RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3857
(349 letters)
>1elk_A Target of MYB1; superhelix of helices, endocytosis/exocytosis
complex; 1.50A {Homo sapiens} SCOP: a.118.9.2
Length = 157
Score = 189 bits (480), Expect = 7e-60
Identities = 98/158 (62%), Positives = 122/158 (77%), Gaps = 4/158 (2%)
Query: 1 MASFFGTAFNPFASPVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKR 60
M S F NPF+SPVG +IE ATD +L SE+WALNMEICDIINETE+GPKDA++A++KR
Sbjct: 3 MGSDFLLG-NPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETEEGPKDALRAVKKR 61
Query: 61 LQQYAGKDYTVIMYTLTVLETCVKNCNRRFHILVCSKDFIQE-LYKLIGPKNEPPIIVQD 119
+ K++ +M LTVLETCVKNC RFH+LV S+DF++ L + I PKN PP IV D
Sbjct: 62 IVGN--KNFHEVMLALTVLETCVKNCGHRFHVLVASQDFVESVLVRTILPKNNPPTIVHD 119
Query: 120 KVLSLIQSWADAFKDIPNLEGVNQIYQELRSKGIEFPM 157
KVL+LIQSWADAF+ P+L GV IY++LR KG+EFPM
Sbjct: 120 KVLNLIQSWADAFRSSPDLTGVVTIYEDLRRKGLEFPM 157
>1x5b_A Signal transducing adaptor molecule 2; VHS domain, ubiquitin
binding, STAM2, structural genomics, NPPSFA; NMR {Homo
sapiens} PDB: 2l0t_B
Length = 163
Score = 180 bits (458), Expect = 2e-56
Identities = 53/153 (34%), Positives = 84/153 (54%), Gaps = 5/153 (3%)
Query: 13 ASPVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVI 72
A+P +E AT+ +E+W+L M+ICD + T +G KD +KAI KR+ K V
Sbjct: 13 ANPFEQDVEKATNEYNTTEDWSLIMDICDKVGSTPNGAKDCLKAIMKRVNH---KVPHVA 69
Query: 73 MYTLTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPKNEPPIIVQDKVLSLIQSWADAF 132
+ LT+L CV NC + FH+ VCS+DF E+ +I KN+ V +K+ SL+ W++ F
Sbjct: 70 LQALTLLGACVANCGKIFHLEVCSRDFATEVRAVI--KNKAHPKVCEKLKSLMVEWSEEF 127
Query: 133 KDIPNLEGVNQIYQELRSKGIEFPMTDLDAMAP 165
+ P ++ + ++ +GI FP P
Sbjct: 128 QKDPQFSLISATIKSMKEEGITFPPAGSQTSGP 160
>1juq_A ADP-ribosylation factor binding protein GGA3; protein-peptide
compelx, VHS domain, DXXLL sorting signal, signaling
protein; 2.20A {Homo sapiens} SCOP: a.118.9.2 PDB:
1jpl_A 1lf8_A*
Length = 171
Score = 172 bits (437), Expect = 3e-53
Identities = 49/172 (28%), Positives = 79/172 (45%), Gaps = 12/172 (6%)
Query: 5 FGTAFNPFASPVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQY 64
G+ + S + AT+P+ E+W + CD IN+ +GP+ A++ + ++Q
Sbjct: 3 MGSMAEAEGESLESWLNKATNPSNRQEDWEYIIGFCDQINKELEGPQIAVRLLAHKIQS- 61
Query: 65 AGKDYTVIMYTLTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPK---NEPPIIVQDKV 121
+ LTVLE C+KNC RRFH V F+ EL K++ PK + V+ KV
Sbjct: 62 --PQEWEALQALTVLEACMKNCGRRFHNEVGKFRFLNELIKVVSPKYLGDRVSEKVKTKV 119
Query: 122 LSLIQSWADAFKDIPNLEGVNQIYQELRSKGIEFPMTDL---DAMAPIITPK 170
+ L+ SW A P + Y L+ +GI + + P P+
Sbjct: 120 IELLYSWTMAL---PEEAKIKDAYHMLKRQGIVQSDPPIPVDRTLIPSPPPR 168
>3rru_A TOM1L1 protein; structural genomics, PSI-biology, northeast
structural genom consortium, NESG, super-helical
protein; 3.00A {Homo sapiens}
Length = 152
Score = 169 bits (430), Expect = 2e-52
Identities = 55/149 (36%), Positives = 95/149 (63%), Gaps = 3/149 (2%)
