Query 035819
Match_columns 122
No_of_seqs 120 out of 691
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 06:42:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035819.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035819hhsearch_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 1.3E-41 2.7E-46 261.5 11.9 107 2-121 22-128 (183)
2 cd00684 Terpene_cyclase_plant_ 100.0 7.5E-37 1.6E-41 264.0 11.1 107 3-121 28-136 (542)
3 PLN02279 ent-kaur-16-ene synth 99.9 6.8E-25 1.5E-29 197.5 8.1 83 29-120 268-350 (784)
4 PLN02592 ent-copalyl diphospha 99.9 1.2E-24 2.7E-29 196.1 8.2 87 29-118 308-394 (800)
5 PF11848 DUF3368: Domain of un 74.7 3.4 7.4E-05 25.0 2.5 25 85-109 20-44 (48)
6 cd07604 BAR_ASAPs The Bin/Amph 68.2 28 0.0006 27.5 6.9 53 3-61 13-68 (215)
7 PF00601 Flu_NS2: Influenza no 59.4 21 0.00045 25.2 4.1 42 6-56 47-88 (94)
8 COG4738 Predicted transcriptio 56.0 27 0.00058 25.8 4.4 54 35-98 14-70 (124)
9 PLN02863 UDP-glucoronosyl/UDP- 52.4 26 0.00056 30.5 4.6 41 2-47 435-475 (477)
10 cd03569 VHS_Hrs_Vps27p VHS dom 45.2 47 0.001 24.3 4.4 22 81-102 120-141 (142)
11 PF08373 RAP: RAP domain; Int 43.2 21 0.00045 21.5 1.9 21 84-104 18-38 (58)
12 cd07641 BAR_ASAP1 The Bin/Amph 42.1 60 0.0013 26.1 4.8 52 5-61 15-68 (215)
13 PF11000 DUF2840: Protein of u 40.7 18 0.00039 27.5 1.6 16 33-48 96-111 (149)
14 PF14164 YqzH: YqzH-like prote 39.3 13 0.00029 24.5 0.6 17 90-106 11-27 (64)
15 PF15508 NAAA-beta: beta subun 37.5 1.3E+02 0.0028 20.3 5.7 48 4-57 25-75 (95)
16 PF02005 TRM: N2,N2-dimethylgu 36.7 61 0.0013 27.6 4.4 68 30-106 278-359 (377)
17 cd07603 BAR_ACAPs The Bin/Amph 35.9 1.1E+02 0.0023 23.8 5.3 51 5-61 15-66 (200)
18 PF02847 MA3: MA3 domain; Int 35.0 1E+02 0.0023 20.5 4.6 45 11-62 1-46 (113)
19 PF07862 Nif11: Nitrogen fixat 33.0 32 0.00068 20.4 1.5 13 92-104 35-47 (49)
20 PF09278 MerR-DNA-bind: MerR, 29.8 85 0.0018 19.1 3.2 24 32-58 1-24 (65)
21 PF13369 Transglut_core2: Tran 29.6 2.2E+02 0.0048 20.6 7.6 82 2-102 1-87 (152)
22 PF03578 HGWP: HGWP repeat; I 29.2 18 0.00039 20.2 -0.0 15 91-105 7-21 (28)
23 smart00027 EH Eps15 homology d 29.2 1.7E+02 0.0037 19.2 7.9 62 29-103 24-85 (96)
24 PF05384 DegS: Sensor protein 29.1 1.9E+02 0.0041 22.0 5.5 49 7-62 35-87 (159)
25 PF08513 LisH: LisH; InterPro 29.0 33 0.0007 18.3 1.0 21 87-107 5-25 (27)
26 PF10390 ELL: RNA polymerase I 27.6 91 0.002 25.5 3.8 46 10-63 198-243 (284)
27 PF12627 PolyA_pol_RNAbd: Prob 26.8 69 0.0015 19.4 2.4 40 9-58 25-64 (64)
28 PF00233 PDEase_I: 3'5'-cyclic 26.3 50 0.0011 25.9 2.0 47 42-101 45-91 (237)
29 PF02084 Bindin: Bindin; Inte 26.2 57 0.0012 26.6 2.3 17 80-96 124-140 (238)
30 PF15469 Sec5: Exocyst complex 26.0 1.8E+02 0.004 21.4 5.0 38 6-48 135-172 (182)
31 COG1060 ThiH Thiamine biosynth 24.5 63 0.0014 27.6 2.4 36 8-48 180-215 (370)
32 smart00544 MA3 Domain in DAP-5 24.2 1.2E+02 0.0026 20.3 3.4 40 12-58 2-41 (113)
33 PRK10941 hypothetical protein; 24.0 1.9E+02 0.0041 23.5 5.0 40 3-48 33-74 (269)
34 PF07582 AP_endonuc_2_N: AP en 23.5 48 0.001 21.0 1.2 11 89-99 5-15 (55)
35 cd07642 BAR_ASAP2 The Bin/Amph 23.3 1.7E+02 0.0037 23.4 4.6 49 8-61 18-68 (215)
36 cd03568 VHS_STAM VHS domain fa 23.3 1.9E+02 0.0041 21.2 4.5 21 81-101 116-136 (144)
37 PF01963 TraB: TraB family; I 22.9 40 0.00086 25.8 0.9 13 90-102 246-258 (259)
38 PF00382 TFIIB: Transcription 22.9 2E+02 0.0044 17.9 6.3 60 42-110 6-65 (71)
39 PHA00438 hypothetical protein 22.9 45 0.00097 23.0 1.0 11 89-99 40-50 (81)
40 PF08041 PetM: PetM family of 22.9 95 0.0021 17.7 2.2 16 82-97 14-29 (31)
41 COG1400 SEC65 Signal recogniti 21.9 62 0.0013 22.7 1.6 15 35-49 35-49 (93)
42 COG3023 ampD N-acetyl-anhydrom 21.8 38 0.00083 27.9 0.6 84 6-109 126-223 (257)
43 cd07640 BAR_ASAP3 The Bin/Amph 21.5 1.3E+02 0.0028 24.2 3.5 38 8-50 18-55 (213)
44 cd04783 HTH_MerR1 Helix-Turn-H 21.4 1.1E+02 0.0025 21.4 2.9 28 29-59 41-68 (126)
45 PF01585 G-patch: G-patch doma 21.1 68 0.0015 19.0 1.5 14 87-100 3-16 (45)
46 PLN02554 UDP-glycosyltransfera 20.5 1.7E+02 0.0037 25.4 4.3 21 2-22 442-462 (481)
47 PF11121 DUF2639: Protein of u 20.3 76 0.0016 19.1 1.5 20 35-54 6-25 (40)
48 PF09633 DUF2023: Protein of u 20.0 36 0.00078 24.4 0.1 39 7-51 6-44 (101)
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=1.3e-41 Score=261.51 Aligned_cols=107 Identities=47% Similarity=0.717 Sum_probs=93.6
Q ss_pred chHHHHHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCccchHHHHHHHHHHHHhhccCCCcccccccccccc
Q 035819 2 ESCAQRIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSYHFEGEIKRFLNSIYNKRNSRRSSTYHAKENQES 81 (122)
Q Consensus 2 ~~~~~~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~~~~~~~ 81 (122)
+.|.+++++||++||.||.... .+++++|+|||+||||||+|||++||+++|+.||+.|..... ...
