RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5853
(217 letters)
>2efe_A Similarity to vacuolar protein sorting-associated VPS9; GEF,
GTPase, VPS9, nucleotide, transport protein; HET: GNH;
2.08A {Arabidopsis thaliana} PDB: 2efd_A 2efc_A* 2efh_A*
Length = 267
Score = 138 bits (348), Expect = 2e-40
Identities = 54/181 (29%), Positives = 91/181 (50%), Gaps = 9/181 (4%)
Query: 43 YSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQVLHEHVKNLAKIITPNHKY 102
+S + +L A +++ V+++ + N + ++ D+ L + + + + I+P +
Sbjct: 69 WSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTE-EVIADEKLFQKMSLVQQFISPEN-- 125
Query: 103 LRIPKMFHSECPWPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLL-----SLTSAVPA 157
L I F +E W AQ E+ I+ YK DK+ C+ I NLL + P
Sbjct: 126 LDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVINNLLLNASIASNENAPG 185
Query: 158 ADDLIPVLVYVLIKANPPSLLSTVQYVNSF-YANKMEGEIQYWWVQFCSAIEFIKTMDYK 216
AD+ +PVL+YV IKANPP L S + Y+ + +K+ GE Y++ SA FI +D K
Sbjct: 186 ADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKLVGEAAYFFTNILSAESFISNIDAK 245
Query: 217 E 217
Sbjct: 246 S 246
>2ot3_A RAB5 GDP/GTP exchange factor; rabex-5, VPS9 domain, vesicular
traffic, protein transport; 2.10A {Homo sapiens} SCOP:
a.222.1.1 PDB: 1txu_A
Length = 274
Score = 131 bits (331), Expect = 6e-38
Identities = 45/184 (24%), Positives = 84/184 (45%), Gaps = 5/184 (2%)
Query: 38 DYRSGYSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQVLHEHVKNLAKIIT 97
+ ++ I++ +++R Y Y P D +D + + ++ L + T
Sbjct: 68 ERMQTRGKVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIRALRWV-T 126
Query: 98 PNHKYLRIPKMF-HSECPWPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLLSLTSAVP 156
P + + + A +I + S + DK+ C+ + I N + +T P
Sbjct: 127 PQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEP 186
Query: 157 A-ADDLIPVLVYVLIKANPPSLLSTVQYVNSFY--ANKMEGEIQYWWVQFCSAIEFIKTM 213
A ADD +P L+Y+++K NPP L S +QY+ F + M GE Y++ C A+ FI+ +
Sbjct: 187 ASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKL 246
Query: 214 DYKE 217
D +
Sbjct: 247 DAQS 250
>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 = 33.5 bits (76), Expect = 0.060
Identities = 25/140 (17%), Positives = 51/140 (36%), Gaps = 34/140 (24%)
Query: 34 NNRRDY-RSGYSDS-NSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQVLHEHVKN 91
N ++ SG S + L+L K P+G D SR + K
Sbjct: 372 NGAKNLVVSGPPQSLYGLNLTLRKAKA--------------PSGL-DQSR--IPFSERK- 413
Query: 92 LAKIITPNHKYLRI--PKMFHSECPWPAAQAEISSISSYKTAHDKVQC---VYRTLNTIL 146
+ ++++L + P FHS PA+ + + + VY T
Sbjct: 414 ----LKFSNRFLPVASP--FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDT-FDGS 466
Query: 147 NLLSLTSAVPAADDLIPVLV 166
+L L+ ++ ++ ++ ++
Sbjct: 467 DLRVLSGSI--SERIVDCII 484
>3sdr_A Alpha-bisabolene synthase; lyase, terpene synthase; HET: 210; 1.86A
{Abies grandis} PDB: 3sdq_A 3sae_A* 3sdt_A* 3sdu_A*
3sdv_A*
Length = 817
