RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1423
(125 letters)
>1wjt_A Transcription elongation factor S-II protein 3; four-helix bundle,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: a.48.3.1
Length = 103
Score = 67.4 bits (164), Expect = 5e-16
Identities = 28/57 (49%), Positives = 38/57 (66%)
Query: 47 QEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
E ALDLLK L + + + +L T IG+ VN +RK D EV++LAK LIKNWK+ +
Sbjct: 30 TEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLL 86
>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA
cleavage, proofreading, BACKTRACKING, gene expression,
multiprotein complex; 3.80A {Saccharomyces cerevisiae}
SCOP: i.8.1.1 PDB: 1eo0_A
Length = 309
Score = 54.8 bits (130), Expect = 4e-10
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 47 QEQALDLLKALQT-LNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFIRP 105
L++L L +L +T +G+ VN +KS+ + E+ L K +I +WK I
Sbjct: 20 DAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKST-NVEISKLVKKMISSWKDAINK 78
Query: 106 YVWRMN 111
Sbjct: 79 NKRSRQ 84
>2xpp_A IWS1, ECU08_0440; transcription, elongation, histone chaperone, RNA
polymerase mRNA export; 1.74A {Encephalitozoon cuniculi}
PDB: 2xpo_A 2xpn_A 2xpl_A
Length = 145
Score = 33.4 bits (76), Expect = 0.008
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 52 DLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVI-NLAKTLIKNWKKFI 103
LL L+T+ I L + +G V + K+ + + AK L++ W +
Sbjct: 86 RLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEV 138
>3nfq_A Transcription factor IWS1; SPN1, RNA polymerase II; 1.85A
{Saccharomyces cerevisiae} PDB: 3o8z_A 3oak_A
Length = 170
Score = 32.3 bits (73), Expect = 0.018
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 52 DLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVI-NLAKTLIKNWKKFI 103
L AL L + L ++ +G V KS + + + LA+ LI W + I
Sbjct: 101 SLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWTRPI 153
>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 = 32.1 bits (72), Expect = 0.034
Identities = 23/146 (15%), Positives = 47/146 (32%), Gaps = 41/146 (28%)
Query: 12 LWSKTR-RPK-RNLIGSAMLTKKKRTSGDNKLTG---LVRQEQALDLLKALQTLNIDLNI 66
L S + + +++ + ++ R DN++ + R + L L +AL L N+
Sbjct: 94 LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNV 153
Query: 67 LTKTHIGM-----------TVN---------------NLRKSSKDDEVI----NLAKTLI 96
L G+ NL+ + + V+ L +
Sbjct: 154 L--ID-GVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID 210
Query: 97 KNWK---KFIRPYVWRMNLPQDVVKR 119
NW R++ Q ++R
Sbjct: 211 PNWTSRSDHSSNIKLRIHSIQAELRR 236
>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 = 30.8 bits (69), Expect = 0.11
Identities = 8/46 (17%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 36 SGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRK 81
+GD + L + ++L ++ ID+ L K+ +++ +
Sbjct: 1856 AGDLR--AL---DTVTNVLNFIKLQKIDIIELQKS---LSLEEVEG 1893
>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat,
glycoprotein, immune response, inflamma response, innate
immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO
MYR NAG GCS; 3.10A {Homo sapiens}
Length = 605
Score = 29.2 bits (66), Expect = 0.32
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 38 DNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRK 81
+ L L + + LK L+ LN+ N++ + +NL
Sbjct: 109 ETNLASL--ENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTN 150
>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS,
immune system; HET: NAG FUL; 2.00A {Homo sapiens}
Length = 570
Score = 28.9 bits (65), Expect = 0.43
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 38 DNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRK 81
+ L L + + LK L+ LN+ N++ + +NL
Sbjct: 109 ETNLASL--ENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTN 150
>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid
recognition, receptor immunity, lipid binding,
glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO
MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*
Length = 606
Score = 27.3 bits (61), Expect = 1.3
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 38 DNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRK 81
+ KL L + + L L+ LN+ N + + +NL