Query: 5 FGTAFNPFASPVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQY 64
+ +P+A+ VG IE AT + +E+W M ICDIIN T+DGPKDA+KA++KR+ +
Sbjct: 6 HHHSHDPYATSVGHLIEKATFAGVQTEDWGQFMHICDIINTTQDGPKDAVKALKKRISK- 64
Query: 65 AGKDYTVIMYTLTVLETCVKNCNRRFHILVCSKDFIQE-LYKLIGPKNEPPIIVQDKVLS 123
++ I TL++++ CV+NC F L+ K+F++E L KL+ P+ P+ +Q+++L+
Sbjct: 65 -NYNHKEIQLTLSLIDMCVQNCGPSFQSLIVKKEFVKENLVKLLNPRYNLPLDIQNRILN 123
Query: 124 LIQSWADAFKDIPNLEGVNQIYQELRSKG 152
I++W+ F ++ V ++Y +L KG
Sbjct: 124 FIKTWSQGFPGGVDVSEVKEVYLDLVKKG 152
>3ldz_A STAM-1, signal transducing adapter molecule 1; ubiquitin-binding,
cytoplasm, UBL conjugation, endosome, membrane, protein
transport, SH3 domain; 2.60A {Homo sapiens}
Length = 140
Score = 168 bits (427), Expect = 4e-52
Identities = 48/144 (33%), Positives = 82/144 (56%), Gaps = 6/144 (4%)
Query: 13 ASPVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVI 72
+P +E AT +E+W L ++ICD + ++ GPKD +++I +R+ KD V
Sbjct: 3 TNPFDQDVEKATSEMNTAEDWGLILDICDKVGQSRTGPKDCLRSIMRRVNH---KDPHVA 59
Query: 73 MYTLTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPKNEPPIIVQDKVLSLIQSWADAF 132
M LT+L CV NC + FH+ VCS+DF E+ ++ + V +K+ +L+ W D F
Sbjct: 60 MQALTLLGACVSNCGKIFHLEVCSRDFASEVSNVLNKGHPK---VCEKLKALMVEWTDEF 116
Query: 133 KDIPNLEGVNQIYQELRSKGIEFP 156
K+ P L ++ + + L+ +G+ FP
Sbjct: 117 KNDPQLSLISAMIKNLKEQGVTFP 140
>1mhq_A ADP-ribosylation factor binding protein GGA2; super helix, protein
transport; 2.20A {Homo sapiens} SCOP: a.118.9.2
Length = 148
Score = 163 bits (415), Expect = 3e-50
Identities = 40/151 (26%), Positives = 71/151 (47%), Gaps = 11/151 (7%)
Query: 18 SKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVIMYTLT 77
+ ATDP+++ ++W+ C+ +N +GP A + ++Q +Y LT
Sbjct: 4 LWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQS---PQEKEALYALT 60
Query: 78 VLETCVKNCNRRFHILVCSKDFIQELYKLIGPKNEP---PIIVQDKVLSLIQSWADAFKD 134
VLE C+ +C +FH V F+ EL K++ PK V+ +V+ ++ SW F +
Sbjct: 61 VLEMCMNHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTVWFPE 120
Query: 135 IPNLEGVNQIYQELRSKGIEF--PMTDLDAM 163
+ YQ L+ +GI P +D +
Sbjct: 121 DI---KIRDAYQMLKKQGIIKQDPKLPVDKI 148
>3g2s_A C-terminal fragment of sortilin-related receptor; ADP-ribosylation
factor binding protein GGA1, VHS, acidic- cluster
dileucine signal, sorla; 1.70A {Homo sapiens} PDB:
3g2t_A* 3g2u_A 3g2v_A* 3g2w_A 1ujk_A* 1jwf_A 1ujj_A
1jwg_A* 1py1_A*
Length = 149
Score = 162 bits (410), Expect = 2e-49
Identities = 44/146 (30%), Positives = 72/146 (49%), Gaps = 9/146 (6%)
Query: 11 PFASPVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYT 70
+ ++I AT+P +WA C+ +NE +GP A + + ++Q
Sbjct: 7 MEPETLEARINRATNPLNKELDWASINGFCEQLNEDFEGPPLATRLLAHKIQS---PQEW 63
Query: 71 VIMYTLTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPK---NEPPIIVQDKVLSLIQS 127
+ LTVLETC+K+C +RFH V F+ EL K++ PK + V++K+L L+ S