T Consensus 22 ~~~~~~~~~Lk~~v~~~l~~~~-----~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~--------~~~ 88 (183)
T PF01397_consen 22 EKCKERAEELKEEVRNMLPASY-----PDPLEKLELIDTLQRLGISYHFEDEIKEILDSIYRSWDEDNE--------EID 88 (183)
T ss_dssp HHHHHHHHHHHHHHHHHHHSSS-----SHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHHTTTTTSH--------TSS
T ss_pred HHHHHHHHHHHHHHHHHHhhcC-----CCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhhhcccccc--------ccC
Confidence 5788999999999999998764 589999999999999999999999999999999999876531 234
Q ss_pred hHHHHHHHHHHHHhcCCccChhhhhcccCCCCcccccccc
Q 035819 82 LLYAASLEFRLLRQHGYDIHAHVVSDGAHLEQQYHESLFN 121 (122)
Q Consensus 82 dL~~~AL~FRLLRqhGy~VS~DVF~~F~d~~g~f~~~l~~ 121 (122)
|||+|||+|||||||||+||||||++|+|++|+|++++.+
T Consensus 89 dL~~~AL~FRLLRqhGy~VS~DvF~~F~d~~g~F~~~l~~ 128 (183)
T PF01397_consen 89 DLYTTALRFRLLRQHGYYVSSDVFNKFKDEKGNFKESLSN 128 (183)
T ss_dssp CHHHHHHHHHHHHHTT----GGGGGGGBETTSSBSGGGGG
T ss_pred chhHHHHHHHHHHHcCCcccHHHHhCcccCCCccchhhhH
Confidence 9999999999999999999999999999999999998764
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=7.5e-37 Score=264.03 Aligned_cols=107 Identities=45% Similarity=0.701 Sum_probs=96.0
Q ss_pred hHHHHHHHHHHHHHHHHhhc--ccCCcccchhhhHHHHHHHHHhCCccchHHHHHHHHHHHHhhccCCCccccccccccc
Q 035819 3 SCAQRIEKLKGEVRLMLDNY--KEVDDYVDALHCLEIVDNLQRLGVSYHFEGEIKRFLNSIYNKRNSRRSSTYHAKENQE 80 (122)
Q Consensus 3 ~~~~~~~~LkeeVr~ml~~~--~~~~~~~d~~~~L~lID~LqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~~~~~~ 80 (122)
.+.+++++||++||.||... + .+++++|+|||+||||||+|||++||+++|+.||+.|...+ ....
T Consensus 28 ~~~~~~~~lk~~v~~~~~~~~~~-----~~~~~~l~liD~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~-------~~~~ 95 (542)
T cd00684 28 ELEEEIEELKEEVRKMLEDSEYP-----VDLFERLWLIDRLQRLGISYHFEDEIKEILDYIYRYWTERG-------ESNE 95 (542)
T ss_pred HHHHHHHHHHHHHHHHHHhcccC-----CCHHHHHHHHHHHHHcCchhhhHHHHHHHHHHHHHhhcccc-------cccC
Confidence 47889999999999999863 3 68999999999999999999999999999999999886432 1235
Q ss_pred chHHHHHHHHHHHHhcCCccChhhhhcccCCCCcccccccc
Q 035819 81 SLLYAASLEFRLLRQHGYDIHAHVVSDGAHLEQQYHESLFN 121 (122)
Q Consensus 81 ~dL~~~AL~FRLLRqhGy~VS~DVF~~F~d~~g~f~~~l~~ 121 (122)
.|||+|||+|||||||||+||||||++|+|++|+|++++.+
T Consensus 96 ~dl~~~al~FRlLR~~Gy~vs~dvf~~F~~~~g~f~~~~~~ 136 (542)
T cd00684 96 DDLYTTALGFRLLRQHGYNVSSDVFKKFKDEDGKFKESLTQ 136 (542)
T ss_pred CCHHHHHHHHHHHHHcCCCcCHHHHhhhcCCCCCcCchhhh
Confidence 79999999999999999999999999999999999998754
No 3
>PLN02279 ent-kaur-16-ene synthase
Probab=99.91 E-value=6.8e-25 Score=197.53 Aligned_cols=83 Identities=34% Similarity=0.490 Sum_probs=73.6
Q ss_pred cchhhhHHHHHHHHHhCCccchHHHHHHHHHHHHhhccCCCcccccccccccchHHHHHHHHHHHHhcCCccChhhhhcc
Q 035819 29 VDALHCLEIVDNLQRLGVSYHFEGEIKRFLNSIYNKRNSRRSSTYHAKENQESLLYAASLEFRLLRQHGYDIHAHVVSDG 108 (122)
Q Consensus 29 ~d~~~~L~lID~LqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~DVF~~F 108 (122)
.++++++++||+||||||+|||++||+++|+.+|+.|.... .+...||++|||+|||||||||+||||||++|
T Consensus 268 ~~~fe~l~lvd~L~rlGi~~hF~~EI~~~L~~~~~~~~~~~-------~~~~~Dl~~tAl~FRLLR~hGy~VS~dvf~~F 340 (784)
T PLN02279 268 LDQYARLSMVDTLERLGIDRHFRKEIKSVLDETYRYWLQGE-------EEIFLDLATCALAFRILRLNGYDVSSDPLKQF 340 (784)
T ss_pred ccHHHHhHHHHHHHHhCCccccHHHHHHHHHHHHHhhcccc-------cCCCCCHHHHHHHHHHHHHcCCCCChhHHhhc
Confidence 46899999999999999999999999999999999876421 13457999999999999999999999999999
Q ss_pred cCCCCccccccc
Q 035819 109 AHLEQQYHESLF 120 (122)
Q Consensus 109 ~d~~g~f~~~l~ 120 (122)
+|++ |++++.
T Consensus 341 ~~~~--F~~~l~ 350 (784)
T PLN02279 341 AEDH--FSDSLG 350 (784)
T ss_pred CCCc--ccchhc
Confidence 9764 998873
No 4
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.91 E-value=1.2e-24 Score=196.12 Aligned_cols=87 Identities=29% Similarity=0.381 Sum_probs=74.6
Q ss_pred cchhhhHHHHHHHHHhCCccchHHHHHHHHHHHHhhccCCCcccccccccccchHHHHHHHHHHHHhcCCccChhhhhcc
Q 035819 29 VDALHCLEIVDNLQRLGVSYHFEGEIKRFLNSIYNKRNSRRSSTYHAKENQESLLYAASLEFRLLRQHGYDIHAHVVSDG 108 (122)
Q Consensus 29 ~d~~~~L~lID~LqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~DVF~~F 108 (122)
.+++++|+|||+||||||+|||++||+++|+.+|+.|...+ .+++......|+++|||+|||||||||+||||||++|
T Consensus 308 ~d~fE~LwlVDtLqRLGIs~hF~~EI~~iLd~iy~~w~~~g--~~~a~~~~~~Dld~TALaFRLLRqhGy~VS~DvF~~F 385 (800)
T PLN02592 308 VDLFEHIWAVDRLQRLGISRYFEPEIKECIDYVHRYWTENG--ICWARNSHVHDIDDTAMGFRLLRLHGHQVSADVFKHF 385 (800)
T ss_pred CcHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhcC--cccccCCCcCCHHHHHHHHHHHHHcCCCCChHHHHhh
Confidence 47899999999999999999999999999999999775432 1222223357999999999999999999999999999
Q ss_pred cCCCCccccc
Q 035819 109 AHLEQQYHES 118 (122)
Q Consensus 109 ~d~~g~f~~~ 118 (122)
++ +|.|+..
