RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3858
(180 letters)
>3tig_A TTL protein; ATP-grAsp, ligase, tubulin; 2.50A {Silurana} PDB:
3tii_A* 3tin_A*
Length = 380
Score = 85.0 bits (210), Expect = 4e-20
Identities = 39/187 (20%), Positives = 61/187 (32%), Gaps = 45/187 (24%)
Query: 1 MSLHHRVNHFPGMANLESKAILAYHLNRMK------YFFPDEYNIFPKSWSLPRQWKEVI 54
L VN++ G L KA L + +FP+ Y I+P + P
Sbjct: 59 PGLVQLVNYYRGADKLCRKASLVKLIKTSPELTETCTWFPESYVIYPTNEKTPAMRARNG 118
Query: 55 SYNREHMNHFPGMANLESKAILAYHLNRMKYFFPDEYNIFPKSWSLPRQWKEVISYNREH 114
+ + DE F S++
Sbjct: 119 LPDLANAP------------------------RTDEREEFRSSFN---------KKKENE 145
Query: 115 ADETLILKPTRGAEGKGIKILNFIPE----HEVMDQDASCQVYLSNVLLIN--GFKFDLR 168
I K + GA+G+GI I + E + Q Q YL + LL+ KFD+R
Sbjct: 146 EGNVWIAKSSSGAKGEGILISSDATELLDFIDNQGQVHVIQKYLESPLLLEPGHRKFDIR 205
Query: 169 VYVLMTS 175
+VL+ +
Sbjct: 206 SWVLVDN 212
>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 = 38.7 bits (89), Expect = 6e-04
Identities = 26/135 (19%), Positives = 44/135 (32%), Gaps = 24/135 (17%)
Query: 4 HHRVNHF-PGMANLESKAILAYHLNRMKYF-FPDE-YNIFPKSWSL--------PRQWKE 52
H ++H + E K++L +L+ + P E P+ S+ W
Sbjct: 288 HISLDHHSMTLTPDEVKSLLLKYLD-CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN 346
Query: 53 VISYNREHMNHFPGMANLESKAILAYHLNRMKYFFPDEYNIFPKSWSLPRQ-----WKEV 107
N + + S +L R K F D ++FP S +P W +V
Sbjct: 347 WKHVNCDKLTTIIES----SLNVLEPAEYR-KMF--DRLSVFPPSAHIPTILLSLIWFDV 399
Query: 108 ISYNREHADETLILK 122
I + L
Sbjct: 400 IKSDVMVVVNKLHKY 414
Score = 33.3 bits (75), Expect = 0.036
Identities = 26/165 (15%), Positives = 59/165 (35%), Gaps = 35/165 (21%)
Query: 2 SLHHR-VNHFPGMANLESKAI------------LAYHLNRMKYFFPDEYNIFPKSWSLPR 48
+LH V+H+ +S + + +HL +++ P+ +F L
Sbjct: 444 ALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEH--PERMTLFRM-VFLDF 500
Query: 49 QWKEV-ISYNREHMNHFPGMANLESKAILAYHLNRMKYFFPDEYNIFPKSWSLPRQWKEV 107
++ E I ++ N + N L ++K++ Y I R +
Sbjct: 501 RFLEQKIRHDSTAWNASGSILNT---------LQQLKFY--KPY-ICDNDPKYERLVNAI 548
Query: 108 ISYNREHADETLILKPTRGAEGKGIKILNFIPEHEVMDQDASCQV 152
+ + + + + K T + + + E E + ++A QV
Sbjct: 549 LDFLPKIEENLICSKYTD------LLRIALMAEDEAIFEEAHKQV 587
Score = 26.7 bits (58), Expect = 5.2
Identities = 25/174 (14%), Positives = 59/174 (33%), Gaps = 54/174 (31%)
Query: 37 YN---IFPKSWSLPR-----QWKEVISYNREHMN---HFPGMANLESKAILAYHL---NR 82
YN +F K +++ R + ++ + R N G+ K +A + +
Sbjct: 120 YNDNQVFAK-YNVSRLQPYLKLRQALLELRPAKNVLID--GVLGS-GKTWVALDVCLSYK 175
Query: 83 MKYFFPDEYNIFPKSWSLPRQWKEVISYNREHADETLI---------LKPTRGAEGKGIK 133
++ IF W ++ ++ ET++ + P +
Sbjct: 176 VQCKMDF--KIF---------W---LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS 221
Query: 134 ILNFIPEHEVMDQDA---SCQVYLSNVLLI-------NGFK-FDLRVYVLMTSK 176
+ + H + + + Y N LL+ + F+L +L+T++
Sbjct: 222 NI-KLRIHSIQAELRRLLKSKPY-ENCLLVLLNVQNAKAWNAFNLSCKILLTTR 273
>2p0a_A Synapsin-3, synapsin III; neurotransmitter release, schizophrenia,
