RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy936
(344 letters)
>3kg2_A Glutamate receptor 2; ION channel, membrane protein, cell membrane,
glycoprotein, transport, membrane, postsynaptic cell
membrane, editing; HET: ZK1 NAG BMA; 3.60A {Rattus
norvegicus}
Length = 823
Score = 104 bits (259), Expect = 1e-24
Identities = 58/297 (19%), Positives = 112/297 (37%), Gaps = 46/297 (15%)
Query: 64 SFLFQDQKPMSWVTTNNK--TGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDG 121
+ P + N+ G G ++ ++ F Y++ + +D
Sbjct: 387 VVTTILESPYVMMKANHAALAGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDA 446
Query: 122 S------IMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWG 175
++ L G+ D+ A + + + + ++ K
Sbjct: 447 DTKIWNGMVGELVYGKADIAIAPLTI-TLVREEVIDFSKPFMS----------------- 488
Query: 176 IELGQSQYVVMMKRPHESATGS-GLLAPFEIEVWFLILISLVLIGPIMHAIMRV------ 228
+M+K+P +S G L P E+W I+ + + + ++ + R
Sbjct: 489 -----LGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWH 543
Query: 229 -------RRWLSGTQSELYPISACTWFVYGALMKQGSTLNPRTDSTRIMFASWWIFIMIL 281
R S + + I WF GA M+QG+ ++PR+ S RI+ WW F +I+
Sbjct: 544 TEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGADISPRSLSGRIVGGVWWFFTLII 603
Query: 282 TAFYTANLTAFLTLSQFTLPIHSVEDIANPTN-TWCAEAGGAVEYSIKLYRFQTPEH 337
+ YTANL AFLT+ + PI S ED++ T + G+ + + + +
Sbjct: 604 ISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDK 660
>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 = 45.0 bits (106), Expect = 3e-05
Identities = 61/393 (15%), Positives = 113/393 (28%), Gaps = 168/393 (42%)
Query: 4 SQPLTIRSACQVYLIPDEHTRYQVDLTLTGRPDQAYQQSGLPDSWLIIEQLR------LP 57
++PLT+ H + L + P S+ I QL+ LP
Sbjct: 6 TRPLTL-----------SHGSLEHVLLV---P---------TASFFIASQLQEQFNKILP 42
Query: 58 IEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLL 117
EPT D +P + +L G + + + + + ++ +L L
Sbjct: 43 -EPT--EGFAADDEPTTPA-------ELVGKFLGY-VSSLVEPSKVGQFDQVL---NLCL 88
Query: 118 DQDGSIMNILKTGEV-DMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGI 176
+ + L+ ++ + A + + K L+K+
Sbjct: 89 TEFEN--CYLEGNDIHALAAKLLQENDTTLVKTKELIKN--------------------- 125
Query: 177 ELGQSQYV---VMMKRPHESATGSGLL-----------APF----EIEVWFLILISL--- 215
Y+ +M KRP + + S L A F + +F L L
Sbjct: 126 ------YITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQT 179
Query: 216 --VLIGPIMHAI---------------------MRVRRWLSGTQS---ELY----PIS-- 243
VL+G ++ + + WL + + Y PIS
Sbjct: 180 YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCP 239
Query: 244 ------ACTWFVY--------GALMK--QGSTLNPRTDSTRIMFA-------SWWIFIMI 280
+ V G L +G+T S ++ A SW
Sbjct: 240 LIGVIQLAHYVVTAKLLGFTPGELRSYLKGAT----GHSQGLVTAVAIAETDSW------ 289
Query: 281 LTAFYTANLTAFLTL-------SQFTLPIHSVE 306
+F+ + A +T+ P S+
Sbjct: 290 -ESFFVSVRKA-ITVLFFIGVRCYEAYPNTSLP 320
Score = 30.8 bits (69), Expect = 0.93
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 130 GEVDMVAAFVPVLN---IKKNKMAALVKS-EEEELKLQL 164
G++ + VLN ++K + L KS EE++ L
Sbjct: 1857 GDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGHL 1895
>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 = 32.9 bits (74), Expect = 0.19
Identities = 19/117 (16%), Positives = 34/117 (29%), Gaps = 26/117 (22%)
Query: 8 TIRSACQVYLIPDEHTRYQVDLTLTGRPDQAYQQSGLPDSWLIIEQLRLPI-----EPTI 62
TI + L P E+ + L++ P S I L L + +
Sbjct: 357 TIIESSLNVLEPAEYRKMFDRLSV------------FPPSAHIPTIL-LSLIWFDVIKSD 403
Query: 63 PSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQ 119
+ S V K + I E+ L +Y ++++D
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL--------HRSIVDH 452
>2yjp_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-binding protein; 2.26A
{Neisseria gonorrhoeae}
Length = 291
Score = 30.4 bits (69), Expect = 0.69
Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 27/81 (33%)
Query: 66 LFQDQKPMSWVTTNNKTGKLEGHGIAFEI---------LNTLSAKYEFSYEIILPSRKTL 116
+F D+ P +V + GK +G F++ L K EF ++ +
Sbjct: 61 VFGDKPPFGYV---DANGKNQG----FDVEIAKDLAKDLLGSPDKVEF---VLTEA---- 106
Query: 117 LDQDGSIMNILKTGEVDMVAA 137
+ + +++G+VD++ A
Sbjct: 107 ----ANRVEYVRSGKVDLILA 123
>1ii5_A SLR1257 protein; membrane protein; HET: GLU; 1.60A {Synechocystis
SP} SCOP: c.94.1.1 PDB: 1iit_A 1iiw_A
Length = 233
Score = 29.2 bits (66), Expect = 1.5
