Query 029478
Match_columns 192
No_of_seqs 121 out of 786
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 13:33:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029478.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029478hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0859 Synaptobrevin/VAMP-lik 100.0 8.4E-46 1.8E-50 302.5 16.4 150 4-174 1-151 (217)
2 KOG0862 Synaptobrevin/VAMP-lik 99.9 2.3E-26 5.1E-31 190.9 16.0 150 5-174 1-160 (216)
3 KOG0861 SNARE protein YKT6, sy 99.9 1.5E-23 3.3E-28 169.1 14.4 146 4-174 1-163 (198)
4 PF13774 Longin: Regulated-SNA 99.8 4.9E-19 1.1E-23 127.1 9.9 71 31-101 1-73 (83)
5 COG5143 SNC1 Synaptobrevin/VAM 99.6 1.8E-15 3.9E-20 124.2 12.1 147 5-174 2-155 (190)
6 KOG0860 Synaptobrevin/VAMP-lik 97.9 1.6E-05 3.5E-10 60.8 4.4 28 147-174 28-55 (116)
7 PF00957 Synaptobrevin: Synapt 97.6 9.3E-05 2E-09 53.5 4.1 28 147-174 2-29 (89)
8 PF04086 SRP-alpha_N: Signal r 91.6 0.33 7.1E-06 41.8 4.9 66 30-97 6-73 (279)
9 PF04099 Sybindin: Sybindin-li 91.4 3 6.6E-05 32.7 9.8 58 33-91 46-113 (142)
10 KOG0781 Signal recognition par 89.8 0.73 1.6E-05 43.6 5.7 87 7-95 4-96 (587)
11 PF01217 Clat_adaptor_s: Clath 86.4 13 0.00028 28.5 12.9 87 6-94 2-96 (141)
12 KOG0938 Adaptor complexes medi 84.4 22 0.00048 32.5 11.7 87 7-95 5-94 (446)
13 PF09426 Nyv1_N: Vacuolar R-SN 78.2 5.5 0.00012 31.5 5.0 57 31-87 46-110 (141)
14 smart00096 UTG Uteroglobin. 77.5 6.2 0.00014 27.6 4.7 46 133-178 21-66 (69)
15 PF01099 Uteroglobin: Uteroglo 77.2 4.1 8.9E-05 27.9 3.7 47 131-177 17-63 (67)
16 cd00633 Secretoglobin Secretog 74.3 8.4 0.00018 26.2 4.6 47 131-177 17-63 (67)
17 PRK11546 zraP zinc resistance 68.4 23 0.00051 28.2 6.5 48 131-181 75-122 (143)
18 PF10436 BCDHK_Adom3: Mitochon 54.6 37 0.0008 27.2 5.6 51 126-182 81-136 (164)
19 cd07634 BAR_GAP10-like The Bin 53.0 50 0.0011 27.8 6.3 56 126-181 39-107 (207)
20 PF05491 RuvB_C: Holliday junc 42.7 21 0.00045 25.5 2.1 43 131-180 12-55 (76)
21 PF10504 DUF2452: Protein of u 42.0 15 0.00033 29.7 1.5 56 28-83 64-126 (159)
22 PF09182 PuR_N: Bacterial puri 40.4 1.3E+02 0.0027 21.2 5.7 53 132-184 5-57 (70)
23 PF10112 Halogen_Hydrol: 5-bro 34.5 1.1E+02 0.0023 24.9 5.4 49 131-179 136-187 (199)
24 cd04889 ACT_PDH-BS-like C-term 33.4 67 0.0014 20.1 3.3 22 168-189 12-33 (56)
25 KOG3369 Transport protein part 32.1 3E+02 0.0065 22.9 9.0 54 35-90 110-167 (199)
26 PF03164 Mon1: Trafficking pro 32.1 2.2E+02 0.0048 26.2 7.6 68 27-94 36-104 (415)
27 KOG2740 Clathrin-associated pr 31.7 1.6E+02 0.0034 27.3 6.3 44 52-95 54-97 (418)
28 PF03179 V-ATPase_G: Vacuolar 31.7 1E+02 0.0022 22.4 4.4 29 150-178 72-100 (105)
29 cd07636 BAR_GRAF The Bin/Amphi 31.1 1.4E+02 0.0031 25.1 5.6 56 126-181 39-107 (207)
30 cd07638 BAR_ACAP2 The Bin/Amph 29.7 1.8E+02 0.0038 24.4 6.0 56 126-181 39-101 (200)
31 cd04908 ACT_Bt0572_1 N-termina 29.1 78 0.0017 20.7 3.1 20 168-187 15-34 (66)
32 cd07601 BAR_APPL The Bin/Amphi 27.6 1.9E+02 0.0041 24.5 5.8 56 126-181 39-105 (215)
33 PF11074 DUF2779: Domain of un 26.8 1.9E+02 0.0041 22.3 5.3 16 52-67 27-42 (130)
34 PF02520 DUF148: Domain of unk 26.4 2.6E+02 0.0057 20.4 6.7 45 127-175 19-63 (113)
35 KOG3368 Transport protein part 26.2 2.5E+02 0.0053 22.3 5.8 55 31-87 44-102 (140)
36 cd07635 BAR_GRAF2 The Bin/Amph 25.1 2.9E+02 0.0064 23.2 6.5 56 126-181 39-107 (207)
37 cd07604 BAR_ASAPs The Bin/Amph 24.6 1.7E+02 0.0038 24.5 5.1 56 126-181 39-103 (215)
38 PF08900 DUF1845: Domain of un 24.6 2.5E+02 0.0054 23.5 6.1 46 128-173 41-87 (217)
39 cd07603 BAR_ACAPs The Bin/Amph 24.2 2.3E+02 0.005 23.5 5.7 56 126-181 39-101 (200)
40 PHA02604 rI.-1 hypothetical pr 23.8 3.6E+02 0.0077 21.1 6.6 81 70-169 36-121 (126)
41 cd07639 BAR_ACAP1 The Bin/Amph 23.4 2.6E+02 0.0057 23.3 5.9 56 126-181 39-101 (200)
42 cd07642 BAR_ASAP2 The Bin/Amph 22.1 2.7E+02 0.0058 23.7 5.7 53 127-179 40-101 (215)
43 TIGR01478 STEVOR variant surfa 22.0 90 0.002 27.7 3.0 36 130-167 57-92 (295)
44 PF02252 PA28_beta: Proteasome 21.4 2.6E+02 0.0055 22.3 5.2 26 148-173 115-140 (150)
45 KOG0058 Peptide exporter, ABC 21.0 1.1E+02 0.0024 30.5 3.7 58 128-186 227-284 (716)
46 PTZ00370 STEVOR; Provisional 20.7 1E+02 0.0022 27.4 3.0 36 130-167 56-91 (296)
No 1
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=8.4e-46 Score=302.49 Aligned_cols=150 Identities=60% Similarity=1.051 Sum_probs=142.5
Q ss_pred ccEEEEEEEeCCeeeeeeecCcccHHHHHHHHHhcCCCC-CCeeEEEECCeEEEEEeeCCEEEEEEecCCCCcccHHHHH
Q 029478 4 KGLIYSFVSKGTVVLAEHTSYSGNFSTIAIQCLQKLPAS-SSKYTYSCDGHTFNFLLDSGFVFLVVADESVGRSVPFVFL 82 (192)
Q Consensus 4 m~I~Ya~Var~~~iLae~~~~~~nf~~ia~~iL~ki~~~-~~k~s~~~~~~~fh~l~~~gl~ylcitd~~yp~rvaF~fL 82 (192)
|+|+||+||||++|||||++.+|||.++|+++|+|+|++ ++|.+|.+|+|+|||+++||++|+||+|++.+|++||.||
T Consensus 1 m~iiYs~VARGTvvLaeft~~~gNf~sva~qiL~klp~~~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFL 80 (217)
T KOG0859|consen 1 MSIIYSFVARGTVILAEFTEFSGNFSSIAAQILQKLPSSSNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFL 80 (217)
T ss_pred CceeEEEEecceEEEEeeeeccCCHHHHHHHHHHhCCCCCCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHH
Confidence 789999999999999999999999999999999999998 5699999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhccccccccCCCCCCCCCCchhhhhhhhhccccccchhHHHHHHHHHhcCCchhhhHHHHHHHHHHHHHH
Q 029478 83 ERVKDDFKQRYGASIQNEESHPLADDDEDDDLFEDRFSIAYNLDREFGPRLKEHMQYCMSHPEEMSKLSKLKAQITEVKG 162 (192)
Q Consensus 83 ~ei~~~F~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~~~~~~~F~~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~ 162 (192)
++|+.+|.++||..+.+ +++|+++.+|++.|++.|+||.++|+ .|+|++++.|++|||+
T Consensus 81 e~Ik~~F~k~YG~~a~t--------------------a~AysmN~EFs~vL~qqm~y~s~~p~-id~lskvkaqv~evk~ 139 (217)
T KOG0859|consen 81 ERIKEDFKKRYGGGAHT--------------------AVAYSMNKEFSSVLKQQMQYCSEHPE-ISKLAKVKAQVTEVKG 139 (217)
T ss_pred HHHHHHHHHHhccchhH--------------------HHHhHhHHHHHHHHHHHHHHHHcCcc-hhHHHHHHHHHHHHHH
Confidence 99999999999877543 45677799999999999999999997 7999999999999999
Q ss_pred HHHHhHHHHHHH
Q 029478 163 IMMDNIEKVRVF 174 (192)
Q Consensus 163 IM~~NIdkiL~~ 174 (192)
||++||||+|+|
T Consensus 140 vM~eNIekvldR 151 (217)
T KOG0859|consen 140 VMMENIEKVLDR 151 (217)
T ss_pred HHHHHHHHHHhc
Confidence 999999999986
No 2
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.94 E-value=2.3e-26 Score=190.85 Aligned_cols=150 Identities=26% Similarity=0.467 Sum_probs=136.1
Q ss_pred cEEEEEEEeC--Ceeeeeeec---Cccc----HHHHHHHHHhcCCCC-CCeeEEEECCeEEEEEeeCCEEEEEEecCCCC
Q 029478 5 GLIYSFVSKG--TVVLAEHTS---YSGN----FSTIAIQCLQKLPAS-SSKYTYSCDGHTFNFLLDSGFVFLVVADESVG 74 (192)
Q Consensus 5 ~I~Ya~Var~--~~iLae~~~---~~~n----f~~ia~~iL~ki~~~-~~k~s~~~~~~~fh~l~~~gl~ylcitd~~yp 74 (192)
||++++|+|. ..+||...+ .+++ .+..++.+++|+.+. +.|.|++.+.|+|||++++|+||+||||+.||
T Consensus 1 mi~~T~I~RV~DGLPLa~s~d~~e~~~~s~~e~r~q~K~L~kkLs~~s~~r~Sietg~f~fHfli~~~Vcylvicd~~yP 80 (216)
T KOG0862|consen 1 MILLTLIARVRDGLPLAASTDDNEQSGDSLLEYRQQAKSLFKKLSQQSPTRCSIETGPFVFHFLIESGVCYLVICDKSYP 80 (216)
T ss_pred CceeEEEEEecCCcccccccCcccCCCchHHHHHHHHHHHHHhccCCCCcccccccCCeEEEEEecCCEEEEEEecCCCc
Confidence 6899999995 599998765 1333 456999999999988 78999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHhhhccccccccCCCCCCCCCCchhhhhhhhhccccccchhHHHHHHHHHhcCCchhhhHHHHHH
Q 029478 75 RSVPFVFLERVKDDFKQRYGASIQNEESHPLADDDEDDDLFEDRFSIAYNLDREFGPRLKEHMQYCMSHPEEMSKLSKLK 154 (192)
Q Consensus 75 ~rvaF~fL~ei~~~F~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~~~~~~~F~~~Lk~lm~~yn~~p~~~Dkl~klq 154 (192)
+++||.||+++.++|.+.|+....+...+|++ +-+|.+.|++.-+.|| |++..+++.++.