Sbjct: 64 EAIQALTVLETCMKSCGKRFHDEVGKFRFLNELIKVVSPKYLGSRTSEKVKNKILELLYS 123
Query: 128 WADAFKDIPNLEGVNQIYQELRSKGI 153
W P + + YQ L+ +GI
Sbjct: 124 WTVGL---PEEVKIAEAYQMLKKQGI 146
>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate;
signaling; 1.48A {Homo sapiens} PDB: 4avx_A*
Length = 226
Score = 164 bits (416), Expect = 2e-49
Identities = 47/168 (27%), Positives = 82/168 (48%), Gaps = 5/168 (2%)
Query: 13 ASPVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVI 72
+ ++ AT L +W ++ICD+I + + K A+ +I+K++ K+ V
Sbjct: 6 SGTFERLLDKATSQLLLETDWESILQICDLIRQGDTQAKYAVNSIKKKVND---KNPHVA 62
Query: 73 MYTLTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPKNEPPIIVQDKVLSLIQSWADAF 132
+Y L V+E+ VKNC + H V +K ++EL L+ K + + V++K+L LIQ+WA AF
Sbjct: 63 LYALEVMESVVKNCGQTVHDEVANKQTMEELKDLL--KRQVEVNVRNKILYLIQAWAHAF 120
Query: 133 KDIPNLEGVNQIYQELRSKGIEFPMTDLDAMAPIITPKKSKEVASSHP 180
++ P + V YQ ++ +G FP A
Sbjct: 121 RNEPKYKVVQDTYQIMKVEGHVFPEFKESDAMFAAERAPDWVDAEECH 168
>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate;
VHS, FYVE, zinc finger, superhelix, transferase; HET:
CIT; 2.00A {Drosophila melanogaster} SCOP: a.118.9.2
g.50.1.1
Length = 220
Score = 161 bits (409), Expect = 2e-48
Identities = 44/160 (27%), Positives = 71/160 (44%), Gaps = 5/160 (3%)
Query: 12 FASPVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTV 71
F S +E AT +W + ICD IN+ + PK+A AI+K++ +
Sbjct: 2 FRSSFCKNLENATSHLRLEPDWPSILLICDEINQKDVTPKNAFAAIKKKMNS---PNPHS 58
Query: 72 IMYTLTVLETCVKNCNRRFHILVCSKDFIQELYKLIGPKNEPPIIVQDKVLSLIQSWADA 131
Y+L VLE+ VKNC H V +K+ + + ++ P V+ K+L L+Q+WA A
Sbjct: 59 SCYSLLVLESIVKNCGAPVHEEVFTKENCEMFSSFL--ESTPHENVRQKMLELVQTWAYA 116
Query: 132 FKDIPNLEGVNQIYQELRSKGIEFPMTDLDAMAPIITPKK 171
F+ + + L++KG FP
Sbjct: 117 FRSSDKYQAIKDTMTILKAKGHTFPELREADAMFTADTAP 156
>1wrd_A TOM1, target of MYB protein 1; three-helix bundle,
ubiquitin-binding protein, protein trans signaling
protein complex; 1.75A {Homo sapiens} SCOP: a.7.8.1
Length = 103
Score = 114 bits (286), Expect = 1e-31
Identities = 46/100 (46%), Positives = 65/100 (65%)
Query: 198 LTPEQVTKLHKDLEVVQANMAVFNEMLNTLIPGQEHSSDIELITELHATCKAMQERIVQL 257
L EQ+ KL +LE+V N+ V +EML L+P Q +D+EL+ EL+ TC+AMQ+R+++L
Sbjct: 3 LGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLEL 62
Query: 258 ISKYSQEDFITELLQVNDQLNNLFLRFNRYESNREAAIGK 297
I + + E ELL VND LNN+FLR R+E R K
Sbjct: 63 IPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTGQTTK 102
>1wr6_A ADP-ribosylation factor binding protein GGA3; three-helix bundle,
clathrin coat adaptor protein, protein
transport/signaling protein complex; 2.60A {Homo
sapiens} SCOP: a.7.8.1 PDB: 1yd8_G
Length = 111
Score = 98.8 bits (246), Expect = 8e-26
Identities = 22/95 (23%), Positives = 43/95 (45%), Gaps = 1/95 (1%)
Query: 201 EQVTKLHKDLEVVQANMAVFNEMLNTLIPGQEHSSDIELITELHATCKAMQERIVQLISK 260
++VTK LE V N+ + +EML D EL+ EL C+ + + +L S+