T Consensus 386 ~~-~g~F~~~ 394 (800)
T PLN02592 386 EK-GGEFFCF 394 (800)
T ss_pred cC-CCCcccc
Confidence 98 8999754
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=74.69 E-value=3.4 Score=25.04 Aligned_cols=25 Identities=16% Similarity=0.271 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhcCCccChhhhhccc
Q 035819 85 AASLEFRLLRQHGYDIHAHVVSDGA 109 (122)
Q Consensus 85 ~~AL~FRLLRqhGy~VS~DVF~~F~ 109 (122)
.+.-.+.-|+++||++|++++..+.
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L 44 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEIL 44 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHH
Confidence 3444456669999999999987653
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=68.20 E-value=28 Score=27.50 Aligned_cols=53 Identities=17% Similarity=0.211 Sum_probs=37.5
Q ss_pred hHHHHHHHHHHHHHHHHhhcccCCcccc-hhhhHHHHHHHHHhCCccc--hHHHHHHHHHHH
Q 035819 3 SCAQRIEKLKGEVRLMLDNYKEVDDYVD-ALHCLEIVDNLQRLGVSYH--FEGEIKRFLNSI 61 (122)
Q Consensus 3 ~~~~~~~~LkeeVr~ml~~~~~~~~~~d-~~~~L~lID~LqRLGI~yh--Fe~EI~~~L~~i 61 (122)
.+..+.++++.-+|.|..+. .+ .-....++++|+.||=..- -+.+|..+|.+.
T Consensus 13 ~~~~~l~Kl~K~~k~~~~~g------~~~~~~~~~F~~aL~~~g~~~~~~~~~~i~~~l~kF 68 (215)
T cd07604 13 GDRVGLQKLKKAVKAIHNSG------LAHVENELQFAEALEKLGSKALSREEEDLGAAFLKF 68 (215)
T ss_pred HHHHHHHHHHHHHHHHHHhH------HHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHH
Confidence 34567888999999988764 33 4467899999999993222 333578877654
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=59.38 E-value=21 Score=25.22 Aligned_cols=42 Identities=26% Similarity=0.284 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCccchHHHHHH
Q 035819 6 QRIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSYHFEGEIKR 56 (122)
Q Consensus 6 ~~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~yhFe~EI~~ 56 (122)
+++.-|.+++|..|..+ .+.++++-+..+||-| +--++||+.
T Consensus 47 e~IrwlI~e~r~~l~~t------ensf~qItfmqaLqlL---lEve~eirt 88 (94)
T PF00601_consen 47 EEIRWLIEEHRHRLKIT------ENSFEQITFMQALQLL---LEVEQEIRT 88 (94)
T ss_dssp HHHHHHHHHHHHC----------TTSHHHHHHHHHHHHH---HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh------hhhHHHHHHHHHHHHH---HHHHHHHHH
Confidence 56777888888888776 5777777766666655 556666654
No 8
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=56.02 E-value=27 Score=25.80 Aligned_cols=54 Identities=28% Similarity=0.399 Sum_probs=31.7
Q ss_pred HHHHHHHHHhCCccchHHHHHHHHHHHHhhccCCCccccccccc-ccchH--HHHHHHHHHHHhcCC
Q 035819 35 LEIVDNLQRLGVSYHFEGEIKRFLNSIYNKRNSRRSSTYHAKEN-QESLL--YAASLEFRLLRQHGY 98 (122)
Q Consensus 35 L~lID~LqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~~~~-~~~dL--~~~AL~FRLLRqhGy 98 (122)
-.+|+.|+.|||++.- ++--+|-.......+ ++- ....| ..+|++-|.||..|+
T Consensus 14 ~~~ie~L~~lgi~R~v------A~tlv~L~~~~E~sS----~~IE~~sgLRQPEVSiAMr~Lre~gW 70 (124)
T COG4738 14 YEIIELLRILGIPRNV------ATTLVCLAKGDEASS----REIERVSGLRQPEVSIAMRYLRENGW 70 (124)
T ss_pred HHHHHHHHHcCCCchH------HHHHHHHhcCcchhh----hhhHHhhcCCCchhHHHHHHHHHccc
Confidence 4699999999999865 222232222211100 000 01222 369999999999995
No 9
>PLN02863 UDP-glucoronosyl/UDP-glucosyl transferase family protein
Probab=52.42 E-value=26 Score=30.53 Aligned_cols=41 Identities=12% Similarity=0.135 Sum_probs=30.3
Q ss_pred chHHHHHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCc
Q 035819 2 ESCAQRIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVS 47 (122)
Q Consensus 2 ~~~~~~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~ 47 (122)
+.|.+++.+|++.++..+...+ ...-.--+||+.|+++|+.
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 5678899999999888876542 2223335689999999985
No 10
>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=45.19 E-value=47 Score=24.32 Aligned_cols=22 Identities=14% Similarity=0.223 Sum_probs=18.0
Q ss_pred chHHHHHHHHHHHHhcCCccCh
Q 035819 81 SLLYAASLEFRLLRQHGYDIHA 102 (122)
Q Consensus 81 ~dL~~~AL~FRLLRqhGy~VS~ 102 (122)
.++-.+.=.|..||..||..|+
T Consensus 120 ~~l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 120 PQLKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred cccHHHHHHHHHHHHcCCCCCC
Confidence 4666777789999999998875
No 11
>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=43.23 E-value=21 Score=21.54 Aligned_cols=21 Identities=24% Similarity=0.370 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHhcCCccChhh
Q 035819 84 YAASLEFRLLRQHGYDIHAHV 104 (122)
Q Consensus 84 ~~~AL~FRLLRqhGy~VS~DV 104 (122)
-.++|.=|+|+..||.|-+=-
T Consensus 18 g~t~lk~r~L~~~G~~Vi~Ip 38 (58)
T PF08373_consen 18 GSTKLKHRHLKALGYKVISIP 38 (58)
T ss_pred hHHHHHHHHHHHCCCEEEEec
Confidence 579999999999999986543
No 12
>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=42.08 E-value=60 Score=26.10 Aligned_cols=52 Identities=10% Similarity=0.196 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCcc--chHHHHHHHHHHH
Q 035819 5 AQRIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSY--HFEGEIKRFLNSI 61 (122)
Q Consensus 5 ~~~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~y--hFe~EI~~~L~~i 61 (122)
..++++||.-|+.|..+.. .=.-..-.+|+.|.+||=.. -=+.+|.++|.+.