vesicle T structural genomics, structural genomics
consortium, SGC, neuropeptide; HET: ANP; 1.90A {Homo
sapiens}
Length = 344
Score = 30.1 bits (67), Expect = 0.37
Identities = 15/113 (13%), Positives = 38/113 (33%), Gaps = 7/113 (6%)
Query: 61 MNHFPGMANLESKAILAYHLNRMKYFFPDEYNIFPKSWSLPRQWKEVISYNREHADETLI 120
+N + N SK + L ++ + K + + + ++
Sbjct: 119 VNSLYSVYNFCSKPWVFSQLIKIFHSLGP-----EKFPLVEQTFFPNHKPMVTAPHFPVV 173
Query: 121 LKPTRGAEGKGIKILNFIPE-HEVMDQDASCQVYLSNVLLINGFKFDLRVYVL 172
+K G G + + ++ A + Y + I+ K+D+R+ +
Sbjct: 174 VKLGHAHAGMGKIKVENQLDFQDITSVVAMAKTYATTEAFID-SKYDIRIQKI 225
>1uc8_A LYSX, lysine biosynthesis enzyme; alpha-aminoadipate pathway, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; 2.00A {Thermus thermophilus} SCOP:
c.30.1.6 d.142.1.7 PDB: 1uc9_A*
Length = 280
Score = 28.6 bits (64), Expect = 1.2
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 119 LILKPTRGAEGKGI-------KILNFIPEHEVMDQDASCQVYLSNVLLINGFKFDLRVYV 171
++LKP G+ G+ + EV+ Y+ + D+RV+V
Sbjct: 126 VVLKPVIGSWGRLLAXXXXXXXXXXXXXXKEVLGGFQHQLFYIQEY--VEKPGRDIRVFV 183
Query: 172 L 172
+
Sbjct: 184 V 184
>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex,
single-stranded DNA, isomerase/DNA complex; HET: DNA;
2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A*
2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*
Length = 659
Score = 28.0 bits (63), Expect = 2.2
Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 8/33 (24%)
Query: 25 HLNRMKYFFPDEYNIFPKSWSL------PRQWK 51
HL PD Y+ W+L P +W+
Sbjct: 44 HLLEQAQ--PDAYDSRYARWNLADLPIVPEKWQ 74
Score = 28.0 bits (63), Expect = 2.2
Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 8/33 (24%)
Query: 79 HLNRMKYFFPDEYNIFPKSWSL------PRQWK 105
HL PD Y+ W+L P +W+
Sbjct: 44 HLLEQAQ--PDAYDSRYARWNLADLPIVPEKWQ 74
>1i7n_A Synapsin II; synapse, phosphorylation, neuropeptide; 1.90A {Rattus
norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1i7l_A 1auv_A
1aux_A*
Length = 309
Score = 27.4 bits (60), Expect = 2.8
Identities = 16/116 (13%), Positives = 32/116 (27%), Gaps = 13/116 (11%)
Query: 61 MNHFPGMANLESKAILAYHLNRMKYFFPDEYNIFPKSWSLPRQ-WKEVISYNREHADETL 119
+N + N K + + + + + + L Q + +
Sbjct: 102 INSLESIYNFCDKPWVFAQMVAI------FKTLGGEKFPLIEQTYYPNHREMLTLPTFPV 155
Query: 120 ILKPTRGAEGKGIKILNFIPEHEVMDQDASCQVYLSNVLLINGF---KFDLRVYVL 172
++K G G + H AS F K+D+RV +
Sbjct: 156 VVKIGHAHSGMGKV---KVENHYDFQDIASVVALTQTYATAEPFIDAKYDIRVQKI 208
>2io8_A Bifunctional glutathionylspermidine synthetase/amidase; ligase,
hydrolase; HET: ADP; 2.10A {Escherichia coli} SCOP:
c.30.1.7 d.3.1.15 d.142.1.8 PDB: 2io7_A* 2io9_A* 2ioa_A*
2iob_A 3o98_A*
Length = 619
Score = 26.9 bits (59), Expect = 4.1
Identities = 16/78 (20%), Positives = 26/78 (33%), Gaps = 16/78 (20%)
Query: 70 LESKAILAYHLNRMKYFFPDEYNIFPKSWSLPRQWKEVISYNREHADETLILKPTRGAEG 129
+KAIL + FP + + N E +KP G G