Sbjct: 1 QKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASE 60
Query: 261 YSQ-EDFITELLQVNDQLNNLFLRFNRYESNREAA 294
++ + ++LQ +D L+ + + +
Sbjct: 61 TEDNDNSLGDILQASDNLSRVINSYKTIIEGQVIN 95
>1oxz_A ADP-ribosylation factor binding protein GGA1; GAT domain, membrane
protein; 2.80A {Homo sapiens} SCOP: a.7.8.1
Length = 186
Score = 94.3 bits (234), Expect = 3e-23
Identities = 28/139 (20%), Positives = 55/139 (39%), Gaps = 15/139 (10%)
Query: 191 AGDHDERLTPEQVTKLHKDLEVVQANMAVFNEMLNTLIPGQEHSSD-IELITELHATCKA 249
+ +R E+++K +E V N+ + EM+ + G + +L+ EL+ C+
Sbjct: 61 VQEDQKR--MEKISKRVNAIEEVNNNVKLLTEMVMSHSQGGAAAGSSEDLMKELYQRCER 118
Query: 250 MQERIVQLISKYSQ-EDFITELLQVNDQLNNLFLRFNRYESNREAAIGKQNPDAASKLSK 308
M+ + +L S ++ + E+LQ ND L + + + E
Sbjct: 119 MRPTLFRLASDTEDNDEALAEILQANDNLTQVINLYKQLVRGEEVNGDATAGSIPG---- 174
Query: 309 KPDVAADSGPSLIDLDDDD 327
S +L+DL D
Sbjct: 175 -------STSALLDLSGLD 186
>1o3x_A ADP-ribosylation factor binding protein GGA1; protein transport;
2.10A {Homo sapiens} SCOP: a.7.8.1 PDB: 1nwm_X 1x79_A
Length = 140
Score = 89.9 bits (223), Expect = 3e-22
Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 4/106 (3%)
Query: 191 AGDHDERLTPEQVTKLHKDLEVVQANMAVFNEMLNTLIPGQEHSSD-IELITELHATCKA 249
+ +R E+++K +E V N+ + EM+ + G + +L+ EL+ C+
Sbjct: 36 VQEDQKR--MEKISKRVNAIEEVNNNVKLLTEMVMSHSQGGAAAGSSEDLMKELYQRCER 93
Query: 250 MQERIVQLISKYSQ-EDFITELLQVNDQLNNLFLRFNRYESNREAA 294
M+ + +L S ++ + E+LQ ND L + + + E
Sbjct: 94 MRPTLFRLASDTEDNDEALAEILQANDNLTQVINLYKQLVRGEEVN 139
>1naf_A ADP-ribosylation factor binding protein GGA1, golgi-localized,
gamma EAR-; clathrin-adaptor, GAT domain, helical
paper-CLIP, three-helix bundle; 2.80A {Homo sapiens}
SCOP: a.7.8.1
Length = 158
Score = 90.0 bits (223), Expect = 5e-22
Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 4/106 (3%)
Query: 191 AGDHDERLTPEQVTKLHKDLEVVQANMAVFNEMLNTLIPGQEHSSD-IELITELHATCKA 249
+ +R E+++K +E V N+ + EM+ + G + +L+ EL+ C+
Sbjct: 45 VQEDQKR--MEKISKRVNAIEEVNNNVKLLTEMVMSHSQGGAAAGSSEDLMKELYQRCER 102
Query: 250 MQERIVQLISKYSQ-EDFITELLQVNDQLNNLFLRFNRYESNREAA 294
M+ + +L S ++ + E+LQ ND L + + + E
Sbjct: 103 MRPTLFRLASDTEDNDEALAEILQANDNLTQVINLYKQLVRGEEVN 148
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 57.4 bits (138), Expect = 3e-09
Identities = 54/325 (16%), Positives = 93/325 (28%), Gaps = 124/325 (38%)
Query: 17 GS-KIEMATD----PTLASENW---------ALNMEICDII--NETE-----DGPKDAIK 55
GS + M D A + W I DI+ N G K K
Sbjct: 1625 GSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKG--K 1682
Query: 56 AIRKRLQQYAGKDYTVIMYTLTVLETCVKNCNRRFHILVCSKDFIQELYKLI--GPKNEP 113
IR+ Y+ +++ ET V + I K+ + K
Sbjct: 1683 RIREN--------YSAMIF-----ETIVDGKLKTEKIF---KEINEHSTSYTFRSEKGL- 1725
Query: 114 PIIVQDKVLSLIQ---------SWADAFKDIPNLEGVNQIYQELRSKGIEFPMTD----- 159
LS Q A +++L+SKG+ P
Sbjct: 1726 --------LSATQFTQPALTLMEKA--------------AFEDLKSKGL-IPADATFAGH 1762