T Consensus 15 e~~L~Kl~K~~kam~~SG~-----~yv~n~~~f~~~l~~Lg~~~~~~dd~~i~~a~~kf 68 (215)
T cd07641 15 RTALQKVKKSVKAIYNSGQ-----DHVQNEENYAQALDKFGSNFLSRDNPDLGTAFVKF 68 (215)
T ss_pred HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHhhccCCchhHHHHHHHH
Confidence 4578899999999998753 23345678999999999444 3356777777665
No 13
>PF11000 DUF2840: Protein of unknown function (DUF2840); InterPro: IPR021263 This bacterial family of proteins have no known function.
Probab=40.70 E-value=18 Score=27.53 Aligned_cols=16 Identities=25% Similarity=0.584 Sum_probs=13.9
Q ss_pred hhHHHHHHHHHhCCcc
Q 035819 33 HCLEIVDNLQRLGVSY 48 (122)
Q Consensus 33 ~~L~lID~LqRLGI~y 48 (122)
.-|..||+++.|||+-
T Consensus 96 ~VL~~IDaiEalGidp 111 (149)
T PF11000_consen 96 RVLQAIDAIEALGIDP 111 (149)
T ss_pred HHHHHHhHHHHcCCCh
Confidence 4599999999999974
No 14
>PF14164 YqzH: YqzH-like protein
Probab=39.32 E-value=13 Score=24.45 Aligned_cols=17 Identities=41% Similarity=0.647 Sum_probs=13.2
Q ss_pred HHHHHhcCCccChhhhh
Q 035819 90 FRLLRQHGYDIHAHVVS 106 (122)
Q Consensus 90 FRLLRqhGy~VS~DVF~ 106 (122)
=+-|||+||++++.-+.
T Consensus 11 ~~~l~QYg~d~~~~pls 27 (64)
T PF14164_consen 11 INCLRQYGYDVECMPLS 27 (64)
T ss_pred HHHHHHhCCcccCCCCC
Confidence 36789999998887554
No 15
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=37.47 E-value=1.3e+02 Score=20.30 Aligned_cols=48 Identities=21% Similarity=0.318 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHh---CCccchHHHHHHH
Q 035819 4 CAQRIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRL---GVSYHFEGEIKRF 57 (122)
Q Consensus 4 ~~~~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRL---GI~yhFe~EI~~~ 57 (122)
|..++..+.+.++.++... ...-.-+.+|+.+-+. -++..|.+||+-+
T Consensus 25 ~k~~i~~l~~~~~~~~~~~------~~~~~~~~~v~~~~~~l~~~~~~~~~~EirGI 75 (95)
T PF15508_consen 25 YKDEIRELIEVLKDLLQSF------VPSGKVLDFVDKLLPHLLRYLPQPYAEEIRGI 75 (95)
T ss_pred HHHHHHHHHHHHHHHHHHh------CCchHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 4455556666666666542 1111234555554433 3466677777766
No 16
>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=36.74 E-value=61 Score=27.58 Aligned_cols=68 Identities=16% Similarity=0.150 Sum_probs=43.1
Q ss_pred chhhhHHHHHHHHHhCCc---cchHHHHHHHHHHHHhhccCCCcccccccccccchHHHHH-----------HHHHHHHh
Q 035819 30 DALHCLEIVDNLQRLGVS---YHFEGEIKRFLNSIYNKRNSRRSSTYHAKENQESLLYAAS-----------LEFRLLRQ 95 (122)
Q Consensus 30 d~~~~L~lID~LqRLGI~---yhFe~EI~~~L~~i~~~~~~~~~~~~~~~~~~~~dL~~~A-----------L~FRLLRq 95 (122)
.++..-++|+.+...... ..+...|...|..+..+..... ..-+++.+| .-..-||+
T Consensus 278 GpL~d~~fl~~ml~~~~~~~~~~~~~ri~~lL~~i~eE~~~~P---------~yY~l~~ias~lk~~~P~~~~ii~aL~~ 348 (377)
T PF02005_consen 278 GPLHDKEFLEKMLEEAEEMPELNTSKRIEKLLETIKEELIDPP---------FYYDLHEIASRLKCNPPPLDKIISALRN 348 (377)
T ss_dssp S-SB-HHHHHHHHHHHCT-S-TTTHHHHHHHHHHHHHCHS-SS---------S-EEHHHHHHHHT-SC--HHHHHHHHHH
T ss_pred cccCCHHHHHHHHhhhhccchhhhHHHHhhhcchhhhhcccce---------eEEeHHHHHHhcCCCCCCHHHHHHHHhh
Confidence 456666677766666555 4668899999999876532211 123455544 23566999
Q ss_pred cCCccChhhhh
Q 035819 96 HGYDIHAHVVS 106 (122)
Q Consensus 96 hGy~VS~DVF~ 106 (122)
.||.+|.-.|+
T Consensus 349 ~Gy~aSrTH~~ 359 (377)
T PF02005_consen 349 AGYRASRTHFD 359 (377)
T ss_dssp TTTTEEEETTC
T ss_pred cceEEEecccC
Confidence 99999987775
No 17
>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=35.86 E-value=1.1e+02 Score=23.81 Aligned_cols=51 Identities=22% Similarity=0.182 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHhhcccCCcccch-hhhHHHHHHHHHhCCccchHHHHHHHHHHH
Q 035819 5 AQRIEKLKGEVRLMLDNYKEVDDYVDA-LHCLEIVDNLQRLGVSYHFEGEIKRFLNSI 61 (122)
Q Consensus 5 ~~~~~~LkeeVr~ml~~~~~~~~~~d~-~~~L~lID~LqRLGI~yhFe~EI~~~L~~i 61 (122)
..++++|+..++.|+... ... .....++++|+.||-.+-=+..|..+|.+.
T Consensus 15 ~~~l~kl~K~~~~~~~ag------~~~~~a~~~F~~~L~~~~~~~~~d~~i~~~l~kF 66 (200)
T cd07603 15 ETRLEKLLKLCNGMVDSG------KTYVNANSLFVNSLNDLSDYFRDDSLVQNCLNKF 66 (200)
T ss_pred HHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH
Confidence 356677777777777654 232 347889999999997543345566666554
No 18
>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=34.97 E-value=1e+02 Score=20.53 Aligned_cols=45 Identities=22% Similarity=0.282 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCccchHHHH-HHHHHHHH
Q 035819 11 LKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSYHFEGEI-KRFLNSIY 62 (122)
Q Consensus 11 LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~yhFe~EI-~~~L~~i~ 62 (122)
+|+.++..|.+. -+.-..-+.+..|+.|+++ .+..++ ..++....