T Consensus 81 ~kLAF~YLedL~~EF~~~~~~~~~~~~~RPY~-------------------FieFD~~IQk~Kk~yn-d~r~~~n~~~~n 140 (216)
T KOG0862|consen 81 RKLAFSYLEDLAQEFDKSYGKNIIQPASRPYA-------------------FIEFDTFIQKTKKRYN-DTRSQRNLLKLN 140 (216)
T ss_pred HHHHHHHHHHHHHHHHHhcccccCCccCCCee-------------------EEehhHHHHHHHHHhc-CcHHHHHHHHHH
Confidence 99999999999999999999988887788987 7899999999999996 787779999999
Q ss_pred HHHHHHHHHHHHhHHHHHHH
Q 029478 155 AQITEVKGIMMDNIEKVRVF 174 (192)
Q Consensus 155 ~ei~eVk~IM~~NIdkiL~~ 174 (192)
.++.+|+.||.+||+++|++
T Consensus 141 ~el~~v~~im~~niedvl~r 160 (216)
T KOG0862|consen 141 QELQDVQRIMVENLEDVLQR 160 (216)
T ss_pred HHHHHHHHHHHHhHHHHHhh
Confidence 99999999999999999985
No 3
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.91 E-value=1.5e-23 Score=169.06 Aligned_cols=146 Identities=21% Similarity=0.254 Sum_probs=118.4
Q ss_pred ccEEEEEEEeCC----eeeeeeecCc----------ccHHH-HHHHHHhcCCCCCCeeEEEECCeEEEEEee-CCEEEEE
Q 029478 4 KGLIYSFVSKGT----VVLAEHTSYS----------GNFST-IAIQCLQKLPASSSKYTYSCDGHTFNFLLD-SGFVFLV 67 (192)
Q Consensus 4 m~I~Ya~Var~~----~iLae~~~~~----------~nf~~-ia~~iL~ki~~~~~k~s~~~~~~~fh~l~~-~gl~ylc 67 (192)
|.|++-.|.+.. ++|+.-++.+ ++|.. +++++.+|++|+ +|++++++.|.+|.... +|+++++
T Consensus 1 Mki~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F~sktvaeRt~~g-~rqsvk~~~Y~~h~yvrndgL~~V~ 79 (198)
T KOG0861|consen 1 MKIYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTFISKTVAERTGPG-QRQSVKHEEYLVHVYVRNDGLCGVL 79 (198)
T ss_pred CceEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHHHHHHHHHhcCcc-cccccccceeEEEEEEecCCeeEEE
Confidence 567777777762 5777655422 34544 889999999994 79999999999997766 5999999
Q ss_pred EecCCCCcccHHHHHHHHHHHHHhhhcc-ccccccCCCCCCCCCCchhhhhhhhhccccccchhHHHHHHHHHhcCCchh
Q 029478 68 VADESVGRSVPFVFLERVKDDFKQRYGA-SIQNEESHPLADDDEDDDLFEDRFSIAYNLDREFGPRLKEHMQYCMSHPEE 146 (192)
Q Consensus 68 itd~~yp~rvaF~fL~ei~~~F~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~i~~~~~~~F~~~Lk~lm~~yn~~p~~ 146 (192)
++|.+||.|+||.+|+++.++|..+.+. +|...... +.. .|.|..++..| |||.+
T Consensus 80 ~~D~eYP~rvA~tLL~kvld~~~~k~~~~~W~~~~~~----------------------~~~-~~~L~~~l~ky-qdP~e 135 (198)
T KOG0861|consen 80 IADDEYPVRVAFTLLNKVLDEFTTKVPATQWPVGETA----------------------DLS-YPYLDTLLSKY-QDPAE 135 (198)
T ss_pred EecCcCchhHHHHHHHHHHHHHhhcCcccccCcCCCc----------------------CCC-chhHHHHHHHh-cChhh
Confidence 9999999999999999999999777654 44321111 122 48899999777 89999
Q ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 029478 147 MSKLSKLKAQITEVKGIMMDNIEKVRVF 174 (192)
Q Consensus 147 ~Dkl~klq~ei~eVk~IM~~NIdkiL~~ 174 (192)
+|+|.++|+|+||+|.||+++|+.+|+|
T Consensus 136 ad~l~kvQ~EldETKiiLhkTiesVL~R 163 (198)
T KOG0861|consen 136 ADPLLKVQNELDETKIILHKTIESVLER 163 (198)
T ss_pred hChHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 9999999999999999999999999986
No 4
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=99.80 E-value=4.9e-19 Score=127.06 Aligned_cols=71 Identities=32% Similarity=0.688 Sum_probs=63.3
Q ss_pred HHHHHHhcCCCCC-CeeEEEECCeEEEEEeeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhc-ccccccc
Q 029478 31 IAIQCLQKLPASS-SKYTYSCDGHTFNFLLDSGFVFLVVADESVGRSVPFVFLERVKDDFKQRYG-ASIQNEE 101 (192)
Q Consensus 31 ia~~iL~ki~~~~-~k~s~~~~~~~fh~l~~~gl~ylcitd~~yp~rvaF~fL~ei~~~F~~~~~-~~~~~~~ 101 (192)
+|++||+|+++.+ +|.+++.++|+||+++++|++|+||||++||+|+||.||++|+++|.++|+ .++..+.