Query: 160 -------LDAMAPIITP-----------KKSKEVASSHPVQRSKVPMGA-------AGDH 194
L ++A +++ + + RS M A A
Sbjct: 1763 SLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFS 1822
Query: 195 DERLTP--EQVTKLHKDLEVVQ-ANMAVFNEMLNTLIPGQE-----HSSDIELITELHAT 246
E L E+V K + +V+ N +N + Q+ ++ +T +
Sbjct: 1823 QEALQYVVERVGK--RTGWLVEIVN---YN------VENQQYVAAGDLRALDTVTNVLNF 1871
Query: 247 CKAMQERIVQLISKYSQEDFITELL 271
K + I++L S E+ + L
Sbjct: 1872 IKLQKIDIIELQKSLSLEE-VEGHL 1895
Score = 40.0 bits (93), Expect = 0.001
Identities = 52/277 (18%), Positives = 87/277 (31%), Gaps = 87/277 (31%)
Query: 100 IQELYKLIGPKNEPPIIVQDKVL-SLIQSWADAFK------DIPN-LEGVNQI----YQE 147
+++LY+ I + L LI++ DA K +I LE + Y
Sbjct: 173 LRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDY-- 230
Query: 148 LRSKGIEFPMTDLDAMAP-IITPKKSKEVASSHPVQRSKVPMGAAGDHDERLTPEQVTKL 206
L S I P+ + +A ++T K + P + GA G H + L
Sbjct: 231 LLSIPISCPLIGVIQLAHYVVTAK----LLGFTPGELRSYLKGATG-HSQGL-------- 277
Query: 207 HKDLEVVQANMAV------FNEMLNTLIP--------GQEHSSDIELITELHATCKAMQE 252
V +A F + I E + L
Sbjct: 278 -----VTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSL-----------PP 321
Query: 253 RIVQLISKYSQEDFITELLQVND----QLNNLFLRFNRY-ESNREAAIGKQN-PDAASKL 306
I++ S + E + +L +++ Q+ + + N + + ++ I N
Sbjct: 322 SILE-DSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNL--- 377
Query: 307 SKKPDVAADSGP--SLIDLDDDDPVDVGLNSNLSKLK 341
V SGP SL GLN L K K
Sbjct: 378 -----VV--SGPPQSL----------YGLNLTLRKAK 397
Score = 36.6 bits (84), Expect = 0.012
Identities = 21/122 (17%), Positives = 38/122 (31%), Gaps = 27/122 (22%)
Query: 198 LTPEQVTKLHKDLEVVQANMAVFNEMLNT----LIPGQEHSSDIELITELHATCKAMQER 253
L P T +Q FN++L E ++ EL+ +
Sbjct: 21 LVP---TASFFIASQLQEQ---FNKILPEPTEGFAADDEPTTPAELVG-----------K 63
Query: 254 IVQLISKYSQEDFITELLQVNDQLNNLFLRFNR-YESNRE--AAIGKQNPDAASKLSKKP 310
+ +S + + + QV LN F Y + A K + + L K
Sbjct: 64 FLGYVSSLVEPSKVGQFDQV---LNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTK 120
Query: 311 DV 312
++
Sbjct: 121 EL 122
Score = 35.0 bits (80), Expect = 0.045
Identities = 30/114 (26%), Positives = 42/114 (36%), Gaps = 32/114 (28%)
Query: 5 FGTAFNPFASPVGSKI-EMATDPT---LASENWALNMEICDI-INETEDGPKDAIKAIRK 59
F F P ASP S + A+D L N + N + I + +T DG D
Sbjct: 416 FSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDG-SD------- 467
Query: 60 RLQQYAGKDYTVIMYTLTVL----ETCVKNCNRRFHILVCSKDFIQELYKLIGP 109
L+ +G I+ + L ET + + HIL DF GP
Sbjct: 468 -LRVLSGSISERIVDCIIRLPVKWETTTQ--FKATHIL----DF--------GP 506
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 56.4 bits (135), Expect = 8e-09
Identities = 72/516 (13%), Positives = 132/516 (25%), Gaps = 210/516 (40%)
Query: 4 FFGTAFNPFASPVGSKIEMAT-DPTLASENWALNMEICDIINETEDGPK------DAIKA 56
F + S I+ P++ + + + + N+ + K
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMY--IEQRDRLYNDNQVFAKYNVSRLQPYLK 139