T Consensus 1 ~rk~i~~~l~ey------~~~~d~~ea~~~l~el~~~-~~~~~vv~~~l~~~l 46 (113)
T PF02847_consen 1 LRKKIFSILMEY------FSSGDVDEAVECLKELKLP-SQHHEVVKVILECAL 46 (113)
T ss_dssp HHHHHHHHHHHH------HHHT-HHHHHHHHHHTT-G-GGHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHH------hcCCCHHHHHHHHHHhCCC-ccHHHHHHHHHHHHh
Confidence 466777777654 3333446788889999999 555554 44444444
No 19
>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=33.04 E-value=32 Score=20.43 Aligned_cols=13 Identities=38% Similarity=0.685 Sum_probs=10.7
Q ss_pred HHHhcCCccChhh
Q 035819 92 LLRQHGYDIHAHV 104 (122)
Q Consensus 92 LLRqhGy~VS~DV 104 (122)
+.|.+||.+|++-
T Consensus 35 lA~~~Gy~ft~~e 47 (49)
T PF07862_consen 35 LAREAGYDFTEEE 47 (49)
T ss_pred HHHHcCCCCCHHH
Confidence 5699999999763
No 20
>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=29.79 E-value=85 Score=19.10 Aligned_cols=24 Identities=33% Similarity=0.618 Sum_probs=18.9
Q ss_pred hhhHHHHHHHHHhCCccchHHHHHHHH
Q 035819 32 LHCLEIVDNLQRLGVSYHFEGEIKRFL 58 (122)
Q Consensus 32 ~~~L~lID~LqRLGI~yhFe~EI~~~L 58 (122)
+++|.+|=.++.||++- +||++.|
T Consensus 1 v~rL~~I~~~r~lGfsL---~eI~~~l 24 (65)
T PF09278_consen 1 VERLQFIRRLRELGFSL---EEIRELL 24 (65)
T ss_dssp HHHHHHHHHHHHTT--H---HHHHHHH
T ss_pred ChHHHHHHHHHHcCCCH---HHHHHHH
Confidence 36799999999999985 7888888
No 21
>PF13369 Transglut_core2: Transglutaminase-like superfamily
Probab=29.60 E-value=2.2e+02 Score=20.59 Aligned_cols=82 Identities=24% Similarity=0.323 Sum_probs=52.5
Q ss_pred chHHHHHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHH--HHhCCccch---HHHHHHHHHHHHhhccCCCccccccc
Q 035819 2 ESCAQRIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNL--QRLGVSYHF---EGEIKRFLNSIYNKRNSRRSSTYHAK 76 (122)
Q Consensus 2 ~~~~~~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~L--qRLGI~yhF---e~EI~~~L~~i~~~~~~~~~~~~~~~ 76 (122)
|.+.++++.+-.+||..+... .++.++++.|..+ +.+|....- .+--+..|..+......
T Consensus 1 ~~~~~~Ld~la~~v~~~~~~~------~~~~~~l~al~~~l~~~~gF~~~~~~y~~~~n~~l~~vL~~r~G--------- 65 (152)
T PF13369_consen 1 EAVLQRLDALAAQVRQRLPAR------ASPREKLEALNDVLYQELGFSGNSENYYDPENSFLHKVLERRRG--------- 65 (152)
T ss_pred ChHHHHHHHHHHHHHHHcccc------CCHHHHHHHHHHHHHHHcCCCCCccccCChHhhhHHHHHhcCCC---------
Confidence 468899999999999998765 4677777766654 688876422 22225556666543221
Q ss_pred ccccchHHHHHHHHHHHHhcCCccCh
Q 035819 77 ENQESLLYAASLEFRLLRQHGYDIHA 102 (122)
Q Consensus 77 ~~~~~dL~~~AL~FRLLRqhGy~VS~ 102 (122)
.-+--++|.=-+.|.-|.++.+
T Consensus 66 ----~Pi~L~ily~~va~rlGl~~~~ 87 (152)
T PF13369_consen 66 ----IPISLAILYLEVARRLGLPAEP 87 (152)
T ss_pred ----CcHHHHHHHHHHHHHcCCeEEE
Confidence 1233455555677888877665
No 22
>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=29.20 E-value=18 Score=20.21 Aligned_cols=15 Identities=33% Similarity=0.567 Sum_probs=11.6
Q ss_pred HHHHhcCCccChhhh
Q 035819 91 RLLRQHGYDIHAHVV 105 (122)
Q Consensus 91 RLLRqhGy~VS~DVF 105 (122)
+-||.||..|.|-..
T Consensus 7 Wc~rLhGW~i~ppll 21 (28)
T PF03578_consen 7 WCLRLHGWPIMPPLL 21 (28)
T ss_pred hheeeccCcccCcce
Confidence 458999999998543
No 23
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=29.16 E-value=1.7e+02 Score=19.21 Aligned_cols=62 Identities=15% Similarity=0.164 Sum_probs=37.0
Q ss_pred cchhhhHHHHHHHHHhCCccchHHHHHHHHHHHHhhccCCCcccccccccccchHHHHHHHHHHHHhcCCccChh
Q 035819 29 VDALHCLEIVDNLQRLGVSYHFEGEIKRFLNSIYNKRNSRRSSTYHAKENQESLLYAASLEFRLLRQHGYDIHAH 103 (122)
Q Consensus 29 ~d~~~~L~lID~LqRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~D 103 (122)
+..+..-++...+.++|++ +.|++.++..+- ...+. ....+=+-.++..--..+.|+.||+.
T Consensus 24 ~G~Is~~el~~~l~~~~~~---~~ev~~i~~~~d-~~~~g---------~I~~~eF~~~~~~~~~~~~g~~~~~~ 85 (96)
T smart00027 24 DGTVTGAQAKPILLKSGLP---QTLLAKIWNLAD-IDNDG---------ELDKDEFALAMHLIYRKLNGYPIPAS 85 (96)
T ss_pred CCeEeHHHHHHHHHHcCCC---HHHHHHHHHHhc-CCCCC---------CcCHHHHHHHHHHHHHHHcCCCCCcc
Confidence 3456667788888889976 467776665431 11111 11223334555666667789999975
No 24
>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=29.08 E-value=1.9e+02 Score=21.97 Aligned_cols=49 Identities=27% Similarity=0.295 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCccch----HHHHHHHHHHHH
Q 035819 7 RIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSYHF----EGEIKRFLNSIY 62 (122)
Q Consensus 7 ~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~yhF----e~EI~~~L~~i~ 62 (122)
.++.+|.+|...+... |.++..+.--...-.-||.+| +++|+++-+...