T Consensus 1 ~a~~il~~i~~~~~~k~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~~~~~~~a~ 73 (83)
T PF13774_consen 1 QARKILKRIPPNGNSKMSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYGGDQIKSAS 73 (83)
T ss_dssp HHHHHHHTS-TTSESEEEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCTTTTTTTST
T ss_pred CHHHHHHhcCCCCCCeEEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcCcchhcccC
Confidence 6899999999765 899999999999999999999999999999999999999999999999998 4555444
No 5
>COG5143 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
Probab=99.65 E-value=1.8e-15 Score=124.18 Aligned_cols=147 Identities=20% Similarity=0.294 Sum_probs=111.9
Q ss_pred cEEEEEEEeCC--eeeeeee-cCcccHH--HHHHHHHhcCCCC-CCeeEEEECCeEEEEEeeC-CEEEEEEecCCCCccc
Q 029478 5 GLIYSFVSKGT--VVLAEHT-SYSGNFS--TIAIQCLQKLPAS-SSKYTYSCDGHTFNFLLDS-GFVFLVVADESVGRSV 77 (192)
Q Consensus 5 ~I~Ya~Var~~--~iLae~~-~~~~nf~--~ia~~iL~ki~~~-~~k~s~~~~~~~fh~l~~~-gl~ylcitd~~yp~rv 77 (192)
.++|..+.++. .+|++-. ..+..|. ..++.+|.++.|. ..+.+++.++|.|||...+ |++|+|+|+++||+++
T Consensus 2 ~s~~~~~~~~~~~~~~~~~~s~~~~~ff~~~~v~~~l~~~~~~~a~~~~ies~~~~~~~~~~s~gi~y~~~~~~e~p~~l 81 (190)
T COG5143 2 ASISLFRVKGEPLRTLSDAESLSSFSFFHRSKVKEVLRFLSKTSASRASIESGDYFFHYLKMSSGIVYVPISDKEYPNKL 81 (190)
T ss_pred ceEEEEeecCCcceeeccccccCcccccccchHHHHHHHhcccccchhccccCceEEEEEecCCCceeEEecccccchhh
Confidence 45666666664 4555433 2233333 3788888888765 4578899999999998765 9999999999999999
Q ss_pred HHHHHHHHHHHHHhhhccccccccCCCCCCCCCCchhhhhhhhhccccccchhHHHHHHHHHhcCCchhhhHHHHHHHHH
Q 029478 78 PFVFLERVKDDFKQRYGASIQNEESHPLADDDEDDDLFEDRFSIAYNLDREFGPRLKEHMQYCMSHPEEMSKLSKLKAQI 157 (192)
Q Consensus 78 aF~fL~ei~~~F~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~~~~~~~F~~~Lk~lm~~yn~~p~~~Dkl~klq~ei 157 (192)
||+.++++..+|....+.+.+....+++. ...|.+.+++ . | ++|...|++.+++.++
T Consensus 82 a~~~~~~~~~~~~~s~~~~~~~d~~~~~~-------------------~~~~d~~~e~--~-y-~d~s~~D~~d~l~~el 138 (190)
T COG5143 82 AYGYLNSIATEFLKSSALEQLIDDTVGIM-------------------RVNIDKVIEK--G-Y-RDPSIQDKLDQLQQEL 138 (190)
T ss_pred hhHHHHhhccHhhhhhhHhhcccCccchh-------------------hhhHHHHHHh--h-c-CCchhhhHHHHHHHHH
Confidence 99999999999988876554433333421 3455666654 2 5 6898889999999999
Q ss_pred HHHHHHHHHhHHHHHHH
Q 029478 158 TEVKGIMMDNIEKVRVF 174 (192)
Q Consensus 158 ~eVk~IM~~NIdkiL~~ 174 (192)
++||.+|++||+++|++
T Consensus 139 ~e~K~~l~k~ie~~l~R 155 (190)
T COG5143 139 EETKRVLNKNIEKVLYR 155 (190)
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 99999999999999985
No 6
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.90 E-value=1.6e-05 Score=60.83 Aligned_cols=28 Identities=43% Similarity=0.478 Sum_probs=26.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 029478 147 MSKLSKLKAQITEVKGIMMDNIEKVRVF 174 (192)
Q Consensus 147 ~Dkl~klq~ei~eVk~IM~~NIdkiL~~ 174 (192)
.+++.++|+|+|+|++||.+||+|+|+|
T Consensus 28 ~~k~~~tq~QvdeVv~IMr~NV~KVlER 55 (116)
T KOG0860|consen 28 NDKLQQTQAQVDEVVDIMRENVEKVLER 55 (116)
T ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHh
Confidence 4899999999999999999999999996
No 7
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=97.58 E-value=9.3e-05 Score=53.53 Aligned_cols=28 Identities=39% Similarity=0.540 Sum_probs=26.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 029478 147 MSKLSKLKAQITEVKGIMMDNIEKVRVF 174 (192)
Q Consensus 147 ~Dkl~klq~ei~eVk~IM~~NIdkiL~~ 174 (192)
.|++.++++++++|+++|.+||++++++
T Consensus 2 ~dkl~~i~~~v~~v~~im~~Ni~~ll~R 29 (89)
T PF00957_consen 2 NDKLEQIQEQVEEVKNIMRENIDKLLER 29 (89)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3899999999999999999999999986
No 8
>PF04086 SRP-alpha_N: Signal recognition particle, alpha subunit, N-terminal; InterPro: IPR007222 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents the alpha subunit of the SR receptor.; GO: 0003924 GTPase activity, 0005047 signal recognition particle binding, 0005525 GTP binding, 0006184 GTP catabolic process, 0006886 intracellular protein transport, 0005785 signal recognition particle receptor complex; PDB: 2FH5_A 2GO5_1.
Probab=91.56 E-value=0.33 Score=41.78 Aligned_cols=66 Identities=23% Similarity=0.395 Sum_probs=42.3
Q ss_pred HHHHHHHhcCCCCCCeeEEEECCeEEEEEeeC--CEEEEEEecCCCCcccHHHHHHHHHHHHHhhhcccc
Q 029478 30 TIAIQCLQKLPASSSKYTYSCDGHTFNFLLDS--GFVFLVVADESVGRSVPFVFLERVKDDFKQRYGASI 97 (192)
Q Consensus 30 ~ia~~iL~ki~~~~~k~s~~~~~~~fh~l~~~--gl~ylcitd~~yp~rvaF~fL~ei~~~F~~~~~~~~ 97 (192)
.+++.||=.=.. ...+|++++|+.+|...+ ||+|+||-..-.+-.-.=.||+.|+..|...|+...
T Consensus 6 ~LI~~vlleeR~--~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~~l 73 (279)
T PF04086_consen 6 ALIRDVLLEERS--GNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKNQL 73 (279)
T ss_dssp HHHHHTGGG---------------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHHHH
T ss_pred HHHHHhheeecc--CCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhHHh
Confidence 455555533112 345689999999999886 799999999888877777899999999999997653
No 9
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. Syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin []. ; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005801 cis-Golgi network; PDB: 3CUE_C 2J3T_C 2ZMV_B 2JSN_A.
Probab=91.36 E-value=3 Score=32.69 Aligned_cols=58 Identities=17% Similarity=0.228 Sum_probs=34.9
Q ss_pred HHHHhcCCC---------CCCeeEEEECCeEEEEEee-CCEEEEEEecCCCCcccHHHHHHHHHHHHHh
Q 029478 33 IQCLQKLPA---------SSSKYTYSCDGHTFNFLLD-SGFVFLVVADESVGRSVPFVFLERVKDDFKQ 91 (192)
Q Consensus 33 ~~iL~ki~~---------~~~k~s~~~~~~~fh~l~~-~gl~ylcitd~~yp~rvaF~fL~ei~~~F~~ 91 (192)
+.+..++.| .+.-.+++-+.|..|+.-. .|+-|+++||+..+. ..-.++..+.+-|..
T Consensus 46 ~~i~~klsp~~~~~~~~~~~g~~~~~T~~yklh~~eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~d 113 (142)
T PF04099_consen 46 KAIASKLSPVDSKPNEPGSSGFESFETDTYKLHCFETPTGLKFVLITDPNVPS-LRDELLRIYYELYVD 113 (142)
T ss_dssp HHHHHHT-SSSSSS-SSS--SEEEEEESS-EEEEEE-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHH
T ss_pred HHHHHHhCCCCcccccccceeEEEEEeCCEEEEEEEcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHH
Confidence 455555555 1356788899999998854 899999999999863 333344444444433
No 10
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.82 E-value=0.73 Score=43.64 Aligned_cols=87 Identities=20% Similarity=0.327 Sum_probs=65.6
Q ss_pred EEEEEEeCCeeeeeeecCcccHHH----HHHHHHhcCCCCCCeeEEEECCeEEEEEeeC--CEEEEEEecCCCCcccHHH
Q 029478 7 IYSFVSKGTVVLAEHTSYSGNFST----IAIQCLQKLPASSSKYTYSCDGHTFNFLLDS--GFVFLVVADESVGRSVPFV 80 (192)
Q Consensus 7 ~Ya~Var~~~iLae~~~~~~nf~~----ia~~iL~ki~~~~~k~s~~~~~~~fh~l~~~--gl~ylcitd~~yp~rvaF~ 80 (192)
.++.+.+|..||..|.....+|.. +.+.+|-. .+ +.-.+++.+.|+..|-.++ +++|+|+-.+-.-..-+-.
T Consensus 4 ~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~-er-~~~~~~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~yv~~ 81 (587)
T KOG0781|consen 4 QFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLS-ER-GGVNSFTFEAYTLKYQLDNQYSLVFVVVFQKILTLTYVDK 81 (587)
T ss_pred eeeeecCCcEEEEEecccchhccchHHHHHHHHHHH-hh-cCcccCchhheeEeeeecCCccEEEEEEEeccchhhhHHH
Confidence 578889999999999875545443 44444432 11 2233478888998887764 8999999988888888889
Q ss_pred HHHHHHHHHHhhhcc
Q 029478 81 FLERVKDDFKQRYGA 95 (192)
Q Consensus 81 fL~ei~~~F~~~~~~ 95 (192)
+|+++.+-|+..|..
T Consensus 82 ll~~v~~~f~e~~~~ 96 (587)
T KOG0781|consen 82 LLNDVLNLFREKYDT 96 (587)
T ss_pred HHHHHHHHHHHHhcc
Confidence 999999999999965
No 11
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=86.39 E-value=13 Score=28.53 Aligned_cols=87 Identities=17% Similarity=0.238 Sum_probs=61.3
Q ss_pred EEEEEEEe--CCeeeeeeecC-c-----ccHHHHHHHHHhcCCCCCCeeEEEECCeEEEEEeeCCEEEEEEecCCCCccc
Q 029478 6 LIYSFVSK--GTVVLAEHTSY-S-----GNFSTIAIQCLQKLPASSSKYTYSCDGHTFNFLLDSGFVFLVVADESVGRSV 77 (192)
Q Consensus 6 I~Ya~Var--~~~iLae~~~~-~-----~nf~~ia~~iL~ki~~~~~k~s~~~~~~~fh~l~~~gl~ylcitd~~yp~rv 77 (192)
|..-+|.- |+++++-|... + .-++...+.+..+-+. .--.+..+++.+-|..-+++.++++++.+...-.