Score = 32.2 bits (72), Expect = 0.13
Identities = 8/68 (11%), Positives = 25/68 (36%), Gaps = 4/68 (5%)
Query: 25 RRRTYEFVDNNRRDYRSGYSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQV 84
Y ++ ++ + + V + K+ + ++ ++ +GDG
Sbjct: 747 LDHIYSILEPAVKELTREFLKPDDVPFACKKMLFEETRVTMV----IFKDGDGFGVSKLE 802
Query: 85 LHEHVKNL 92
+ +H+K
Sbjct: 803 VKDHIKEC 810
>1n1b_A (+)-bornyl diphosphate synthase; terpene synthase fold, isomerase;
2.00A {Salvia officinalis} SCOP: a.102.4.1 a.128.1.3
PDB: 1n1z_A* 1n20_A* 1n21_A* 1n22_A* 1n23_A* 1n24_A*
Length = 549
Score = 31.7 bits (71), Expect = 0.18
Identities = 10/74 (13%), Positives = 25/74 (33%), Gaps = 6/74 (8%)
Query: 25 RRRTYEFVDNNRRDYRSGYSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQV 84
+ +D + + + A + +++ +Y +GDG +
Sbjct: 480 VEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQF----IYLHGDGFGVQHSK 535
Query: 85 LHEHVKNLAKIITP 98
+EH+ L + P
Sbjct: 536 TYEHIAGL--LFEP 547
>3g4d_A (+)-delta-cadinene synthase isozyme XC1; cyclase, lyase, magnesium,
metal-binding; 2.40A {Gossypium arboreum} PDB: 3g4f_A*
Length = 554
Score = 31.3 bits (70), Expect = 0.22
Identities = 12/83 (14%), Positives = 29/83 (34%), Gaps = 5/83 (6%)
Query: 11 ISNVTGQGGGTAEY-RRRTYEFVDNNRRDYRSGYSDSNSVQLSLAKIAIDRAVISRCYMY 69
I + G TA+ + V++ +D + + + +++ A +
Sbjct: 469 IECYMEEYGVTAQEAYDVFNKHVESAWKDLNQEFLKPTEMPTEVLNRSLNLARVMDV--- 525
Query: 70 AMYPNGDGDISRDQVLHEHVKNL 92
+Y GDG + + +L
Sbjct: 526 -LYREGDGYTYVGKAAKGGITSL 547
>3n0f_A Isoprene synthase; terpene cyclase fold, hemiterpene synthase,
DDXXD motif, NSE motif, lyase; 2.70A {Populus tremula x
populus alba} PDB: 3n0g_A*
Length = 555
Score = 30.9 bits (69), Expect = 0.31
Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 4/68 (5%)
Query: 25 RRRTYEFVDNNRRDYRSGYSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQV 84
+D + + + AI+ A S C Y NGD S D++
Sbjct: 482 TESVMNLIDETWKKMNKEKLGGSLFAKPFVETAINLARQSHC----TYHNGDAHTSPDEL 537
Query: 85 LHEHVKNL 92
+ V ++
Sbjct: 538 TRKRVLSV 545
>2ong_A 4S-limonene synthase; monoterpene synthase, monoterpene cyclase,
geranyl diphosphate, 2 fluorogeranyl diphosphate linalyl
diphosphate; HET: FPG BTB; 2.70A {Mentha spicata} PDB:
2onh_A*
Length = 543
Score = 28.2 bits (62), Expect = 2.6
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 5/71 (7%)
Query: 23 EYRRRTYEFVDNNRRD-YRSGYSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISR 81
E R+ + + S + A+D +++ MY NGDG ++
Sbjct: 471 EARKHVKWLIAEVWKKMNAERVSKDSPFGKDFIGCAVDLGRMAQL----MYHNGDGHGTQ 526
Query: 82 DQVLHEHVKNL 92
++H+ +
Sbjct: 527 HPIIHQQMTRT 537
>2r4g_A Telomerase reverse transcriptase; telomeres, chromosomal protein,
DNA-binding, nucleotidyltransferase, nucleus; 1.71A
{Tetrahymena thermophila}
Length = 267
Score = 27.5 bits (60), Expect = 3.1
Identities = 12/108 (11%), Positives = 24/108 (22%), Gaps = 3/108 (2%)
Query: 71 MYPNGDGDISRDQVLHEHVKNLAKIITPNHKYLRIPKMFHSECPWPAAQAEISSISSYKT 130