T Consensus 35 EL~evk~~v~~~I~ev-------D~Le~~er~aR~rL~eVS~~f~~ysE~dik~AYe~A~ 87 (159)
T PF05384_consen 35 ELEEVKEEVSEVIEEV-------DKLEKRERQARQRLAEVSRNFDRYSEEDIKEAYEEAH 87 (159)
T ss_pred HHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHH
Confidence 4445555555554432 333333333333333457777 899998866654
No 25
>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=29.00 E-value=33 Score=18.35 Aligned_cols=21 Identities=24% Similarity=0.444 Sum_probs=14.0
Q ss_pred HHHHHHHHhcCCccChhhhhc
Q 035819 87 SLEFRLLRQHGYDIHAHVVSD 107 (122)
Q Consensus 87 AL~FRLLRqhGy~VS~DVF~~ 107 (122)
.|-.+=|..+||.-++..|.+
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 345667788888888777753
No 26
>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=27.55 E-value=91 Score=25.50 Aligned_cols=46 Identities=24% Similarity=0.268 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCccchHHHHHHHHHHHHh
Q 035819 10 KLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSYHFEGEIKRFLNSIYN 63 (122)
Q Consensus 10 ~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~yhFe~EI~~~L~~i~~ 63 (122)
-|++-|=++|.- .|+.+-+|+..|+|-||.--=.++|..+|+.|-.
T Consensus 198 plReRvIHLLAL--------kpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~ 243 (284)
T PF10390_consen 198 PLRERVIHLLAL--------KPYKKPELLLRLQKDGLSPKDKDELDSILQEVAN 243 (284)
T ss_dssp -HHHHHHHHHHH--------S-EEHHHHHHHHHHH---HHHHHHHHHHHHHCCE
T ss_pred cccccchhhhhc--------CccccHHHHHHHHhcCCChHHHHHHHHHHHHHhc
Confidence 366667677652 4566779999999999998888889999998854
No 27
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=26.77 E-value=69 Score=19.44 Aligned_cols=40 Identities=20% Similarity=0.262 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCccchHHHHHHHH
Q 035819 9 EKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSYHFEGEIKRFL 58 (122)
Q Consensus 9 ~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~yhFe~EI~~~L 58 (122)
+.+..|+.++|... .+ -..+..+..+|+-.+.=.|++.+|
T Consensus 25 ERi~~El~kil~~~-------~~---~~~~~~l~~~gll~~ifP~l~~a~ 64 (64)
T PF12627_consen 25 ERIREELEKILSSP-------NP---SRAFKLLDELGLLEYIFPELDAAL 64 (64)
T ss_dssp HHHHHHHHHHHTST-------TH---HHHHHHHHHTTCHHHHSTTHHT--
T ss_pred HHHHHHHHHHHcCC-------CH---HHHHHHHHHcCCHHHHCccccccC
Confidence 44567777887753 33 345667788887666546666554
No 28
>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=26.29 E-value=50 Score=25.95 Aligned_cols=47 Identities=28% Similarity=0.338 Sum_probs=33.9
Q ss_pred HHhCCccchHHHHHHHHHHHHhhccCCCcccccccccccchHHHHHHHHHHHHhcCCccC
Q 035819 42 QRLGVSYHFEGEIKRFLNSIYNKRNSRRSSTYHAKENQESLLYAASLEFRLLRQHGYDIH 101 (122)
Q Consensus 42 qRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS 101 (122)
-.=|+.--|.-..+..|-.+|...+ ...-|-+|+.|+||+..|+++-
T Consensus 45 ~HpG~~N~flv~~~~~LA~~Y~d~S-------------vLE~~H~~~~~~lL~~~~~nil 91 (237)
T PF00233_consen 45 DHPGVNNAFLVKTNSPLAILYNDRS-------------VLENHHCALAFQLLRKEECNIL 91 (237)
T ss_dssp T-SSSCHHHHHHTTSHHHHHTTTSS-------------HHHHHHHHHHHHHHTSTTTTTT
T ss_pred CCCccccchhhccccchhhhcCccC-------------CccccHHHHHHHHHHhhhhhhh
Confidence 3457777788888888877764321 3467889999999999888653
No 29
>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=26.23 E-value=57 Score=26.61 Aligned_cols=17 Identities=35% Similarity=0.403 Sum_probs=15.6
Q ss_pred cchHHHHHHHHHHHHhc
Q 035819 80 ESLLYAASLEFRLLRQH 96 (122)
Q Consensus 80 ~~dL~~~AL~FRLLRqh 96 (122)
..|.|+.-|-.|-||.|
T Consensus 124 INDPYDlGLLLRhLRHH 140 (238)
T PF02084_consen 124 INDPYDLGLLLRHLRHH 140 (238)
T ss_pred cCChhhHHHHHHHHHHH
Confidence 46999999999999998
No 30
>PF15469 Sec5: Exocyst complex component Sec5
Probab=25.99 E-value=1.8e+02 Score=21.42 Aligned_cols=38 Identities=18% Similarity=0.195 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCcc
Q 035819 6 QRIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSY 48 (122)
Q Consensus 6 ~~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~y 48 (122)
+.++.+++.+..-|.+.. .+.-+.+.+|..|..||+.-
T Consensus 135 ~ii~~~r~~l~~~L~~~~-----~s~~~~~~~i~~Ll~L~~~~ 172 (182)
T PF15469_consen 135 KIIEEFREKLWEKLLSPP-----SSQEEFLKLIRKLLELNVEE 172 (182)
T ss_pred HHHHHHHHHHHHHHhCCC-----CCHHHHHHHHHHHHhCCCCC
Confidence 344555555555555542 45667888999999998753
No 31
>COG1060 ThiH Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]
Probab=24.47 E-value=63 Score=27.59 Aligned_cols=36 Identities=33% Similarity=0.329 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCcc
Q 035819 8 IEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSY 48 (122)
Q Consensus 8 ~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~y 48 (122)
++.|.++||+.+...+ .++-..|++++...||||.-
T Consensus 180 aeil~e~vr~~~~p~K-----~~~~~wle~~~~Ah~lGI~~ 215 (370)
T COG1060 180 AEILSEEVRKIHCPPK-----KSPEEWLEIHERAHRLGIPT 215 (370)
T ss_pred eeechHHHHHhhCCCC-----CCHHHHHHHHHHHHHcCCCc
Confidence 4567788998887543 58889999999999999863
No 32
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=24.16 E-value=1.2e+02 Score=20.33 Aligned_cols=40 Identities=23% Similarity=0.336 Sum_probs=25.0
Q ss_pred HHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCccchHHHHHHHH
Q 035819 12 KGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSYHFEGEIKRFL 58 (122)
Q Consensus 12 keeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~yhFe~EI~~~L 58 (122)
++.+..++.+. .++-.--+.+..|..|++. +|..|+=..+
T Consensus 2 ~k~i~~~l~ey------~~~~D~~ea~~~l~~L~~~-~~~~~vv~~~ 41 (113)
T smart00544 2 KKKIFLIIEEY------LSSGDTDEAVHCLLELKLP-EQHHEVVKVL 41 (113)
T ss_pred hhHHHHHHHHH------HHcCCHHHHHHHHHHhCCC-cchHHHHHHH
Confidence 34555555543 2222346788899999999 6777765544
No 33
>PRK10941 hypothetical protein; Provisional
Probab=24.02 E-value=1.9e+02 Score=23.54 Aligned_cols=40 Identities=18% Similarity=0.140 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHH--HHhCCcc
Q 035819 3 SCAQRIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNL--QRLGVSY 48 (122)
Q Consensus 3 ~~~~~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~L--qRLGI~y 48 (122)
.+..+++.|..+||..+... .++.+++..+..+ +.+|.+-
T Consensus 33 ~~~~~L~~l~~~~~~~l~~~------~~~~~~l~~L~~~fy~~lgF~G 74 (269)
T PRK10941 33 DVYDELERLVSLAREEISQL------LPQDEQLEKLIALFYGEWGFGG 74 (269)
T ss_pred HHHHHHHHHHHHHHHhcccc------CCHHHHHHHHHHHHHHHhCCCC
Confidence 45667888888888888764 4666666555554 5555543
No 34
>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=23.45 E-value=48 Score=20.97 Aligned_cols=11 Identities=55% Similarity=0.915 Sum_probs=7.9
Q ss_pred HHHHHHhcCCc
Q 035819 89 EFRLLRQHGYD 99 (122)
Q Consensus 89 ~FRLLRqhGy~ 99 (122)
.|+.||+.||.