T Consensus 2 I~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~~~--~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~ 79 (141)
T PF01217_consen 2 IKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRNSK--QSPIFEHDNYRIVYKRYSDLYFVVVGDENENELL 79 (141)
T ss_dssp EEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSSSS--STSEEEETTEEEEEEEETTEEEEEEESSTSBHHH
T ss_pred EEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhcccc--cceeeecccceeeeEeeccEEEEEEeecccchHH
Confidence 34444443 45788877632 2 1234444555555322 1344678899999988999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhc
Q 029478 78 PFVFLERVKDDFKQRYG 94 (192)
Q Consensus 78 aF~fL~ei~~~F~~~~~ 94 (192)
...||..+.+-+..-++
T Consensus 80 ~~e~l~~~v~~l~~~~~ 96 (141)
T PF01217_consen 80 LLEFLHRLVEVLDDYFG 96 (141)
T ss_dssp HHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHhhhhhhhhhc
Confidence 99999999999888765
No 12
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.40 E-value=22 Score=32.49 Aligned_cols=87 Identities=14% Similarity=0.292 Sum_probs=64.3
Q ss_pred EEEEEEeCCeeeeeee--cCcccHHHHHHH-HHhcCCCCCCeeEEEECCeEEEEEeeCCEEEEEEecCCCCcccHHHHHH
Q 029478 7 IYSFVSKGTVVLAEHT--SYSGNFSTIAIQ-CLQKLPASSSKYTYSCDGHTFNFLLDSGFVFLVVADESVGRSVPFVFLE 83 (192)
Q Consensus 7 ~Ya~Var~~~iLae~~--~~~~nf~~ia~~-iL~ki~~~~~k~s~~~~~~~fh~l~~~gl~ylcitd~~yp~rvaF~fL~ 83 (192)
+|..=.||+++++-.- +-.++...+-|- |+..+.-.. -..+.++-+||++..+++--++||.........|.||.
T Consensus 5 lfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~d~r~--PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl~ 82 (446)
T KOG0938|consen 5 LFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNLDVRS--PVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFLY 82 (446)
T ss_pred EEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhccccCC--CeeEecceeEEEEeeccEEEEEEecCCCchhhHHHHHH
Confidence 4555678999998654 335666664442 333322211 23467899999999999999999999999999999999
Q ss_pred HHHHHHHhhhcc
Q 029478 84 RVKDDFKQRYGA 95 (192)
Q Consensus 84 ei~~~F~~~~~~ 95 (192)
++...+..-||.
T Consensus 83 kl~avm~aYfgk 94 (446)
T KOG0938|consen 83 KLDAVMNAYFGK 94 (446)
T ss_pred HHHHHHHHHhcc
Confidence 999999887774
No 13
>PF09426 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro: IPR019005 This entry represents the N-terminal domain of vacuolar R-SNARE Nyv1, which adopts a longin fold []. Vacuolar v-SNARE is required for docking and is only involved in homotypic vacuole fusion. Nyv1 is required for Ca(2+) efflux from the vacuolar lumen, a required signal for subsequent membrane fusion events, by inhibiting vacuolar Ca(2+)-ATPase PMC1 and promoting Ca(2+) release when forming trans-SNARE assemblies during the docking step. In yeast, the N-terminal domain of Nyv1 is sufficient to direct the transport of Nyv1 to limiting membrane of the vacuole []. ; PDB: 2FZ0_A.
Probab=78.18 E-value=5.5 Score=31.48 Aligned_cols=57 Identities=21% Similarity=0.296 Sum_probs=36.6
Q ss_pred HHHHHHhcCCCC-C---CeeEEE-ECCeEEEEEe---eCCEEEEEEecCCCCcccHHHHHHHHHH
Q 029478 31 IAIQCLQKLPAS-S---SKYTYS-CDGHTFNFLL---DSGFVFLVVADESVGRSVPFVFLERVKD 87 (192)
Q Consensus 31 ia~~iL~ki~~~-~---~k~s~~-~~~~~fh~l~---~~gl~ylcitd~~yp~rvaF~fL~ei~~ 87 (192)
+-..|++|+-|- + .|.+.. .+||-..|.. +++-+++|+|..+.|+-+|-..|.+++.
T Consensus 46 i~dmVlPkVV~v~GNKVTK~S~~lIDGyDCYYTT~~~d~~~vlVCFt~~~vPKILPiRlLSeLK~ 110 (141)
T PF09426_consen 46 IHDMVLPKVVPVEGNKVTKMSMHLIDGYDCYYTTEDNDDNKVLVCFTRVDVPKILPIRLLSELKG 110 (141)
T ss_dssp HHHTTGGG----SS-SSEE--S--SSSEEEEE---SS-TTEEEEEEEETTS-SSHHHHHHHHHTT
T ss_pred HhhccccceEEccCCeEEEEEeecccccceeeecccCCCCeEEEEEEecCCcceecHHHHHhhcc
Confidence 445566666553 2 344444 4899998887 4689999999999999999999998863
No 14
>smart00096 UTG Uteroglobin.
Probab=77.51 E-value=6.2 Score=27.62 Aligned_cols=46 Identities=13% Similarity=0.166 Sum_probs=39.1
Q ss_pred HHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHc
Q 029478 133 LKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDNIEKVRVFFLKN 178 (192)
Q Consensus 133 Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~~~~~~ 178 (192)
....++.||.+|+..++-.++|+=+|....-=..||-++|+.|++.
T Consensus 21 Y~~~l~~y~~~~~~~ea~~~lK~cvD~L~~~~k~~i~~ll~kI~~s 66 (69)
T smart00096 21 YEASLKQFKPDPDMLEAGRQLKKLVDTLPQETRENILKLTEKIYTS 66 (69)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHcC
Confidence 4456678888888889999999999998888889999999998864
No 15
>PF01099 Uteroglobin: Uteroglobin family; InterPro: IPR006038 Uteroglobin (or blastokinin) is a mammalian steroid-inducible secreted protein originally isolated from the uterus of rabbits during early pregnancy. The mucosal epithelia of several organs that communicate with the external environment express uteroglobin. Its tissue-specific expression is regulated by steroid hormones, and is augmented in the uterus by non-steroidal prolactin. Uteroglobin may be a multi-functional protein with anti-inflammatory/immunomodulatory properties, acting to inhibit phospholipase A2 activity, and binding to (and possibly sequestering) several hydrophobic ligands such as progesterone, retinols, polychlorinated biphenyls, phospholipids and prostaglandins. In addition, uteroglobin has anti-chemotactic, anti-allergic, anti-tumourigenic and embryo growth-stimulatory properties. Uteroglobin may have a homeostatic role against oxidative damage, inflammation, autoimmunity and cancer [, , , ]. Uteroglobin consists of a disulphide-linked dimer of two identical polypeptides, each polypeptide being composed of four helices. It is a member of the secretoglobin superfamily. This entry represents uteroglobin proteins from several mammalian species, as well as other members of the secretoglobin superfamily, such as lipophilin B [], prostatic steroid-binding protein [], mammaglobin [], and the related allergen Fel d 1 (Felis domesticus allergen 1) [].; GO: 0005488 binding, 0005576 extracellular region; PDB: 1UTR_B 1CCD_A 1UTG_A 2UTG_A 1ZKR_B 1PUO_B 2EJN_B.
Probab=77.20 E-value=4.1 Score=27.85 Aligned_cols=47 Identities=21% Similarity=0.210 Sum_probs=37.2
Q ss_pred HHHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 029478 131 PRLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDNIEKVRVFFLK 177 (192)
Q Consensus 131 ~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~~~~~ 177 (192)
+..+..++.||.+|.......++|+=+++.-.-=..||.++|+.|.+
T Consensus 17 ~~Y~~~l~~y~~~~~~~~A~~~lK~C~d~ls~e~~~~i~~~l~~I~~ 63 (67)
T PF01099_consen 17 EEYKESLQKYNPPPEAVEAKLELKQCVDKLSNETRENILKLLEKIYN 63 (67)
T ss_dssp HHHHHHHHCC---HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHc
Confidence 56777788888778888899999999999999999999999998874
No 16
>cd00633 Secretoglobin Secretoglobins are relatively small, secreted, disulphide-bridged dimeric proteins with encoding genes sharing substantial sequence similarity. Their family subunits may be grouped into five subfamilies, A-E. Uteroglobin (subfamily A), which is identical to Clara cell protein (CC10), forms a globular shaped homodimer with a large hydrophobic pocket located between the two dimers. The uteroglobin monomer structure is composed of four alpha helices that do not form a canonical four helix-bundle motif but rather a boomerang-shaped structure in which helices H1, H3, and H4 are able to bind a homodimeric partner. The hydrophobic pocket binds steroids, particularly progesterone, with high specificity. However, the true biological function of uteroglobin is poorly understood. In mammals, uteroglobin has immunosuppressive and anti-inflammatory properties through the inhibition of phospholipase A2. The other four main subfamilies of secretoglobins are found in heterodimeri
Probab=74.25 E-value=8.4 Score=26.19 Aligned_cols=47 Identities=23% Similarity=0.222 Sum_probs=39.9
Q ss_pred HHHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 029478 131 PRLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDNIEKVRVFFLK 177 (192)
Q Consensus 131 ~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~~~~~ 177 (192)
..++..++.||.+|.......++|+=+++...-=..|+-++++.++.