Identities = 10/84 (11%), Positives = 29/84 (34%), Gaps = 18/84 (21%)
Query: 54 LRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSR 113
L++ + P F+F + K G + ++ ++ +++ E +
Sbjct: 6 LKVGVVGNPP-FVFYGEG---------KNAAFTGISL--DVWRAVAESQKWNSEYVRQ-- 51
Query: 114 KTLLDQDGSIMNILKTGEVDMVAA 137
+ + GE+D++
Sbjct: 52 ---NSISA-GITAVAEGELDILIG 71
>1xt8_A Putative amino-acid transporter periplasmic solut protein; ABC
transport, cysteine uptake; 2.00A {Campylobacter jejuni}
SCOP: c.94.1.1
Length = 292
Score = 28.9 bits (65), Expect = 2.3
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 21/78 (26%)
Query: 66 LFQDQKPMSWVTTNNKTGKLEG------HGIAFEILNTLSAKYEFSYEIILPSRKTLLDQ 119
+F D+ P +V ++ G +G IA E+ K +F +++ +
Sbjct: 50 VFGDKPPFGYV---DEKGNNQGYDIALAKRIAKELFGD-ENKVQF---VLVEA------- 95
Query: 120 DGSIMNILKTGEVDMVAA 137
+ + LK+ +VD++ A
Sbjct: 96 -ANRVEFLKSNKVDIILA 112
>1iyr_A DFF45, DNA fragmentation factor alpha subunit; apoptosis, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; HET: DNA; NMR {Homo sapiens} SCOP:
a.164.1.1 PDB: 1koy_A*
Length = 111
Score = 27.6 bits (60), Expect = 2.6
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 127 LKTGEVDMVA-----AFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMK 171
L + ++++V A LN K + ++ E EL L+LQQ +++
Sbjct: 35 LSSQDLELVTKEDPKALAVALNWDIKKTETVQEACERELALRLQQTQSLH 84
>1ik9_A DNA repair protein XRCC4; DNA END joining, double-strand break
repair, V(D)J recombination, protein-protein complex,
coiled coil; HET: DNA; 2.30A {Homo sapiens} SCOP:
b.59.1.1 h.1.11.1 PDB: 3ii6_A* 1fu1_A* 3rwr_A*
Length = 213
Score = 27.9 bits (61), Expect = 3.7
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 131 EVDMVAAFVPVLNIKKNKMAAL---VKSEEEELKLQLQQE 167
E D+ F+ VLN KK K+ +L + + +E + ++QE
Sbjct: 173 ETDLYKRFILVLNEKKTKIRSLHNKLLNAAQEREKDIKQE 212
>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain,
signaling protein; 2.04A {Bordetella pertussis} PDB:
3mpl_A
Length = 267
Score = 27.7 bits (62), Expect = 4.7
Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 19/84 (22%)
Query: 54 LRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSR 113
+++ + F + GI+ +L L + +EII
Sbjct: 34 VKVAVLNLFAPFTLFRTD-----------EQF--GGISAAVLQLLQLRTGLDFEIIG--- 77
Query: 114 KTLLDQDGSIMNILKTGEVDMVAA 137
+D ++ L++GE DM A
Sbjct: 78 ---VDTVEELIAKLRSGEADMAGA 98
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 27.9 bits (62), Expect = 7.0
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 12/63 (19%)
Query: 3 KSQPLTIRSACQV--------YLIPDEHTRYQVDL-TLTG--RPDQAYQQSGLPDSWLII 51
K+ A Q+ Y I D+ QVD TL +A+ SG+ D + +
Sbjct: 978 KALRFDRLVAGQIPTGWNAKTYGISDDIIS-QVDPITLFVLVSVVEAFIASGITDPYEMY 1036
Query: 52 EQL 54
+ +
Sbjct: 1037 KYV 1039
>2xut_A Proton/peptide symporter family protein; transport protein,
membrane protein, major facilitator super transporter;
3.62A {Shewanella oneidensis}
Length = 524
Score = 27.7 bits (62), Expect = 7.1
Identities = 10/103 (9%), Positives = 27/103 (26%), Gaps = 17/103 (16%)
Query: 207 VWFLILISLVLIGPIMHAIMRVRRWLSGTQSE-------LYPISACTWFVYGALMKQGST 259
++L+ + + R R+ + + + A + ++ ST
Sbjct: 262 CCAMVLVMGFVGAGASLQLERARKSHPDAAVDGVRSVLRILVLFALVTPFWSLFDQKAST 321
Query: 260 LN----PRTDSTRIMFASWW-----IFIMILTAFYTANLTAFL 293
+ + +M+L F L +
Sbjct: 322 WILQANDMVKPQWFE-PAMMQALNPLLVMLLIPFNNFVLYPAI 363
>2jrn_A CHAP domain protein; monomer, putative amidase, structural
genomics, PSI-2, protein structure initiative; NMR
{Staphylococcus saprophyticus} PDB: 2k3a_A 2lrj_A
Length = 163
Score = 26.6 bits (58), Expect = 7.8
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 229 RRWLSGTQSELYPISACTWFVYGAL 253
+ SG+ + LY CTW+VY +
Sbjct: 41 TQSTSGSSANLYTAGQCTWYVYDKV 65
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 0.135 0.415
Gapped
Lambda K H
0.267 0.0558 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,263,835
Number of extensions: 305581
Number of successful extensions: 500
Number of sequences better than 10.0: 1
Number of HSP's gapped: 495
Number of HSP's successfully gapped: 23
Length of query: 344
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 250
Effective length of database: 4,077,219
Effective search space: 1019304750
Effective search space used: 1019304750
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: 58 (26.5 bits)