+ Q + + I N + + C P + S
Sbjct: 37 LLKEYQSKNFSCQEERDLFLEFTEKIVQNFHNINFNYLLKKFCKLPENYQSLKSQVKQIV 96
Query: 131 AHDKVQCVYRTLNTILNLLSLTSAVPAADDLIPVLVYVLIKANPPSLL 178
+ N +L + + L ++ P LL
Sbjct: 97 QSENKANQQSCENLFNSLYDTEISY---KQITNFLRQIIQNCVPNQLL 141
>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 = 26.8 bits (58), Expect = 3.8
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 11/33 (33%)
Query: 151 LTSAV-PAADDLIPVLVYVLIKANPPSLLSTVQ 182
L +++ ADD P L IKA T++
Sbjct: 25 LQASLKLYADDSAPALA---IKA-------TME 47
>3c3r_A Programmed cell death 6-interacting protein; ALIX BRO1 CHMP4C
amphipathic-helix, apoptosis, HOST-virus interaction,
protein transport, transport; 2.02A {Homo sapiens} PDB:
2oew_A 3c3o_A 3c3q_A
Length = 380
Score = 27.5 bits (60), Expect = 4.2
Identities = 16/117 (13%), Positives = 41/117 (35%), Gaps = 19/117 (16%)
Query: 90 KNLAKIITPNHKYLRIPKMFHSECPWPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLL 149
K + ++ H ++ +H + I+ + A + ++ V + +N+
Sbjct: 260 KEVFPVLAAKHCIMQANAEYHQSILAKQQKKFGEEIARLQHAAELIKTVASRYDEYVNVK 319
Query: 150 SLTS-------------------AVPAADDLIPVLVYVLIKANPPSLLSTVQYVNSF 187
+ VP DL P+ L+K+ P ++ + ++ + F
Sbjct: 320 DFSDKINRALAAAKKDNDFIYHDRVPDLKDLDPIGKATLVKSTPVNVPISQKFTDLF 376
>3p5p_A Taxadiene synthase; class I and II terpene cyclase fold, diterpene
cyclase, DDXX NSE/DTE motif, 3-azacopalyl diphosphate;
HET: A3C; 1.82A {Taxus brevifolia} PDB: 3p5r_A*
Length = 764
Score = 27.1 bits (59), Expect = 4.9
Identities = 8/69 (11%), Positives = 24/69 (34%), Gaps = 5/69 (7%)
Query: 25 RRRTYEFVDNNRRDYRSGY-SDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISRDQ 83
+ VD ++ Y SN + + + + + Y DG ++
Sbjct: 685 IKHICRVVDRALKEASFEYFKPSNDIPMGCKSFIFNLRLCVQI----FYKFIDGYGIANE 740
Query: 84 VLHEHVKNL 92
+ ++++ +
Sbjct: 741 EIKDYIRKV 749
>3h9p_A Putative triphosphoribosyl-dephospho-COA synthase; putative
triphosphoribosyl-dephospho synthase, structural
genomics, PSI-2; HET: PG4; 2.30A {Archaeoglobus fulgidus
dsm 4304}
Length = 249
Score = 26.5 bits (58), Expect = 6.2
Identities = 6/49 (12%), Positives = 13/49 (26%)
Query: 33 DNNRRDYRSGYSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNGDGDISR 81
+ R+ G+ S L + Y + + D +
Sbjct: 144 NLIARELVDGFKISIEGAKFLLSFGNSGKAVVELYYHLLSKFPDPLVIA 192
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
0.319 0.134 0.404
Gapped
Lambda K H
0.267 0.0448 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,302,307
Number of extensions: 181403
Number of successful extensions: 374
Number of sequences better than 10.0: 1
Number of HSP's gapped: 368
Number of HSP's successfully gapped: 17
Length of query: 217
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 127
Effective length of database: 4,188,903
Effective search space: 531990681
Effective search space used: 531990681
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.7 bits)