T Consensus 17 ~~y~~~L~~f~~~~~~~~A~~~lK~C~d~~~~e~k~~~~~~m~~I~~ 63 (67)
T cd00633 17 EEYKAELEKFNATPEAVEAKEKLKQCVDEQSLETKENIAKLLEKILA 63 (67)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCHhHHHHHHHHHHHHHc
Confidence 45677778898888888999999999999988888899999988765
No 17
>PRK11546 zraP zinc resistance protein; Provisional
Probab=68.38 E-value=23 Score=28.15 Aligned_cols=48 Identities=13% Similarity=0.215 Sum_probs=33.2
Q ss_pred HHHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHcCcc
Q 029478 131 PRLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDNIEKVRVFFLKNGIG 181 (192)
Q Consensus 131 ~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~~~~~~~~~ 181 (192)
.+|..++.. +.|+. .+|.++.+||.+++.-|.+==-+.=...-|-||+
T Consensus 75 ~ELnALl~~--~~pD~-~kI~aL~kEI~~Lr~kL~e~r~~~~~~~~k~Gv~ 122 (143)
T PRK11546 75 YEYNALLTA--NPPDS-SKINAVAKEMENLRQSLDELRVKRDIAMAEAGIP 122 (143)
T ss_pred HHHHHHHcC--CCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 466667654 45655 7899999999999987765433444466676665
No 18
>PF10436 BCDHK_Adom3: Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase; InterPro: IPR018955 Catabolism and synthesis of leucine, isoleucine and valine are finely balanced, allowing the body to make the most of dietary input but removing excesses to prevent toxic build-up of their corresponding keto-acids. Regulating the activity of the branched-chain alpha-ketoacid dehydrogenase (BCDH) complex is the primary means by which these processes are coordinated. BCDH kinase regulates BCDH by phosphorylation, thereby inactivating it when synthesis is required. Pyruvate dehydrogenase kinase inhibits the pyruvate dehydrogenase complex by phosphorylation of the E1 alpha subunit, thus contributing to the regulation of glucose metabolism. It is also involved in telomere maintenance. This entry is associated with IPR003594 from INTERPRO which is found towards the C terminus. ; PDB: 1GKX_A 1GJV_A 1GKZ_A 1JM6_B 3CRL_B 3CRK_B 1Y8O_A 2PNR_A 1Y8P_A 1Y8N_A ....
Probab=54.63 E-value=37 Score=27.21 Aligned_cols=51 Identities=20% Similarity=0.313 Sum_probs=38.8
Q ss_pred ccchhHHHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHH-----HHhHHHHHHHHHHcCcce
Q 029478 126 DREFGPRLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIM-----MDNIEKVRVFFLKNGIGI 182 (192)
Q Consensus 126 ~~~F~~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM-----~~NIdkiL~~~~~~~~~~ 182 (192)
+..|...|+++.+..+ +.+..+-.=+.|.|.-+ .+.|+.-|++|+..-|||
T Consensus 81 ~~~F~~~l~~i~~~H~------~vv~~lA~G~~E~~~~~~~~~~~~~i~~fLd~f~~sRIgi 136 (164)
T PF10436_consen 81 NEKFTELLERILDRHS------DVVPTLAQGVLELKKYLQSSESEEQIQSFLDRFYRSRIGI 136 (164)
T ss_dssp HHHHHHHHHHHHHHTT------THHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhc------ccHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhHHH
Confidence 4678899999886532 45556666677777766 578999999999998886
No 19
>cd07634 BAR_GAP10-like The Bin/Amphiphysin/Rvs (BAR) domain of Rho GTPase activating protein 10-like. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This group is composed of uncharacterized proteins called Rho GTPase activating protein (GAP) 10-like. GAP10-like may be a GAP with activity towards RhoA and Cdc42. Similar to GRAF and GRAF2, it contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domains of the related proteins GRAF and OPHN1, directly interact with their Rho GAP domains and inhibit theiractivity. The autoinhibited proteins are capable of binding membranes and tubulating liposomes, showing that the membrane-tubulation and GAP-inhibitory functions of the BAR domain
Probab=52.97 E-value=50 Score=27.82 Aligned_cols=56 Identities=20% Similarity=0.421 Sum_probs=38.3
Q ss_pred ccchhHHHHHHHHHhcCCc---------hhhhHHHHHHHHHHHHHHHHHHhHHHHHH----HHHHcCcc
Q 029478 126 DREFGPRLKEHMQYCMSHP---------EEMSKLSKLKAQITEVKGIMMDNIEKVRV----FFLKNGIG 181 (192)
Q Consensus 126 ~~~F~~~Lk~lm~~yn~~p---------~~~Dkl~klq~ei~eVk~IM~~NIdkiL~----~~~~~~~~ 181 (192)
+..|...|.++-.++-.++ .+..+.+++-++|.+-+.+|.+|++.++- -|+|..+|
T Consensus 39 ~~~Fa~sL~~f~~~~igd~~tDde~~i~~~l~~Fs~~l~el~~~~~~L~~~~~~~l~~pL~~f~k~dl~ 107 (207)
T cd07634 39 VQKFSQSLQDFQFECIGDAETDDEISIAQSLKEFARLLIAVEEERRRLIQNANDVLIAPLEKFRKEQIG 107 (207)
T ss_pred HHHHHHHHHHHHhhccCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556777777665554344 24467778888888999999999876654 56666554
No 20
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=42.68 E-value=21 Score=25.47 Aligned_cols=43 Identities=21% Similarity=0.295 Sum_probs=28.5
Q ss_pred HHHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHhHHHHHH-HHHHcCc
Q 029478 131 PRLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDNIEKVRV-FFLKNGI 180 (192)
Q Consensus 131 ~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~-~~~~~~~ 180 (192)
+.|+-+.+.|+..|...+.|+.. -..-.++|+++++ |+++.|.
T Consensus 12 ~yL~~l~~~f~ggPvGl~tlA~~-------l~ed~~Tie~v~EPyLiq~G~ 55 (76)
T PF05491_consen 12 RYLKTLIENFKGGPVGLDTLAAA-------LGEDKETIEDVIEPYLIQIGF 55 (76)
T ss_dssp HHHHHHHHCSTTS-B-HHHHHHH-------TTS-HHHHHHTTHHHHHHTTS
T ss_pred HHHHHHHHHcCCCCeeHHHHHHH-------HCCCHhHHHHHhhHHHHHhhh
Confidence 56777778888889876766533 3334678888999 8888763
No 21
>PF10504 DUF2452: Protein of unknown function (DUF2452); InterPro: IPR019534 This entry contains proteins that have no known function.
Probab=41.98 E-value=15 Score=29.73 Aligned_cols=56 Identities=20% Similarity=0.363 Sum_probs=38.3
Q ss_pred HHHHHHHHHhcCCCC----CCeeEEEE-CCeEEE-EEeeCCEEEEEEecCC-CCcccHHHHHH
Q 029478 28 FSTIAIQCLQKLPAS----SSKYTYSC-DGHTFN-FLLDSGFVFLVVADES-VGRSVPFVFLE 83 (192)
Q Consensus 28 f~~ia~~iL~ki~~~----~~k~s~~~-~~~~fh-~l~~~gl~ylcitd~~-yp~rvaF~fL~ 83 (192)
+++.|++|+++...+ +.++.|+- =|.+|| |..++|-.|+-+..++ .+.++++.||.
T Consensus 64 Lq~QA~~ile~~~~~~~l~~A~cnF~pipG~iYhLY~r~~G~~ylSmisP~EWg~~~p~~flG 126 (159)
T PF10504_consen 64 LQEQARKILEEAERNEELHHAKCNFEPIPGQIYHLYRRENGQDYLSMISPEEWGGSCPHEFLG 126 (159)
T ss_pred HHHHHHHHHHHHHHhHHHhhcccCceecCCCEEEEEECCCCCEEEEeeCHHHhCCCCCcCEEE
Confidence 556889999987754 46777764 378888 5556887776665554 47777765553
No 22
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=40.43 E-value=1.3e+02 Score=21.20 Aligned_cols=53 Identities=21% Similarity=0.423 Sum_probs=39.1
Q ss_pred HHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHcCcceEE
Q 029478 132 RLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDNIEKVRVFFLKNGIGIIY 184 (192)
Q Consensus 132 ~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~~~~~~~~~~~~ 184 (192)
.|-.++++..++|...=.|+-.-+..+.-|....+.+.-|-+-|-+.|+|.|-
T Consensus 5 Rlv~it~~L~~~P~~lisL~~Fae~f~~AKSsISEDl~iik~~~~~~g~G~ie 57 (70)
T PF09182_consen 5 RLVAITKYLLENPNKLISLTYFAERFGAAKSSISEDLSIIKETFEKEGLGRIE 57 (70)
T ss_dssp HHHHHHHHHHTSTT--EEHHHHHHHHT--HHHHHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHcCCcceEcHHHHHHHhcccccchHHHHHHHHHHHHHcCCceEE
Confidence 45556666667787777788888888888888899988888889999999874
No 23
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=34.49 E-value=1.1e+02 Score=24.91 Aligned_cols=49 Identities=16% Similarity=0.201 Sum_probs=36.9
Q ss_pred HHHHHHHHHhc---CCchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHcC
Q 029478 131 PRLKEHMQYCM---SHPEEMSKLSKLKAQITEVKGIMMDNIEKVRVFFLKNG 179 (192)
Q Consensus 131 ~~Lk~lm~~yn---~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~~~~~~~ 179 (192)
|.+.++++.|. +.|...+.+.+..+++.++-+.+.+++++.++.++.+.
T Consensus 136 p~~~~l~~kY~~l~~~~~~~~~~~~~l~e~~~~L~~l~~~f~~~~~~l~~~d 187 (199)
T PF10112_consen 136 PTAVKLLEKYAELESQPVKSEEIKQSLEEIEETLDTLNQAFEKDLDKLLEDD 187 (199)
T ss_pred hHHHHHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 66667775553 23444477888888899999999999999999888764
No 24
>cd04889 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate. Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Also included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem A
Probab=33.40 E-value=67 Score=20.09 Aligned_cols=22 Identities=23% Similarity=0.259 Sum_probs=18.1
Q ss_pred HHHHHHHHHHcCcceEEEEEee
Q 029478 168 IEKVRVFFLKNGIGIIYMYIWY 189 (192)
Q Consensus 168 IdkiL~~~~~~~~~~~~~~~~~ 189 (192)
+.++++-+.++|+.|.|||.+.
