RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4079
(294 letters)
>3hzj_A Rabgap1L, RAB GTPase-activating protein 1-like; structural genomics
consortium, SGC, alternative splicing, GTPase
activation, phosphoprotein; 2.30A {Homo sapiens}
Length = 310
Score = 167 bits (426), Expect = 2e-50
Identities = 40/121 (33%), Positives = 56/121 (46%)
Query: 133 YCQGTGMIAASLLLLMEEEEAFWTLSAIVEDLLPASYYTPNLIGIQADQKVLRSLVASGL 192
YCQG +AA LLL M EE+AF L I+ D Y N + L L+ L
Sbjct: 114 YCQGQSFLAAVLLLHMPEEQAFCVLVKIMYDYGLRDLYRNNFEDLHCKFYQLERLMQEQL 173
Query: 193 PQLELSLLQHDIELSLITLHWFLTLFASVVHFKILLRIWDLLFLDGSMVLFQITLGMLKI 252
P L ++E + WFLTLF + ++ I DLL +G ++F + L +LK
Sbjct: 174 PDLHSHFSDLNLEAHMYASQWFLTLFTAKFPLCMVFHIIDLLLCEGLNIIFHVALALLKT 233
Query: 253 K 253
Sbjct: 234 S 234
>3qye_A TBC1 domain family member 1; rabgap, RAB, myocytes, hydrolase
activator; 2.20A {Homo sapiens} PDB: 3qyb_A
Length = 331
Score = 168 bits (426), Expect = 3e-50
Identities = 44/121 (36%), Positives = 65/121 (53%)
Query: 133 YCQGTGMIAASLLLLMEEEEAFWTLSAIVEDLLPASYYTPNLIGIQADQKVLRSLVASGL 192
YCQG +A LLL M EEEAF L ++ D+ Y P++I +Q L L+
Sbjct: 148 YCQGLSFVAGILLLHMSEEEAFKMLKFLMFDMGLRKQYRPDMIILQIQMYQLSRLLHDYH 207
Query: 193 PQLELSLLQHDIELSLITLHWFLTLFASVVHFKILLRIWDLLFLDGSMVLFQITLGMLKI 252
L L +H+I SL WFLT+FAS + R++D++FL G+ V+F++ L +L
Sbjct: 208 RDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLLGS 267
Query: 253 K 253
Sbjct: 268 H 268
>2qq8_A TBC1 domain family member 14; structural genomics consortium,
RAB-GAP, SGC, GTPase activation, hydrolase activator;
2.00A {Homo sapiens}
Length = 334
Score = 166 bits (421), Expect = 2e-49
Identities = 29/120 (24%), Positives = 55/120 (45%)
Query: 133 YCQGTGMIAASLLLLMEEEEAFWTLSAIVEDLLPASYYTPNLIGIQADQKVLRSLVASGL 192
Y QG IAA L+L ++ +AF S ++ +++ + + L
Sbjct: 153 YVQGMSFIAAVLILNLDTADAFIAFSNLLNKPCQMAFFRVDHGLMLTYFAAFEVFFEENL 212
Query: 193 PQLELSLLQHDIELSLITLHWFLTLFASVVHFKILLRIWDLLFLDGSMVLFQITLGMLKI 252
P+L ++++ + + W TL++ + + RIWD+ DG LF+ LG+LK+
Sbjct: 213 PKLFAHFKKNNLTPDIYLIDWIFTLYSKSLPLDLACRIWDVFCRDGEEFLFRTALGILKL 272
>2qfz_A TBC1 domain family member 22A; RAB-GAP, GTPase activator,
structural genomics, structural genomics consortium,
SGC, hydrolase activator; 2.10A {Homo sapiens} PDB:
3dzx_A
Length = 345
Score = 93.9 bits (233), Expect = 3e-22
Identities = 28/150 (18%), Positives = 48/150 (32%), Gaps = 30/150 (20%)
Query: 130 ESNYCQGTGMIAASLLLLME-------------------------EEEAFWTLSAIVEDL 164
S Y QG + ++ E + +W +S +++ +
Sbjct: 143 ASGYVQGINDLVTPFFVVFICEYIEAEEVDTVDVSGVPAEVLCNIEADTYWCMSKLLDGI 202
Query: 165 LPASYYTPNLIGIQADQKVLRSLVASGLPQLELSLLQHDIELSLITLHWFLTLFASVVHF 224
YT GIQ K+L LV+ Q+ L QH++ W L V
Sbjct: 203 QD--NYTFAQPGIQMKVKMLEELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMREVPL 260
Query: 225 KILLRIWDLLFLDG---SMVLFQITLGMLK 251
+ +R+WD + S + L