Query: 57 IRKRLQQYAGKDYTVI--MY----TLTVLETC-----------------VKNCNRRFHIL 93
+R+ L + +I + T L+ C +KNCN +L
Sbjct: 140 LRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199
Query: 94 VCSKDFIQELYKLIGP---------KNEPPII--VQDKVLSLIQS-------------W- 128
+ +Q+L I P N I +Q ++ L++S
Sbjct: 200 ----EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN 255
Query: 129 ---ADAF----------KDIPNLEGVN-QIYQELRSKGIEFPMTD---LDAMAPIITPKK 171
+AF + + ++ + +T + + +
Sbjct: 256 AKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRP 315
Query: 172 SK---EVASSHPVQRSKVPMGAAGDHD------------------------ERLTPEQVT 204
EV +++P + S + A D L P +
Sbjct: 316 QDLPREVLTTNPRRLS---IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372
Query: 205 KLHKDLEVVQANMAVFNEMLNTLIP--------GQEHSSDIELI-TELHATC-------- 247
K+ L +VF + IP SD+ ++ +LH
Sbjct: 373 KMFDRL-------SVFPP--SAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423
Query: 248 -------------------KAMQERIV---QLISKYSQEDFI------------------ 267
A+ IV + + +D I
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKN 483
Query: 268 TELLQVNDQLNNLFLRFN------RYESNREAAIGKQNPDAASKLSKKPDVAADSGPSLI 321
E + +FL F R++S A G L
Sbjct: 484 IEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNT------------------LQ 525
Query: 322 DLD-------DDDPVDVGLNSNLSKLKFLQ---ENL 347
L D+DP L + + L FL ENL
Sbjct: 526 QLKFYKPYICDNDPKYERLVNAI--LDFLPKIEENL 559
Score = 47.5 bits (112), Expect = 5e-06
Identities = 37/312 (11%), Positives = 83/312 (26%), Gaps = 99/312 (31%)
Query: 43 INETEDGPKDAI----KAIRKRLQQYAGKDYTVIMYTLTVLETCVKNCNRRFHILVCSKD 98
E + KD + A +D + + ++ HI++ SKD
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEID----------HIIM-SKD 59
Query: 99 FIQELYKLIGP-KNEPPIIVQDKVLSLIQ---SW-ADAFKDIPNL-EGVNQIYQELRSKG 152
+ +L ++ +VQ V +++ + K + ++Y E R +
Sbjct: 60 AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDR- 118
Query: 153 IEFPMTDLDAMAPIITPKKSKEVASSHPVQRSKVPMGAAGDHDERLTPEQVTKLHKDLE- 211
L + + V R + KL + L
Sbjct: 119 -------LYNDNQVFAK---------YNVSR----------------LQPYLKLRQALLE 146
Query: 212 -------VVQ----------ANMAVFNEMLNTLIPGQEHSSDIELITELHATCKAMQERI 254
++ A + + + + ++ C + + +
Sbjct: 147 LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNL-------KNCNSPETVL 199
Query: 255 VQLISKYSQEDFITELLQVNDQLNNLFLRFNRYESN-REAAIGKQNPDAASKLSKKPDVA 313
L Q D +D +N+ LR + ++ R K +
Sbjct: 200 EMLQKLLYQID--PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN------------ 245
Query: 314 ADSGPSLIDLDD 325
L+ L +
Sbjct: 246 -----CLLVLLN 252
>2pjw_H Uncharacterized protein YHL002W; GAT domain, core complex, doamin
SWAP, endocytosis/exocytosis complex; 3.01A
{Saccharomyces cerevisiae}
Length = 88
Score = 35.0 bits (80), Expect = 0.004
Identities = 10/75 (13%), Positives = 31/75 (41%), Gaps = 4/75 (5%)
Query: 214 QANMAVFNEMLNTLIP--GQEHSSDIELITELHATCKAMQERIVQLISKYSQEDFITELL 271
+ + + LN I +++ + ++ ++ +++ KY++E ++L