T Consensus 12 l~~i~~~l~~~~inI~~~~~~~ 33 (56)
T cd04889 12 LAEVTEILAEAGINIKAISIAE 33 (56)
T ss_pred HHHHHHHHHHcCCCEeeEEEEE
Confidence 4567788999999999998764
No 25
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.08 E-value=3e+02 Score=22.93 Aligned_cols=54 Identities=17% Similarity=0.228 Sum_probs=36.9
Q ss_pred HHhcCCCC---CCeeEEEECCeEEEEE-eeCCEEEEEEecCCCCcccHHHHHHHHHHHHH
Q 029478 35 CLQKLPAS---SSKYTYSCDGHTFNFL-LDSGFVFLVVADESVGRSVPFVFLERVKDDFK 90 (192)
Q Consensus 35 iL~ki~~~---~~k~s~~~~~~~fh~l-~~~gl~ylcitd~~yp~rvaF~fL~ei~~~F~ 90 (192)
+..++.|. .....++-+.+..|+. .--|+-|++||++..+ .|=.+|+.+..-|.
T Consensus 110 I~~qlsp~~ksSGie~LetdtF~l~~~QTlTG~KFVvis~~~~~--~aD~lLrKiYelYs 167 (199)
T KOG3369|consen 110 ISTQLSPEPKSSGIEVLETDTFTLHIFQTLTGTKFVVIAEPGTQ--GADSLLRKIYELYS 167 (199)
T ss_pred eeeccCCCCCCCceEEEEeccEEEEEEEccCCcEEEEEecCCch--hHHHHHHHHHHHHH
Confidence 34455543 2356667788888866 4589999999999874 45567776666554
No 26
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=32.06 E-value=2.2e+02 Score=26.15 Aligned_cols=68 Identities=9% Similarity=0.090 Sum_probs=50.2
Q ss_pred cHHHHHHHHHhcCCCC-CCeeEEEECCeEEEEEeeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhc
Q 029478 27 NFSTIAIQCLQKLPAS-SSKYTYSCDGHTFNFLLDSGFVFLVVADESVGRSVPFVFLERVKDDFKQRYG 94 (192)
Q Consensus 27 nf~~ia~~iL~ki~~~-~~k~s~~~~~~~fh~l~~~gl~ylcitd~~yp~rvaF~fL~ei~~~F~~~~~ 94 (192)
.+..+...++.-.... +.=.++..++..|.|+.++.+.++||+...-+...--.-|+-+.........
T Consensus 36 ~~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly~qils~lt 104 (415)
T PF03164_consen 36 SLMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLYSQILSILT 104 (415)
T ss_pred HHHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHHHHHHHhcc
Confidence 3445566666655433 3445778899999999999999999999999877777777777776665543
No 27
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.72 E-value=1.6e+02 Score=27.30 Aligned_cols=44 Identities=20% Similarity=0.243 Sum_probs=35.8
Q ss_pred CeEEEEEeeCCEEEEEEecCCCCcccHHHHHHHHHHHHHhhhcc
Q 029478 52 GHTFNFLLDSGFVFLVVADESVGRSVPFVFLERVKDDFKQRYGA 95 (192)
Q Consensus 52 ~~~fh~l~~~gl~ylcitd~~yp~rvaF~fL~ei~~~F~~~~~~ 95 (192)
.|.+.-..++++.+++++.-+.|--.++.||.+|.+.|.+-||.
T Consensus 54 ~hylfsv~~~~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg~ 97 (418)
T KOG2740|consen 54 HHYLFSVYRDLIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFGG 97 (418)
T ss_pred ceeeeeeeccCcEEEEEEeccCCChhHHHHHHHHHHHHHHHhcc
Confidence 34444445678888888888999999999999999999988874
No 28
>PF03179 V-ATPase_G: Vacuolar (H+)-ATPase G subunit; InterPro: IPR005124 This family represents the eukaryotic vacuolar (H+)-ATPase (V-ATPase) G subunit. V-ATPases generate an acidic environment in several intracellular compartments. Correspondingly, they are found as membrane-attached proteins in several organelles. They are also found in the plasma membranes of some specialised cells. V-ATPases consist of peripheral (V1) and membrane integral (V0) heteromultimeric complexes. The G subunit is part of the V1 subunit, but is also thought to be strongly attached to the V0 complex. It may be involved in the coupling of ATP degradation to H+ translocation.; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015992 proton transport, 0016471 vacuolar proton-transporting V-type ATPase complex; PDB: 2KWY_A 2K88_A.
Probab=31.70 E-value=1e+02 Score=22.43 Aligned_cols=29 Identities=24% Similarity=0.270 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHc
Q 029478 150 LSKLKAQITEVKGIMMDNIEKVRVFFLKN 178 (192)
Q Consensus 150 l~klq~ei~eVk~IM~~NIdkiL~~~~~~ 178 (192)
....+.+|.+++....+|.+++++.+++.
T Consensus 72 ~~et~~~i~~i~~~~~~~~~~vv~~ll~~ 100 (105)
T PF03179_consen 72 EKETEEKIEEIKKSASKNKDKVVDMLLSR 100 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 35668889999999999999999999874
No 29
>cd07636 BAR_GRAF The Bin/Amphiphysin/Rvs (BAR) domain of GTPase Regulator Associated with Focal adhesion kinase. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. GTPase Regulator Associated with Focal adhesion kinase (GRAF), also called Rho GTPase activating protein 26 (ARHGAP26), is a GAP with activity towards RhoA and Cdc42 and is only weakly active towards Rac1. It influences Rho-mediated cytoskeletal rearrangements and binds focal adhesion kinase (FAK), which is a critical component of integrin signaling. GRAF contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of GRAF directly interacts with its Rho GAP domain and inhibits its activity. Autoinhibited GRAF is capable o
Probab=31.09 E-value=1.4e+02 Score=25.12 Aligned_cols=56 Identities=21% Similarity=0.412 Sum_probs=38.6
Q ss_pred ccchhHHHHHHHHHhcCCc---------hhhhHHHHHHHHHHHHHHHHHHhHHHHH----HHHHHcCcc
Q 029478 126 DREFGPRLKEHMQYCMSHP---------EEMSKLSKLKAQITEVKGIMMDNIEKVR----VFFLKNGIG 181 (192)
Q Consensus 126 ~~~F~~~Lk~lm~~yn~~p---------~~~Dkl~klq~ei~eVk~IM~~NIdkiL----~~~~~~~~~ 181 (192)
+..|...|.++-.++..++ ....+..++-++|++-+.+|.++.+..| +-|+|..||
T Consensus 39 ~~~Fa~sL~~f~~~~~gd~~~dDe~~I~~~L~kF~~~L~ei~~~r~~L~~qa~~~l~~~L~~F~kedi~ 107 (207)
T cd07636 39 KRKFADSLNEFKFQCIGDAETDDEICIARSLQEFAAVLRNLEDERTRMIENASEVLITPLEKFRKEQIG 107 (207)
T ss_pred HHHHHHHHHHHHhhcCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777765654444 2334667778888888999999976544 477777776
No 30
>cd07638 BAR_ACAP2 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, 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. ACAP2 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 2), also called centaurin beta-2, is an Arf6-specific GTPase activating protein (GAP) which mediates Arf6 signaling. Arf6 is involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration. ACAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=29.75 E-value=1.8e+02 Score=24.35 Aligned_cols=56 Identities=16% Similarity=0.360 Sum_probs=39.1
Q ss_pred ccchhHHHHHHHHHhcCCc---hhhhHHHHHHHHHHHHHHHHHHhHHHHHH----HHHHcCcc
Q 029478 126 DREFGPRLKEHMQYCMSHP---EEMSKLSKLKAQITEVKGIMMDNIEKVRV----FFLKNGIG 181 (192)
Q Consensus 126 ~~~F~~~Lk~lm~~yn~~p---~~~Dkl~klq~ei~eVk~IM~~NIdkiL~----~~~~~~~~ 181 (192)
...|...|+++.+++..|+ ....+.+++-++|.+-+.+|.++++..+- -|+|+.+|
T Consensus 39 ~~~F~~~l~d~~~~~~~De~i~~~l~kF~~~l~ei~~~~~~L~~q~~~~l~~~L~~F~k~dl~ 101 (200)
T cd07638 39 NKQFMNGIRDLAQYSSKDAVIETSLTKFSDTLQEMINYHTILFDQAQRSIKAQLQTFVKEDLR 101 (200)
T ss_pred HHHHHHHHHHHHHhCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 4567777887776654444 23456677778888889999999986654 56666654
No 31
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=29.08 E-value=78 Score=20.68 Aligned_cols=20 Identities=25% Similarity=0.348 Sum_probs=17.4
Q ss_pred HHHHHHHHHHcCcceEEEEE
Q 029478 168 IEKVRVFFLKNGIGIIYMYI 187 (192)
Q Consensus 168 IdkiL~~~~~~~~~~~~~~~ 187 (192)
+.++++-|-++|+-|.|+|.