Sbjct: 261 RCTIRLWDTYQSEPDGFSHFHLYVCAAFLV 290
>3qwl_A TBC1 domain family member 7; RAB GTPase activation, structural
genomics consortium, TBC D SGC, hydrolase activator;
1.90A {Homo sapiens}
Length = 294
Score = 90.9 bits (225), Expect = 2e-21
Identities = 22/128 (17%), Positives = 41/128 (32%), Gaps = 6/128 (4%)
Query: 130 ESNYCQGTGMIAASLLLLMEEEEAFWTLSAIVEDLLPASYYTPNLIGIQADQKVLRSLVA 189
E + + A ++ + + +W V L Y +L + K +
Sbjct: 129 EPDDEVFLAIAKAMEEMVEDSVDCYWITRRFVNQLNT--KYRDSLPQLP---KAFEQYLN 183
Query: 190 SGLPQLELSLLQHDIELSLITLHWFLTLFASVVHFKILLRIWDLLFLDGSMVLFQITLGM 249
+L L L WF FA + L R+WD + +L + + +
Sbjct: 184 LEDGRLLTHLRMCSAAPKLPYDLWFKRCFAGCLPESSLQRVWDKVVSGSCKILVFVAVEI 243
Query: 250 LK-IKDTI 256
L K +
Sbjct: 244 LLTFKIKV 251
>1fkm_A Protein (GYP1P), ORF YOR070C; GAP, YPT/RAB protein, vesicular
trafficking, endocytosis, hydrolase, GTPase activation;
1.90A {Saccharomyces cerevisiae} SCOP: a.69.2.1 a.69.2.1
PDB: 2g77_A*
Length = 396
Score = 82.7 bits (204), Expect = 4e-18
Identities = 24/143 (16%), Positives = 36/143 (25%), Gaps = 31/143 (21%)
Query: 130 ESNYCQGTGMIAASLLLLME-----------------------------EEEAFWTLSAI 160
S Y QG + E + FW L+ +
Sbjct: 126 ASGYVQGINDLVTPFFETFLTEYLPPSQIDDVEIKDPSTYMVDEQITDLEADTFWCLTKL 185
Query: 161 VEDLLPASYYTPNLIGIQADQKVLRSLVASGLPQLELSLLQHDIELSLITLHWFLTLFAS 220
+E + Y GI K L LV L +E W L
Sbjct: 186 LEQITD--NYIHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMR 243
Query: 221 VVHFKILLRIWDLLFLDGSMVLF 243
++R+WD + S +
Sbjct: 244 EFQMGTVIRMWDTYLSETSQEVT 266
>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 = 42.3 bits (99), Expect = 1e-04
Identities = 56/260 (21%), Positives = 89/260 (34%), Gaps = 65/260 (25%)
Query: 88 VVGCPSKSAGNWPKQAIVFLN--LPVDSGVVVNALDFGSGGWWFESNYCQGTGMIAASLL 145
VV K G P + +L G+V A+ W ES + I
Sbjct: 250 VVTA--KLLGFTPGELRSYLKGATGHSQGLVT-AVAIAETDSW-ESFFVSVRKAITVLFF 305
Query: 146 LLMEEEEAFWTLS---AIVEDLLPASYYTP----NLIGI----------------QADQK 182
+ + EA+ S +I+ED L + P ++ + A ++
Sbjct: 306 IGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365
Query: 183 V---L----RSLVASGLPQ----LELSLL---------QHDIELS---LITLHWFLTLFA 219
V L ++LV SG PQ L L+L Q I S L + FL + +
Sbjct: 366 VEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVAS 425
Query: 220 SVVHFKILLRIWDLLFLDGSMVLFQITLGMLKIKDTIYI--------VLSSPIAITMGTC 271
H +L+ DL+ D ++I +Y VLS I+ + C
Sbjct: 426 -PFHSHLLVPASDLINKDLVKNNVSFNAKDIQI--PVYDTFDGSDLRVLSGSISERIVDC 482
Query: 272 VYQLRGLVYMETNMFPHPSH 291
+ +L V ET +H
Sbjct: 483 IIRLP--VKWETTTQFKATH 500
Score = 38.5 bits (89), Expect = 0.003
Identities = 46/222 (20%), Positives = 73/222 (32%), Gaps = 73/222 (32%)
Query: 23 GNSSFM------KRVSLVCIVGSKCAGNWPKQAIVFLNLPVESR---VVGCPSKSAGNWP 73
G S M + + V +K + P V ++L V VV +G P
Sbjct: 333 GVPSPMLSISNLTQEQVQDYV-NKTNSHLPAGKQVEISL-VNGAKNLVV------SG--P 382
Query: 74 KQAIVFLNLPVESRVVGCPSK---SAGNWPKQAIVFLN--LPVDSGVVVNALDFGSGGWW 128