Sbjct: 9 KTTIDQLHNSLNAASKTGNSNEVLQDPHIGDMYGSVTPLRPQVTRMLGKYAKEK--EDML 66
Query: 272 QVNDQLNNLFLRFNR 286
+ L N +N+
Sbjct: 67 SLRQVLANAERSYNQ 81
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 32.2 bits (72), Expect = 0.12
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 6/26 (23%)
Query: 297 KQNPDAASKL--SKKPDVAADSGPSL 320
KQ A KL S K A DS P+L
Sbjct: 19 KQ---ALKKLQASLKL-YADDSAPAL 40
Score = 30.7 bits (68), Expect = 0.37
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 51 KDAIKAIRKRLQQYA 65
K A+K ++ L+ YA
Sbjct: 19 KQALKKLQASLKLYA 33
Score = 27.6 bits (60), Expect = 4.3
Identities = 5/28 (17%), Positives = 13/28 (46%), Gaps = 3/28 (10%)
Query: 97 KDFIQEL---YKLIGPKNEPPIIVQDKV 121
K +++L KL + P + ++ +
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATM 46
>1xgw_A Epsin 4; ENTH, enthoprotin, clathrin-associated, endocytosis; 1.90A
{Homo sapiens} PDB: 2qy7_A 2v8s_E
Length = 176
Score = 29.6 bits (66), Expect = 1.1
Identities = 25/146 (17%), Positives = 55/146 (37%), Gaps = 17/146 (11%)
Query: 14 SPVGSKIEMATDPTLASENWALN----MEICDIINETEDGPKDAIKAIRKRLQQYAGKDY 69
S + SK+ AT+ + W + EI E P+ + + R+ + K++
Sbjct: 33 SEIESKVREATN----DDPWGPSGQLMGEIAKATFMYEQFPE-LMNMLWSRMLKDNKKNW 87
Query: 70 TVIMYTLTVLETCVKN-CNRRFHILVCSKDFIQEL--YKLIGPKNEPP-IIVQDKVLSLI 125
+ +L +L ++N R ++ L Y + + I ++ KV L+
Sbjct: 88 RRVYKSLLLLAYLIRNGSERVVTSAREHIYDLRSLENYHFVDEHGKDQGINIRQKVKELV 147
Query: 126 QSWADAFKDIPNLEGVNQIYQELRSK 151
+ +D L + ++ + K
Sbjct: 148 E----FAQDDDRLREERKKAKKNKDK 169
>2obb_A Hypothetical protein; structural genomics, PSI-2, PR structure
initiative, midwest center for structural genomic
unknown function; 2.20A {Bacteroides thetaiotaomicron}
SCOP: c.108.1.25
Length = 142
Score = 28.8 bits (64), Expect = 1.5
Identities = 15/107 (14%), Positives = 42/107 (39%), Gaps = 10/107 (9%)
Query: 51 KDAIKAIRKRLQQYAGKDYTVIMYT---LTVLETCVKNCNRR---FHILVCSKDFIQELY 104
A++ ++ Q + +I+++ +L+ ++ C R F+ + +
Sbjct: 27 PFAVETLKLL--QQEK--HRLILWSVREGELLDEAIEWCRARGLEFYAANKDYPEEERDH 82
Query: 105 KLIGPKNEPPIIVQDKVLSLIQSWADAFKDIPNLEGVNQIYQELRSK 151
+ K + + + D+ + I W ++ I + IY + R +
Sbjct: 83 QGFSRKLKADLFIDDRNVGGIPDWGIIYEMIKEKKTFADIYSQQREE 129
>1hs7_A Syntaxin VAM3; UP-and-DOWN three-helix bundle insertion preceding
proline in AN alpha-helix, endocytosis/exocytosis
complex; NMR {Saccharomyces cerevisiae} SCOP: a.47.2.1
Length = 97
Score = 27.5 bits (60), Expect = 2.4
Identities = 16/94 (17%), Positives = 36/94 (38%), Gaps = 5/94 (5%)
Query: 199 TPEQVTKLHKDLEVVQANMAVF---NEMLNTLIPGQEHSSDIELITELHATCKAMQERIV 255
T ++ +L +E V + + +E IE TEL C +++++I
Sbjct: 1 TNQKTKELSNLIETFAEQSRVLEKECTKIGSKRDSKELRYKIE--TELIPNCTSVRDKIE 58
Query: 256 QLISKYSQEDFITELLQVNDQLNNLFLRFNRYES 289
I + + + + +L +N+ +S
Sbjct: 59 SNILIHQNGKLSADFKNLKTKYQSLQQSYNQRKS 92
>1avo_B 11S regulator; proteasome activator, cell adhesion, interferon
induction; 2.80A {Homo sapiens} SCOP: a.24.8.1