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 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=23.35 E-value=1.7e+02 Score=23.44 Aligned_cols=49 Identities=10% Similarity=0.132 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCc--cchHHHHHHHHHHH
Q 035819 8 IEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVS--YHFEGEIKRFLNSI 61 (122)
Q Consensus 8 ~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~--yhFe~EI~~~L~~i 61 (122)
..++|.-||.|-.+.. .=.-....+++.|++||=. .+=+++|..+|.+.
T Consensus 18 l~~~kk~~k~~~~sG~-----~yv~~~~~f~~~L~~LG~~~l~~dd~~~~~~l~kf 68 (215)
T cd07642 18 LYKMKKSVKAIHTSGL-----AHVENEEQYTQALEKFGSNCVCRDDPDLGSAFLKF 68 (215)
T ss_pred HHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHH
Confidence 4678888888876642 2234567899999999975 44467777776554
No 36
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=23.29 E-value=1.9e+02 Score=21.20 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=17.6
Q ss_pred chHHHHHHHHHHHHhcCCccC
Q 035819 81 SLLYAASLEFRLLRQHGYDIH 101 (122)
Q Consensus 81 ~dL~~~AL~FRLLRqhGy~VS 101 (122)
.+|--++=.+..|+..||..+
T Consensus 116 ~~l~~i~~~y~~L~~~G~~f~ 136 (144)
T cd03568 116 PSLSLMSDLYKKLKNEGPDLV 136 (144)
T ss_pred cccHHHHHHHHHHHHcCCCCC
Confidence 467777888999999999876
No 37
>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=22.94 E-value=40 Score=25.76 Aligned_cols=13 Identities=38% Similarity=0.889 Sum_probs=11.4
Q ss_pred HHHHHhcCCccCh
Q 035819 90 FRLLRQHGYDIHA 102 (122)
Q Consensus 90 FRLLRqhGy~VS~ 102 (122)
..+||+.||.|++
T Consensus 246 l~lLr~~Gy~V~~ 258 (259)
T PF01963_consen 246 LDLLRKKGYTVEP 258 (259)
T ss_pred HHHHHhCCceeec
Confidence 5899999999975
No 38
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=22.94 E-value=2e+02 Score=17.88 Aligned_cols=60 Identities=13% Similarity=0.135 Sum_probs=38.7
Q ss_pred HHhCCccchHHHHHHHHHHHHhhccCCCcccccccccccchHHHHHHHHHHHHhcCCccChhhhhcccC
Q 035819 42 QRLGVSYHFEGEIKRFLNSIYNKRNSRRSSTYHAKENQESLLYAASLEFRLLRQHGYDIHAHVVSDGAH 110 (122)
Q Consensus 42 qRLGI~yhFe~EI~~~L~~i~~~~~~~~~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~DVF~~F~d 110 (122)
.+||++.+..+.-.++.......+...+. ...-...|--|---|++|.++|..-+....+
T Consensus 6 ~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr---------~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~ 65 (71)
T PF00382_consen 6 SKLGLPEDVRERAKEIYKKAQERGLLKGR---------SPESIAAACIYLACRLNGVPRTLKEIAEAAG 65 (71)
T ss_dssp HHTT--HHHHHHHHHHHHHHHHTTTSTTS----------HHHHHHHHHHHHHHHTTSSSSHHHHHHHCT
T ss_pred hHcCCCHHHHHHHHHHHHHHHHcCCcccC---------CHHHHHHHHHHHHHHHcCCCcCHHHHHHHhC
Confidence 57899998888888888877766543221 2333445555666799999999877665443
No 39
>PHA00438 hypothetical protein
Probab=22.90 E-value=45 Score=22.96 Aligned_cols=11 Identities=73% Similarity=1.174 Sum_probs=9.3
Q ss_pred HHHHHHhcCCc
Q 035819 89 EFRLLRQHGYD 99 (122)
Q Consensus 89 ~FRLLRqhGy~ 99 (122)
..++|||+||.
T Consensus 40 ~i~~lR~~G~S 50 (81)
T PHA00438 40 EIRLLRQAGYS 50 (81)
T ss_pred hHHHHHHcCCc
Confidence 46899999995
No 40
>PF08041 PetM: PetM family of cytochrome b6f complex subunit 7; InterPro: IPR012595 This family consists of the PetM family of cytochrome b6f complex subunit IV. The cytochrome b6f complex consists of 7 subunits and contains 2 beta haem's and 1 chlorophyll alpha per cytochrome f. It is highly active in transferring electrons from decylplastoquinol to oxidised plastocyanin [].; GO: 0009512 cytochrome b6f complex; PDB: 2ZT9_F 1Q90_M 2E76_F 2E75_F 2E74_F 2D2C_S 1VF5_S.
Probab=22.89 E-value=95 Score=17.67 Aligned_cols=16 Identities=38% Similarity=0.623 Sum_probs=13.7
Q ss_pred hHHHHHHHHHHHHhcC
Q 035819 82 LLYAASLEFRLLRQHG 97 (122)
Q Consensus 82 dL~~~AL~FRLLRqhG 97 (122)
-|--.|+.|=|||-+|
T Consensus 14 vlvGla~Gf~LLkiQG 29 (31)
T PF08041_consen 14 VLVGLALGFVLLKIQG 29 (31)
T ss_dssp HHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHhheeec
Confidence 4677899999999887
No 41
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=21.90 E-value=62 Score=22.72 Aligned_cols=15 Identities=33% Similarity=0.516 Sum_probs=12.8
Q ss_pred HHHHHHHHHhCCccc
Q 035819 35 LEIVDNLQRLGVSYH 49 (122)
Q Consensus 35 L~lID~LqRLGI~yh 49 (122)
=+++++++.||+.+-
T Consensus 35 ~ei~~a~~~LGl~~~ 49 (93)
T COG1400 35 EEIAEALRELGLKPK 49 (93)
T ss_pred HHHHHHHHHcCCCee
Confidence 468999999999993
No 42
>COG3023 ampD N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]
Probab=21.81 E-value=38 Score=27.91 Aligned_cols=84 Identities=14% Similarity=0.185 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHhhcc----cCC---cc------cchhhhHHHHHHH-HHhCCccchHHHHHHHHHHHHhhccCCCcc
Q 035819 6 QRIEKLKGEVRLMLDNYK----EVD---DY------VDALHCLEIVDNL-QRLGVSYHFEGEIKRFLNSIYNKRNSRRSS 71 (122)
Q Consensus 6 ~~~~~LkeeVr~ml~~~~----~~~---~~------~d~~~~L~lID~L-qRLGI~yhFe~EI~~~L~~i~~~~~~~~~~ 71 (122)
.|++.|++-.|.++...+ .++ .| .||-...-- +.| +.|||+.+++..=.......++.