Q++ LNL + R PS S + ++ + F N LPV S
Sbjct: 383 PQSLYGLNLTL--RKAKAPSGLDQSRIPFSERKLKFSNRFLPVASP-------------- 426
Query: 129 FESNYCQGTGMIAASLLL--LMEEEEAFWTLSAIVEDL-LPASYYTPNLIGIQADQKVLR 185
F S+ A+ L+ L++ +F +D+ +P Y T D LR
Sbjct: 427 FHSHLLVP----ASDLINKDLVKNNVSFN-----AKDIQIPV-YDT-------FDGSDLR 469
Query: 186 SLVASGLPQLELSLLQHDIELSLIT---LHWFLTLFASVVHF 224
L S ++ + I + W T H
Sbjct: 470 VLSGSISERI----------VDCIIRLPVKWETTTQFKATHI 501
Score = 34.3 bits (78), Expect = 0.058
Identities = 26/151 (17%), Positives = 47/151 (31%), Gaps = 45/151 (29%)
Query: 18 TAQFCGNSSFMKRVSLVCIVGSKCAGNWPKQAIVF----LNLPVESRVVGC-PSKSAGNW 72
+ F +S + S + K + F + +PV G +G+
Sbjct: 424 ASPF--HSHLLVPAS------DLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSI 475
Query: 73 PKQAI-VFLNLPVESRVVGCPSKSAGNWPKQAIVFLNLPVDSGVVVNALDFGSGGWW--- 128
++ + + LPV W + LDFG GG
Sbjct: 476 SERIVDCIIRLPV-------------KWET---------TTQFKATHILDFGPGGASGLG 513
Query: 129 --FESNYCQGTGM---IAASLLLLMEEEEAF 154
N GTG+ +A +L + +++ F
Sbjct: 514 VLTHRN-KDGTGVRVIVAGTLDINPDDDYGF 543
Score = 32.3 bits (73), Expect = 0.20
Identities = 42/193 (21%), Positives = 64/193 (33%), Gaps = 56/193 (29%)
Query: 129 FESNYCQGTG--MIAASLLLLMEEEEAFWTLSAIVEDLLPASYYTPNLIGIQADQKVLRS 186
FE+ Y +G +AA LL E + +++ +Y T ++ + K S
Sbjct: 91 FENCYLEGNDIHALAAK--LLQENDTTLVKTKELIK-----NYITARIMAKRPFDKKSNS 143
Query: 187 L----VASGLPQL---------------EL--------SLLQHDIELSLITLHWFL--TL 217
V G QL EL L+ I+ S TL + TL
Sbjct: 144 ALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTL 203
Query: 218 FASVVHFKIL-LRIW--------DLLFLDG---SMVLFQITLGMLKIKDTIYIVLSSPIA 265
A V + L + W D +L S L I + L Y+V + +
Sbjct: 204 DAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPL--IGVIQL----AHYVVTAKLLG 257
Query: 266 ITMGTCVYQLRGL 278
T G L+G
Sbjct: 258 FTPGELRSYLKGA 270
Score = 28.5 bits (63), Expect = 3.8
Identities = 24/174 (13%), Positives = 53/174 (30%), Gaps = 60/174 (34%)
Query: 135 QGT---GM---------IAASLLLLMEE--EEAF-WTLSAIVEDLLPASYYTPNLIGIQA 179
QG+ GM A + + ++ + +++ IV + P + G +
Sbjct: 1624 QGSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINN-PVNLTI--HFGGEK 1680
Query: 180 DQKV-------LRSLVASGLPQLELSLLQHDIELSLITLHW-----FLT------LFA-S 220
+++ + + G + E + + + T T L
Sbjct: 1681 GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 221 VVHFKILLRIWDLLFLD----G-SMVLFQITLG----------MLKIKDTIYIV 259
F+ L+ L+ D G S LG ++ I+ + +V
Sbjct: 1741 KAAFE-DLKSKGLIPADATFAGHS-------LGEYAALASLADVMSIESLVEVV 1786
>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 = 36.8 bits (84), Expect = 0.008
Identities = 32/181 (17%), Positives = 62/181 (34%), Gaps = 45/181 (24%)
Query: 86 SRVVGCPSKSAGNWPKQAIVFLNLPVDSGVVVNALDFGSGGW--WFESNYCQGTGMIAAS 143
+ + C + P++ + P ++ ++ G W W N + T +I +S
Sbjct: 308 LKYLDCRPQDL---PREVL--TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS 362