Length = 140
Score = 27.6 bits (61), Expect = 3.3
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 263 QEDFITELLQVNDQLNNLFLRFNRYESNREAAIGKQNPDAASKLSKKPDVAADSGPSLID 322
QE + ++ +L + ++Y S R DA +K +K+P V D + +
Sbjct: 51 QEKVFELMTSLHTKLEGFHTQISKYFSER--------GDAVTKAAKQPHV-GDYRQLVHE 101
Query: 323 LD 324
LD
Sbjct: 102 LD 103
>3zym_A Phosphatidylinositol-binding clathrin assembly PR
vesicle-associated membrane protein...; endocytosis,
synaptobrevin, VAMP2, VAMP3, AP180; HET: PO4; 2.03A
{Rattus norvegicus}
Length = 310
Score = 28.3 bits (62), Expect = 3.6
Identities = 12/78 (15%), Positives = 22/78 (28%), Gaps = 3/78 (3%)
Query: 13 ASPVGSKIEMATDPTLASENWALNMEICDIINETEDGPKDAIKAIRKRLQQYAGKDYTVI 72
S V + AT + + NE ++ +R + V+
Sbjct: 26 GSAVSKTVCKATTHEIMGPKKKHLDYLIQCTNEMNVNIPQLADSLFERTTN---SSWVVV 82
Query: 73 MYTLTVLETCVKNCNRRF 90
+L + N RF
Sbjct: 83 FKSLITTHHLMVYGNERF 100
>1jnr_A Adenylylsulfate reductase; oxidoreductase; HET: FAD; 1.60A
{Archaeoglobus fulgidus dsm 4304} SCOP: a.7.3.1 c.3.1.4
d.168.1.1 PDB: 1jnz_A* 2fjb_A* 2fja_A* 2fjd_A* 2fje_A*
Length = 643
Score = 28.6 bits (64), Expect = 3.9
Identities = 7/42 (16%), Positives = 18/42 (42%)
Query: 43 INETEDGPKDAIKAIRKRLQQYAGKDYTVIMYTLTVLETCVK 84
+N P + ++K + +YA T+ +L+ ++
Sbjct: 507 VNPEYILPWQGLVRLQKIMDEYAAGIATIYKTNEKMLQRALE 548
>2l7n_A Talin-1; integrin, bundle, focal adhesion, structural protein; NMR
{Mus musculus}
Length = 168
Score = 26.6 bits (58), Expect = 9.4
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 201 EQVTKLHKDLEVVQANMAVFNEMLNTLIPGQEHSSDIELITELHATCKAMQERIVQLISK 260
V L KDL+ + A + L L PG+ + +L + KA+ I +L+ +
Sbjct: 16 SVVQNLEKDLQ--EIKAAARDGKLKPL-PGETMEKCTQ---DLGNSTKAVSSAIAKLLGE 69
Query: 261 YSQED 265
+Q +
Sbjct: 70 IAQGN 74
>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles,
endocytosis, SELF- assembly, alpha-alpha superhelix;
2.60A {Bos taurus} SCOP: a.118.1.3
Length = 449
Score = 27.2 bits (60), Expect = 9.8
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 12/91 (13%)
Query: 221 NEMLNTLIPGQEHSSDIELITELHATCKAMQERIVQLISKYSQEDFITELLQVNDQLNNL 280
N++L L P +H+ + +++ + L+ Y + VN+ LNNL
Sbjct: 347 NDLLMVLSPRLDHTRAVNYFSKVK---------QLPLVKPYLRSVQNHNNKSVNESLNNL 397
Query: 281 FLRFNRYESNREAAIGKQNPDA---ASKLSK 308
F+ Y++ R + N D A +L K
Sbjct: 398 FITEEDYQALRTSIDAYDNFDNISLAQRLEK 428
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.133 0.377
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,195,496
Number of extensions: 311420
Number of successful extensions: 905
Number of sequences better than 10.0: 1
Number of HSP's gapped: 870
Number of HSP's successfully gapped: 42
Length of query: 349
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 255
Effective length of database: 4,077,219
Effective search space: 1039690845
Effective search space used: 1039690845
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.6 bits)