 2 ~rL~~I~~~r~lGfsL---~eI~~~l 24 (65)
T PF09278_consen 2 ERLQFIRRLRELGFSL---EEIRELL 24 (65)
T ss_dssp HHHHHHHHHHHTT--H---HHHHHHH
T ss_pred hHHHHHHHHHHcCCCH---HHHHHHH
Confidence 5789999999999874 7999998
No 29
>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=23.20 E-value=36 Score=26.48 Aligned_cols=12 Identities=50% Similarity=0.911 Sum_probs=10.5
Q ss_pred HHhhhCCCCCCC
Q 048325 126 RLLRQHGYNVSQ 137 (137)
Q Consensus 126 RLLRQhGy~VS~ 137 (137)
.+||+.||.|.+
T Consensus 247 ~lLr~~Gy~V~~ 258 (259)
T PF01963_consen 247 DLLRKKGYTVEP 258 (259)
T ss_pred HHHHhCCceeec
Confidence 799999999864
No 30
>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=21.75 E-value=67 Score=20.57 Aligned_cols=31 Identities=23% Similarity=0.502 Sum_probs=16.9
Q ss_pred hhhHHHHHHHHhcCcccchHHHHHHHHHHHHh
Q 048325 76 LDQLELIDNLQRLRLAYHFETEIESILHNIYN 107 (137)
Q Consensus 76 ~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~ 107 (137)
+.+-+||+.++.+|++|- +..-.+.|-.+|+
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 445679999999999987 3444455555553
No 31
>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=21.05 E-value=2.6e+02 Score=25.17 Aligned_cols=69 Identities=23% Similarity=0.328 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCC----chhhHHHHHHHHhcCcccchHHHHHHHHHHHHhcCCCCCCCCChHHHHHHH
Q 048325 50 SYKKQGEHLKGKVKTMTNEVSVTNK----PLDQLELIDNLQRLRLAYHFETEIESILHNIYNNKDDKWKNENLYATSLEF 125 (137)
Q Consensus 50 ~~~~~~e~LKeeVr~mL~~~~~~~~----~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~dL~~~AL~F 125 (137)
...++++++|.+|+.++...- .+ ....-.||+.+..|+ +||+++|+..... . ...+|...+=.+
T Consensus 18 ~L~~~i~~~k~eV~~~I~~~y--~df~~~~~~~~~L~~~~~~l~------~eI~d~l~~~~~~--~--i~~~l~~a~~e~ 85 (593)
T PF06248_consen 18 RLSRRIEELKEEVHSMINKKY--SDFSPSLQSAKDLIERSKSLA------REINDLLQSEIEN--E--IQPQLRDAAEEL 85 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhHHHHHHHHHHHH------HHHHHHHHhhccc--h--hHHHHHHHHHHH
Confidence 345788899999999987531 11 123334555555553 7787777763211 1 124677777777
Q ss_pred HHhhh
Q 048325 126 RLLRQ 130 (137)
Q Consensus 126 RLLRQ 130 (137)
..|++
T Consensus 86 ~~L~~ 90 (593)
T PF06248_consen 86 QELKR 90 (593)
T ss_pred HHHHH
Confidence 77765
No 32
>KOG3906 consensus Tryptophan 2,3-dioxygenase [Amino acid transport and metabolism]
Probab=20.64 E-value=2.3e+02 Score=24.35 Aligned_cols=28 Identities=18% Similarity=0.379 Sum_probs=21.7
Q ss_pred HHHHHHhhhccCCCCchhhHHHHHHHHhcC
Q 048325 60 GKVKTMTNEVSVTNKPLDQLELIDNLQRLR 89 (137)
Q Consensus 60 eeVr~mL~~~~~~~~~~~~L~lID~lqRLG 89 (137)
..||+||.+.. .|....|++|--+.|.-
T Consensus 87 DsvR~~l~~~v--~DEtktLkiVsrl~Rv~ 114 (399)
T KOG3906|consen 87 DSVRKLLNNTV--VDETKTLKIVSRLDRVT 114 (399)
T ss_pred HHHHHHhcchh--hcchhHHHHHHhHHHHH
Confidence 88999998764 56777888887777764
Done!