Query: 144 LLLLMEEE--EAFWTLSAIVEDL-LPASYYTPNLIGI-------QADQKVLRSLVASGLP 193
L +L E + F LS +P L+ + V+ L
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPSAHIP-----TILLSLIWFDVIKSDVMVVVNKLHKY--- 414
Query: 194 QLELSLLQHDIELSLITLH-WFLTLFASV-----VHFKIL--------LRIWDLL--FLD 237
SL++ + S I++ +L L + +H I+ DL+ +LD
Sbjct: 415 ----SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLD 470
Query: 238 G 238
Sbjct: 471 Q 471
>1rlj_A NRDI protein; flavoprotein, FMN, thioredoxin, alpha/beta/alpha
sandwich, structural genomics, PSI, protein structure
initiative; HET: FMN; 2.00A {Bacillus subtilis} SCOP:
c.23.5.7
Length = 139
Score = 29.1 bits (65), Expect = 0.92
Identities = 11/57 (19%), Positives = 18/57 (31%), Gaps = 8/57 (14%)
Query: 88 VVGCPSKSAGNWPKQAIVFLNLPVD--SGVVVNALDFGSGGWWFESNYCQGTGMIAA 142
V+ + + G P FL GV SG + N+ + I+
Sbjct: 48 VLVTYTTNFGQVPASTQSFLEKYAHLLLGVA------ASGNKVWGDNFAKSADTISR 98
>2jvm_A Uncharacterized protein; alpha+beta, structural genomics, unknown
function, PSI-2, protein structure initiative; NMR
{Rhodobacter sphaeroides 2}
Length = 80
Score = 27.3 bits (60), Expect = 1.5
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 46 PKQAIVFLNLP----VESRVVGCPS-KSAGNWPKQAIVFLNLPVESRVVGCP 92
+ A + + P V + V C + A P+ V+L++P E+ V C
Sbjct: 9 QESARMSIEAPETVVVSTWKVACDGGEGALGHPR---VWLSIPHETGFVECG 57
>2fz5_A Flavodoxin; alpha/beta doubly-wound topology, non-covalently bound
FMN, electron transport; HET: FNR; NMR {Megasphaera
elsdenii} SCOP: c.23.5.1
Length = 137
Score = 27.8 bits (62), Expect = 2.5
Identities = 11/60 (18%), Positives = 17/60 (28%), Gaps = 9/60 (15%)
Query: 88 VVGCPSKSAGNWPKQAIVFLNL---PVDSGVVVNALDFGSGGWWFESNYCQGTGMIAASL 144
++GCP+ + + P G V FGS GW +
Sbjct: 51 LLGCPAMGSEELEDSVVEPFFTDLAPKLKGKKVGL--FGSYGWG----SGEWMDAWKQRT 104
>2xod_A NRDI protein, NRDI; flavoprotein, redox protein, ribonucleotide
reductase; HET: FMN; 0.96A {Bacillus anthracis} PDB:
2xoe_A* 2x2o_A* 2x2p_A*
Length = 119
Score = 26.7 bits (59), Expect = 4.6
Identities = 10/55 (18%), Positives = 20/55 (36%), Gaps = 4/55 (7%)
Query: 88 VVGCPSKSAGNWPKQAIVFLNLPVDSGVVVNALDFGSGGWWFESNYCQGTGMIAA 142
++ + GN P++ + FL + V SG + + I+A
Sbjct: 37 ILITYTTGFGNVPERVLEFLERNNEKLKGV----SASGNRNWGDMFGASADKISA 87
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
0.325 0.139 0.439
Gapped
Lambda K H
0.267 0.0651 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,457,162
Number of extensions: 260876
Number of successful extensions: 564
Number of sequences better than 10.0: 1
Number of HSP's gapped: 557
Number of HSP's successfully gapped: 18
Length of query: 294
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 201
Effective length of database: 4,105,140
Effective search space: 825133140
Effective search space used: 825133140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.9 bits)