Sbjct: 495 PGNKAILPI----LWSLFPHHRYLLDTD----------FTVNDELVKTGYAVKPIAGRCG 540
Query: 130 KGIKILNFIPEHEVMDQD 147
I +++ EV+D+
Sbjct: 541 SNIDLVS--HHEEVLDKT 556
>3df7_A Putative ATP-grAsp superfamily protein; putative protein, PSI-II,
nysgrc., structural genomics, protein structure
initiative; 1.87A {Archaeoglobus fulgidus}
Length = 305
Score = 26.6 bits (58), Expect = 5.0
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 119 LILKPTRGAEGKGIKILNFIPEHEVM 144
I+KP G+GI + +P+ +
Sbjct: 136 FIIKPRTACAGEGIGFSDEVPDGHIA 161
>3g02_A Epoxide hydrolase; alpha/beta hydrolase fold, enantioselective,
mutant, directed evolution; 1.50A {Aspergillus niger}
PDB: 1qo7_A 3g0i_A*
Length = 408
Score = 26.6 bits (59), Expect = 5.8
Identities = 8/37 (21%), Positives = 14/37 (37%), Gaps = 3/37 (8%)
Query: 32 FFPDEYNIFPKSWSLPRQWKEVISYNR-EHMNHFPGM 67
FFP + P+SW ++ + HF +
Sbjct: 345 FFPKDLVPVPRSWI--ATTGNLVFFRDHAEGGHFAAL 379
>1gsa_A Glutathione synthetase; ligase; HET: ADP GSH; 2.00A {Escherichia
coli} SCOP: c.30.1.3 d.142.1.1 PDB: 1gsh_A 2glt_A 1glv_A
Length = 316
Score = 26.5 bits (59), Expect = 5.9
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 28/82 (34%)
Query: 102 RQWKEVISYNREHADETLILKPTRGAEGKGI-----------KILNFIPEHE---VMDQD 147
R ++ ++ +H+D +ILKP G G I I + EH M
Sbjct: 142 RNKAQLKAFWEKHSD--IILKPLDGMGGASIFRVKEGDPNLGVIAETLTEHGTRYCM--- 196
Query: 148 ASCQVYLSNV-------LLING 162
Q YL + L+++G
Sbjct: 197 --AQNYLPAIKDGDKRVLVVDG 216
>2qwv_A UPF0217 protein VC_A1059; unknown function, structural genomics,
PSI- 2, protein structure initiative; 2.60A {Vibrio
cholerae o1 biovar eltor str} SCOP: c.116.1.7
Length = 208
Score = 26.1 bits (57), Expect = 5.9
Identities = 6/55 (10%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 125 RGAEGKGIKILNFIPEHEVMDQDASCQVYLSNVLLINGFKFDLRVYVLMTSKPNP 179
R A ++L+ I + ++++ + D+ +++++ S +
Sbjct: 16 RSAPTDSQRLLDEIGGKCHTE--ILAHCMMNSLFTAQSHREDVVIHLVLESTRDY 68
>3aia_A UPF0217 protein MJ1640; DUF358, rRNA methyltransferase, spout-class
fold, transferas; HET: SAM; 1.40A {Methanocaldococcus
jannaschii} PDB: 3ai9_X*
Length = 211
Score = 25.8 bits (56), Expect = 7.8
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 147 DASCQVYLSNVLLINGFKFDLRVYVLMTSKPNP 179
D C+ L + + D+ Y ++ +PNP
Sbjct: 36 DLLCRCVSDAFFLSHDIRRDVVFYAVLYGQPNP 68
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
0.322 0.137 0.434
Gapped
Lambda K H
0.267 0.0562 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,932,438
Number of extensions: 165359
Number of successful extensions: 351
Number of sequences better than 10.0: 1
Number of HSP's gapped: 341
Number of HSP's successfully gapped: 23
Length of query: 180
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 92
Effective length of database: 4,244,745
Effective search space: 390516540
Effective search space used: 390516540
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 (21.9 bits)
S2: 54 (25.0 bits)