T Consensus 15 La~v~~~l~~~~inI~~i~~ 34 (66)
T cd04908 15 LAAVTEILSEAGINIRALSI 34 (66)
T ss_pred HHHHHHHHHHCCCCEEEEEE
Confidence 56788889999999999986
No 32
>cd07601 BAR_APPL The Bin/Amphiphysin/Rvs (BAR) domain of Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing (APPL) proteins are effectors of the small GTPase Rab5 that function in endosome-mediated signaling. They contain BAR, pleckstrin homology (PH) and phosphotyrosine binding (PTB) domains. They form homo- and hetero-oligomers that are mediated by their BAR domains, and are localized to cytoplasmic membranes. Vertebrates contain two APPL proteins, APPL1 and APPL2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=27.58 E-value=1.9e+02 Score=24.45 Aligned_cols=56 Identities=9% Similarity=0.239 Sum_probs=34.5
Q ss_pred ccchhHHHHHHHHH----hcCCch---hhhHHHHHHHHHHHHHHHHHHhHHHHHH----HHHHcCcc
Q 029478 126 DREFGPRLKEHMQY----CMSHPE---EMSKLSKLKAQITEVKGIMMDNIEKVRV----FFLKNGIG 181 (192)
Q Consensus 126 ~~~F~~~Lk~lm~~----yn~~p~---~~Dkl~klq~ei~eVk~IM~~NIdkiL~----~~~~~~~~ 181 (192)
...|...|+++-++ +.+||. ...+.+.+-++|.+-+.+|.+|++..|- -|+|..++
T Consensus 39 ~~~F~~~L~ef~~~~f~~~~dDe~~~~~l~kFs~~l~El~~~~~~L~~q~~~~l~~pL~~F~k~Dl~ 105 (215)
T cd07601 39 TQALSKKLGEYEKQKFELGRDDEILVSTLKQFSKVVDELSTMHSTLSSQLADTVLHPISQFMESDLA 105 (215)
T ss_pred HHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 44566666666443 433432 3345566677788888888888876654 56665554
No 33
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=26.76 E-value=1.9e+02 Score=22.32 Aligned_cols=16 Identities=6% Similarity=0.289 Sum_probs=11.0
Q ss_pred CeEEEEEeeCCEEEEE
Q 029478 52 GHTFNFLLDSGFVFLV 67 (192)
Q Consensus 52 ~~~fh~l~~~gl~ylc 67 (192)
++..|....+|+.+-.
T Consensus 27 Q~Slhi~~~~g~~~~~ 42 (130)
T PF11074_consen 27 QFSLHITDNDGIIYKE 42 (130)
T ss_pred EEEEEEEcCCCcccCc
Confidence 5888888888844333
No 34
>PF02520 DUF148: Domain of unknown function DUF148; InterPro: IPR003677 This entry represents the domain DUF148, which has no known function.
Probab=26.41 E-value=2.6e+02 Score=20.45 Aligned_cols=45 Identities=20% Similarity=0.186 Sum_probs=32.3
Q ss_pred cchhHHHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 029478 127 REFGPRLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDNIEKVRVFF 175 (192)
Q Consensus 127 ~~F~~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~~~ 175 (192)
.+....+.+..+.|+ -.+.+...+.++..-+.-+.+|+..++..+
T Consensus 19 ~e~~~~l~~Wa~~~~----v~~~~~~f~~~~~~~~~~~~~~~~~vi~~L 63 (113)
T PF02520_consen 19 AEIEEQLDEWAEKYG----VQDQYNEFKAQVQAQKEEVRKNVTAVISNL 63 (113)
T ss_pred HHHHHHHHHHHHHCC----cHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666666543 237888888888888888888888888755
No 35
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.17 E-value=2.5e+02 Score=22.29 Aligned_cols=55 Identities=16% Similarity=0.249 Sum_probs=40.5
Q ss_pred HHHHHHhcCCCCC---CeeEEEECCeEEEEEee-CCEEEEEEecCCCCcccHHHHHHHHHH
Q 029478 31 IAIQCLQKLPASS---SKYTYSCDGHTFNFLLD-SGFVFLVVADESVGRSVPFVFLERVKD 87 (192)
Q Consensus 31 ia~~iL~ki~~~~---~k~s~~~~~~~fh~l~~-~gl~ylcitd~~yp~rvaF~fL~ei~~ 87 (192)
-.|.+.+|+.|++ +-.++.-+.|-.||+.. .|+=++-+||+..+. --..|+.|..
T Consensus 44 SlkS~v~Kls~~d~k~~f~sy~Ts~YklhfyeTptglk~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 44 SLKSFVSKLSPGDVKDGFLSYKTSKYKLHFYETPTGLKFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred hHHHHHHhcCCCCcccCeeEEeeceeEEEEEEcCCCcEEEEecCCCccc--HHHHHHHHHH
Confidence 3577888998874 45677778999998865 899999999998764 2234555555
No 36
>cd07635 BAR_GRAF2 The Bin/Amphiphysin/Rvs (BAR) domain of GTPase Regulator Associated with Focal adhesion 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. GTPase Regulator Associated with Focal adhesion kinase 2 (GRAF2), also called Rho GTPase activating protein 10 (ARHGAP10) or PS-GAP, is a GAP with activity towards Cdc42 and RhoA which regulates caspase-activated p21-activated protein kinase-2 (PAK-2p34). GRAF2 interacts with PAK-2p34, leading to its stabilization and decrease of cell death. It is highly expressed in skeletal muscle and also interacts with PKNbeta, which is a target of Rho. GRAF2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of the related prote
Probab=25.11 E-value=2.9e+02 Score=23.21 Aligned_cols=56 Identities=20% Similarity=0.337 Sum_probs=33.3
Q ss_pred ccchhHHHHHHHHHhcCCc---------hhhhHHHHHHHHHHHHHHHHHHhHHHH----HHHHHHcCcc
Q 029478 126 DREFGPRLKEHMQYCMSHP---------EEMSKLSKLKAQITEVKGIMMDNIEKV----RVFFLKNGIG 181 (192)
Q Consensus 126 ~~~F~~~Lk~lm~~yn~~p---------~~~Dkl~klq~ei~eVk~IM~~NIdki----L~~~~~~~~~ 181 (192)
...|...|+++-.++..++ ....+..++..+|.+-+..|..|++.. |+-|.|..||
T Consensus 39 ~~~Fa~~L~~f~~~~~gd~~~dde~~i~~sl~ef~~~~~el~d~r~~L~~~~~~~l~~pL~~F~kedl~ 107 (207)
T cd07635 39 QRKFAHSLRDFKFEFIGDAETDDERCIDASLQEFSNFLKNLEEQREIMALNVTETLIKPLERFRKEQLG 107 (207)
T ss_pred HHHHHHHHHHHHhhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445556666554443222 112344566778888898888886544 4467777665
No 37
>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=24.65 E-value=1.7e+02 Score=24.53 Aligned_cols=56 Identities=16% Similarity=0.281 Sum_probs=38.0
Q ss_pred ccchhHHHHHHHHHhcC--Cc---hhhhHHHHHHHHHHHHHHHHHHhHHHHHH----HHHHcCcc
Q 029478 126 DREFGPRLKEHMQYCMS--HP---EEMSKLSKLKAQITEVKGIMMDNIEKVRV----FFLKNGIG 181 (192)
Q Consensus 126 ~~~F~~~Lk~lm~~yn~--~p---~~~Dkl~klq~ei~eVk~IM~~NIdkiL~----~~~~~~~~ 181 (192)
...|...|+++-..+.. +| ....+.+++.++|.+-+.+|++|++.+|- -|+|.+++
T Consensus 39 ~~~F~~aL~~~g~~~~~~~~~~i~~~l~kF~~~l~El~~~~~~L~~~~~~~i~~pL~~f~k~dL~ 103 (215)
T cd07604 39 ELQFAEALEKLGSKALSREEEDLGAAFLKFSVFTKELAALFKNLMQNLNNIIMFPLDSLLKGDLK 103 (215)
T ss_pred HHHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 45666777766544321 11 33467788999999999999999988765 56666554
No 38
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=24.60 E-value=2.5e+02 Score=23.55 Aligned_cols=46 Identities=17% Similarity=0.237 Sum_probs=34.6
Q ss_pred chhHHHHHHH-HHhcCCchhhhHHHHHHHHHHHHHHHHHHhHHHHHH
Q 029478 128 EFGPRLKEHM-QYCMSHPEEMSKLSKLKAQITEVKGIMMDNIEKVRV 173 (192)
Q Consensus 128 ~F~~~Lk~lm-~~yn~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~ 173 (192)
.|...++.+- ..-++||-+...|.+++++|++++..|.+-++.+=+
T Consensus 41 ~~~~~~~~i~~~a~~DdPyAD~~L~~iEe~i~~~~~~l~~~~~~l~~ 87 (217)
T PF08900_consen 41 GFASRLNRIWRDARQDDPYADWWLLRIEEKINEARQELQELIARLDA 87 (217)
T ss_pred HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666655 344477877688999999999999999988876644
No 39
>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=24.21 E-value=2.3e+02 Score=23.46 Aligned_cols=56 Identities=16% Similarity=0.300 Sum_probs=38.1
Q ss_pred ccchhHHHHHHHHHhcCCc---hhhhHHHHHHHHHHHHHHHHHHhHHHHHH----HHHHcCcc
Q 029478 126 DREFGPRLKEHMQYCMSHP---EEMSKLSKLKAQITEVKGIMMDNIEKVRV----FFLKNGIG 181 (192)
Q Consensus 126 ~~~F~~~Lk~lm~~yn~~p---~~~Dkl~klq~ei~eVk~IM~~NIdkiL~----~~~~~~~~ 181 (192)
...|...|.++-.++.+|| ....+....-+++..-+.+|.+|++.++- -|+|..++
T Consensus 39 ~~~F~~~L~~~~~~~~~d~~i~~~l~kF~~~l~el~~~~~~L~~q~~~~i~~pL~~F~k~dL~ 101 (200)
T cd07603 39 NSLFVNSLNDLSDYFRDDSLVQNCLNKFIQALQEMNNFHTILLDQAQRTVSTQLQNFVKEDIK 101 (200)
T ss_pred HHHHHHHHHHHhcccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 4567777887776665454 23355567777888888888888887765 56665554
No 40
>PHA02604 rI.-1 hypothetical protein; Provisional
Probab=23.82 E-value=3.6e+02 Score=21.08 Aligned_cols=81 Identities=19% Similarity=0.243 Sum_probs=42.9
Q ss_pred cCCCCcccHHHH----HHHHHHHHHhhh-ccccccccCCCCCCCCCCchhhhhhhhhccccccchhHHHHHHHHHhcCCc
Q 029478 70 DESVGRSVPFVF----LERVKDDFKQRY-GASIQNEESHPLADDDEDDDLFEDRFSIAYNLDREFGPRLKEHMQYCMSHP 144 (192)
Q Consensus 70 d~~yp~rvaF~f----L~ei~~~F~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~~i~~~~~~~F~~~Lk~lm~~yn~~p 144 (192)
..+|.+..|+.+ |.++-+.|.++| |-...+..+ .+. ..+ ..++...|+++++..+ .