T Consensus 126 AQiqal~~L~k~i~~ryP~I~~~~I~GHsDIAP~RK~DPG~~FpW-k~l~~~~gigaw~~~~~~~~~~~~~~~------- 197 (257)
T COG3023 126 AQIQALIALLKDIIARYPNITPERIVGHSDIAPGRKTDPGPLFPW-KRLAEALGIGAWLDTAQVQKYLALLKG------- 197 (257)
T ss_pred HHHHHHHHHHHHHHHHccCCCHHHcccccccCcccCCCCCCCCCH-HHHHhhcCcccCCcHhhhhhhhhhhcc-------
Confidence 478888877777775541 111 01 122222211 223 44599999966544433222211
Q ss_pred cccccccccchHHHHHHHHHHHHhcCCccChhhhhccc
Q 035819 72 TYHAKENQESLLYAASLEFRLLRQHGYDIHAHVVSDGA 109 (122)
Q Consensus 72 ~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~DVF~~F~ 109 (122)
-.++--=-.|+.+||.|++++|+.+.
T Consensus 198 ------------~~v~~lq~~L~~YGY~v~~~~~d~~t 223 (257)
T COG3023 198 ------------EDVAALQEMLARYGYGVEIGVFDQET 223 (257)
T ss_pred ------------CCHHHHHHHHHHhCcCCCcchhhHHH
Confidence 23333446789999999999998764
No 43
>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=21.50 E-value=1.3e+02 Score=24.18 Aligned_cols=38 Identities=16% Similarity=0.142 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCccch
Q 035819 8 IEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSYHF 50 (122)
Q Consensus 8 ~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~yhF 50 (122)
..++|.-||.|-.+.- .-.-....+++.|++||=++--
T Consensus 18 L~k~kk~vkai~~sg~-----~hv~ne~~~~~~le~lg~~~l~ 55 (213)
T cd07640 18 LQRIKKIVKAIHNSGL-----NHVENEEQYTEALENLGNSHLS 55 (213)
T ss_pred HHHHHHHHHHHHHhhH-----HHHhHHHHHHHHHHHHhhhhhc
Confidence 4678888888776541 1223357899999999965543
No 44
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.40 E-value=1.1e+02 Score=21.38 Aligned_cols=28 Identities=25% Similarity=0.462 Sum_probs=23.2
Q ss_pred cchhhhHHHHHHHHHhCCccchHHHHHHHHH
Q 035819 29 VDALHCLEIVDNLQRLGVSYHFEGEIKRFLN 59 (122)
Q Consensus 29 ~d~~~~L~lID~LqRLGI~yhFe~EI~~~L~ 59 (122)
.+.+..|.+|-.++.+|++- +||+++|.
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL---~eI~~~l~ 68 (126)
T cd04783 41 EETVTRLRFIKRAQELGFTL---DEIAELLE 68 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCH---HHHHHHHh
Confidence 35678899999999999886 78888775
No 45
>PF01585 G-patch: G-patch domain; InterPro: IPR000467 The D111/G-patch domain [] is a short conserved region of about 40 amino acids which occurs in a number of putative RNA-binding proteins, including tumor suppressor and DNA-damage-repair proteins, suggesting that this domain may have an RNA binding function. This domain has seven highly conserved glycines. A multiple alignment of a small subset of D111/G-patch domains is shown in Fig. 2b of [].; GO: 0003676 nucleic acid binding, 0005622 intracellular
Probab=21.08 E-value=68 Score=19.02 Aligned_cols=14 Identities=29% Similarity=0.766 Sum_probs=12.0
Q ss_pred HHHHHHHHhcCCcc
Q 035819 87 SLEFRLLRQHGYDI 100 (122)
Q Consensus 87 AL~FRLLRqhGy~V 100 (122)
+..||||++.||.-
T Consensus 3 ~~g~~lm~kmGw~~ 16 (45)
T PF01585_consen 3 SIGFKLMKKMGWKP 16 (45)
T ss_pred cHHHHHHHHCCCCC
Confidence 56899999999974
No 46
>PLN02554 UDP-glycosyltransferase family protein
Probab=20.48 E-value=1.7e+02 Score=25.36 Aligned_cols=21 Identities=10% Similarity=0.256 Sum_probs=14.5
Q ss_pred chHHHHHHHHHHHHHHHHhhc
Q 035819 2 ESCAQRIEKLKGEVRLMLDNY 22 (122)
Q Consensus 2 ~~~~~~~~~LkeeVr~ml~~~ 22 (122)
+.|.+++.++++.+|..+...
T Consensus 442 ~~~r~~a~~l~~~~~~av~~g 462 (481)
T PLN02554 442 SDVRKRVKEMSEKCHVALMDG 462 (481)
T ss_pred HHHHHHHHHHHHHHHHHhcCC
Confidence 457777777777777776544
No 47
>PF11121 DUF2639: Protein of unknown function (DUF2639); InterPro: IPR022580 This family is conserved in the Bacillaceae family. Several members are named as being YflJ, but the function is not known.
Probab=20.30 E-value=76 Score=19.11 Aligned_cols=20 Identities=25% Similarity=0.328 Sum_probs=15.8
Q ss_pred HHHHHHHHHhCCccchHHHH
Q 035819 35 LEIVDNLQRLGVSYHFEGEI 54 (122)
Q Consensus 35 L~lID~LqRLGI~yhFe~EI 54 (122)
=|.|..|..+||.+|=..-+
T Consensus 6 Gw~V~eLKk~GI~~h~~rKl 25 (40)
T PF11121_consen 6 GWYVKELKKLGIRRHEGRKL 25 (40)
T ss_pred hHHHHHHHHhCccccchhHH
Confidence 47899999999999864433
No 48
>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=20.04 E-value=36 Score=24.36 Aligned_cols=39 Identities=21% Similarity=0.250 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHhhcccCCcccchhhhHHHHHHHHHhCCccchH
Q 035819 7 RIEKLKGEVRLMLDNYKEVDDYVDALHCLEIVDNLQRLGVSYHFE 51 (122)
Q Consensus 7 ~~~~LkeeVr~ml~~~~~~~~~~d~~~~L~lID~LqRLGI~yhFe 51 (122)
.+-+.++-||.|+.-+ ...-..-..+..|++-||+|+.+
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 4456677788887544 33334455889999999999975
Done!