T Consensus 36 T~SYa~HkA~d~~y~~~~dLiD~F~E~yiG~~Gr~Y~P-~l~----------~~s------~~d~~~~l~~~l~~a~--~ 96 (126)
T PHA02604 36 TKSYARHKAYEFFYEEMPDLIDKFAEQYIGISGRKYKP-SLP----------SAS------ELDTIAFLDELLQEAE--E 96 (126)
T ss_pred hhhHhhhhHHHHHHHHhhHHHHHHHHHHHhhcccCcCc-ccc----------ccc------ccCHHHHHHHHHHHHH--H
Confidence 477888888875 466778999888 422111110 110 000 1144556666553321 1
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHhHH
Q 029478 145 EEMSKLSKLKAQITEVKGIMMDNIE 169 (192)
Q Consensus 145 ~~~Dkl~klq~ei~eVk~IM~~NId 169 (192)
--..-.+.|++-+||++....+.+=
T Consensus 97 i~~~l~s~L~N~~DdI~~~~~qt~Y 121 (126)
T PHA02604 97 IYKELPSALQSTLDDITGLCYQTKY 121 (126)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 0002235688888888887776653
No 41
>cd07639 BAR_ACAP1 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ACAP1 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 1), also called centaurin beta-1, is an Arf6-specific GTPase activating protein (GAP) which mediates Arf6 signaling. Arf6 is involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration. ACAP1 also participates in the cargo sorting and recycling of the transferrin receptor and integrin beta1. It may also play a role in innate immune responses. ACAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=23.41 E-value=2.6e+02 Score=23.33 Aligned_cols=56 Identities=14% Similarity=0.157 Sum_probs=36.2
Q ss_pred ccchhHHHHHHHHHhcCCch---hhhHHHHHHHHHHHHHHHHHHhHHHHHH----HHHHcCcc
Q 029478 126 DREFGPRLKEHMQYCMSHPE---EMSKLSKLKAQITEVKGIMMDNIEKVRV----FFLKNGIG 181 (192)
Q Consensus 126 ~~~F~~~Lk~lm~~yn~~p~---~~Dkl~klq~ei~eVk~IM~~NIdkiL~----~~~~~~~~ 181 (192)
...|...|.++-.++-.||. ...+.+..-++|.+-+..|.+|++.+|- -|+|..+|
T Consensus 39 ~~~F~~~L~~f~~~~~~D~~i~~~l~kFs~~l~ei~~~~~~Ll~~~~~~l~~~L~~F~k~dl~ 101 (200)
T cd07639 39 SRAFVDGLCDLAHHGPKDPMMAECLEKFSDGLNHILDSHAELLEATQFSFKQQLQLLVKEDLR 101 (200)
T ss_pred HHHHHHHHHHHhccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 45567777777655555553 3345566667777778888888776544 57777665
No 42
>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=22.12 E-value=2.7e+02 Score=23.69 Aligned_cols=53 Identities=17% Similarity=0.346 Sum_probs=34.6
Q ss_pred cchhHHHHHHHHH--hcCCc---hhhhHHHHHHHHHHHHHHHHHHhHHHHHH----HHHHcC
Q 029478 127 REFGPRLKEHMQY--CMSHP---EEMSKLSKLKAQITEVKGIMMDNIEKVRV----FFLKNG 179 (192)
Q Consensus 127 ~~F~~~Lk~lm~~--yn~~p---~~~Dkl~klq~ei~eVk~IM~~NIdkiL~----~~~~~~ 179 (192)
..|...|.++=.+ +++|| ....++.+++.||.....+.++|+..++- -|||..
T Consensus 40 ~~f~~~L~~LG~~~l~~dd~~~~~~l~kf~~~~~El~~l~~~L~~~~~~~I~~pl~s~lK~d 101 (215)
T cd07642 40 EQYTQALEKFGSNCVCRDDPDLGSAFLKFSVFTKELTALFKNLVQNMNNIITFPLDSLLKGD 101 (215)
T ss_pred HHHHHHHHHHhhcccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence 4566666666554 54454 24467778888888888888888877765 455543
No 43
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=22.00 E-value=90 Score=27.74 Aligned_cols=36 Identities=19% Similarity=0.312 Sum_probs=21.0
Q ss_pred hHHHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHh
Q 029478 130 GPRLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDN 167 (192)
Q Consensus 130 ~~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~N 167 (192)
.|++|+.|+.+| .++..|..+.++.-+|.++.|.+|
T Consensus 57 DpEmK~iid~~n--~eaikkyqqT~~~f~e~~e~~~k~ 92 (295)
T TIGR01478 57 DPELKEIIDKLN--EEAIKKYQETHDPYEQLQELVEKN 92 (295)
T ss_pred cHHHHHHHHHHh--HHHhhhhhhhcchHHHHHHHHHhc
Confidence 488898888775 233344445555555555555444
No 44
>PF02252 PA28_beta: Proteasome activator pa28 beta subunit; InterPro: IPR003186 PA28 activator complex (also known as 11S regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha (PA28alpha) and beta (PA28beta) subunits. The catalytic properties of PA28alpha and PA28beta-activated proteosome are similar [, ]. This entry represents the beta subunit. The activator complex binds to the 20S proteasome and stimulates peptidase activity in and ATP-independent manner.; GO: 0008537 proteasome activator complex; PDB: 1AVO_N.
Probab=21.39 E-value=2.6e+02 Score=22.28 Aligned_cols=26 Identities=19% Similarity=0.318 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHHHHHHHHHhHHHHHH
Q 029478 148 SKLSKLKAQITEVKGIMMDNIEKVRV 173 (192)
Q Consensus 148 Dkl~klq~ei~eVk~IM~~NIdkiL~ 173 (192)
.-+..+...-..+.+++.+|++|+..
T Consensus 115 ~~~~elRn~Y~~l~D~i~KN~eKi~~ 140 (150)
T PF02252_consen 115 LIVLELRNNYATLYDIISKNFEKIKK 140 (150)
T ss_dssp HHHHHHHHHHHHHHHHHHHTHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHhcC
Confidence 56778888888899999999999865
No 45
>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.97 E-value=1.1e+02 Score=30.46 Aligned_cols=58 Identities=14% Similarity=0.218 Sum_probs=46.1
Q ss_pred chhHHHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHcCcceEEEE
Q 029478 128 EFGPRLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDNIEKVRVFFLKNGIGIIYMY 186 (192)
Q Consensus 128 ~F~~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~NIdkiL~~~~~~~~~~~~~~ 186 (192)
-|...|++-+..|..+..+ |-++++-.+-..|.+-+.+|+...+....+-=+|+++|.
T Consensus 227 lF~sil~QdiaFFD~nktG-eL~SRLtsD~~~vs~svs~nls~~lR~~~~~~g~~~~M~ 284 (716)
T KOG0058|consen 227 LFRSLLRQDIAFFDENKTG-ELISRLTSDTQIVSNSVSQNLSDGLRNLVQGFGGLGFMF 284 (716)
T ss_pred HHHHHHhhhhhhhccCCcc-HHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHHHHh
Confidence 4667788888888544444 999999999999999999999999997776655555553
No 46
>PTZ00370 STEVOR; Provisional
Probab=20.70 E-value=1e+02 Score=27.44 Aligned_cols=36 Identities=22% Similarity=0.345 Sum_probs=19.6
Q ss_pred hHHHHHHHHHhcCCchhhhHHHHHHHHHHHHHHHHHHh
Q 029478 130 GPRLKEHMQYCMSHPEEMSKLSKLKAQITEVKGIMMDN 167 (192)
Q Consensus 130 ~~~Lk~lm~~yn~~p~~~Dkl~klq~ei~eVk~IM~~N 167 (192)
.|++|+.|+.+|. ++..|..+.++.-+|.++.|.+|
T Consensus 56 DpemK~i~d~~n~--eaikkyqqT~~~f~e~~e~~~k~ 91 (296)
T PTZ00370 56 DPELKEIIDKMNE--EAIKKYQQTHDPYEQLKEVVEKN 91 (296)
T ss_pred cHHHHHHHHHHhH--HHhhhhhhhcchHHHHHHHHHhc
Confidence 4788888877752 23334444444444444444443
Done!