Sbjct: 113 ETKLASL--ESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTN 154
Score = 25.8 bits (57), Expect = 5.0
Identities = 7/62 (11%), Positives = 21/62 (33%), Gaps = 2/62 (3%)
Query: 37 GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLI 96
N + L L +++ N + + LR++ + + ++++ I
Sbjct: 136 AHNFIHSCKLPA-YFSNLTNLVHVDLSYNYIQTITVNDL-QFLRENPQVNLSLDMSLNPI 193
Query: 97 KN 98
Sbjct: 194 DF 195
>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat,
asymmetric homodimer, glycoprotein, immune system; HET:
NAG FUC; 26.00A {Homo sapiens}
Length = 844
Score = 27.5 bits (61), Expect = 1.4
Identities = 9/44 (20%), Positives = 18/44 (40%)
Query: 38 DNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRK 81
L+ V ++ LKAL L++ N + ++ + L
Sbjct: 106 FCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNS 149
>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein;
HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A*
1xcd_A*
Length = 330
Score = 26.1 bits (58), Expect = 3.1
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 37 GDNKLTGLVRQEQALDLLKALQTLNIDLNILTK 69
G N L + A +K L + I +T
Sbjct: 153 GTNPLKSSGIENGAFQGMKKLSYIRIADTNITT 185
>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1,
lipopeptide, innate immunity, glycoPro immune response,
inflammatory response, leucine-rich repeat membrane,
receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}
Length = 520
Score = 26.4 bits (58), Expect = 3.2
Identities = 9/44 (20%), Positives = 19/44 (43%)
Query: 38 DNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRK 81
N+L L + + +K+LQ L+I N ++ + +
Sbjct: 357 MNQLKELSKIAEMTTQMKSLQQLDISQNSVSYDEKKGDCSWTKS 400
>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding;
HET: NAG; 2.00A {Anopheles gambiae}
Length = 317
Score = 25.7 bits (57), Expect = 4.0
Identities = 8/45 (17%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 37 GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRK 81
+NK+T L ++ +Q L++ LN + + +
Sbjct: 128 ANNKITML--RDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDT 170
>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse;
HET: NAG BMA MAN; 3.25A {Homo sapiens}
Length = 440
Score = 25.9 bits (57), Expect = 4.6
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 36 SGDNKLTGLVRQEQALDLLKALQTLNIDLNILTK 69
+L+ + E A + L L+ LN+ + L +
Sbjct: 168 GELKRLSYI--SEGAFEGLSNLRYLNLAMCNLRE 199
>2jdq_A Importin alpha-1 subunit; transport, PB2 subunit, nuclear protein,
protein transport, armadillo repeats; 2.2A {Homo
sapiens} PDB: 3tj3_A
Length = 450
Score = 25.6 bits (56), Expect = 4.8
Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 23/78 (29%)
Query: 21 RNLIGSAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLR 80
N++ K+ +G N L+ + LD ++ LQ
Sbjct: 386 ENILRLGEQEAKRNGTGINPYCALIEEAYGLDKIEFLQ---------------------- 423
Query: 81 KSSKDDEVINLAKTLIKN 98
S ++ E+ A LI++
Sbjct: 424 -SHENQEIYQKAFDLIEH 440
>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix,
leucine-rich repeat, protein; HET: NAG MAN; 2.70A
{Anopheles gambiae}
Length = 487
Score = 26.0 bits (57), Expect = 4.9
Identities = 8/45 (17%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 37 GDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRK 81
+NK+T L ++ +Q L++ LN + + +
Sbjct: 128 ANNKITML--RDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDT 170
>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2
related L recognition, receptor, innate immunity,
glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus
musculus} PDB: 3b2d_A* 3rg1_A*
Length = 606
Score = 25.4 bits (56), Expect = 6.6
Identities = 5/37 (13%), Positives = 14/37 (37%), Gaps = 2/37 (5%)
Query: 38 DNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGM 74
++ + L K L++L + N ++ +
Sbjct: 114 QTGISSI--DFIPLHNQKTLESLYLGSNHISSIKLPK 148
>3gdg_A Probable NADP-dependent mannitol dehydrogenase; rossmann fold,
beta-alpha-beta motifs, open twisted sheet, A NADP,
oxidoreductase; 2.30A {Cladosporium herbarum} PDB:
3gdf_A
Length = 267
Score = 24.8 bits (55), Expect = 8.4
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 88 VINLAKTLIKNWKKFIR 104
I++A++L W+ F R
Sbjct: 182 CIHMARSLANEWRDFAR 198
>3b46_A Aminotransferase BNA3; kynurenine aminotransferase, LLP, PLP,
cytoplasm, mitochondrion, pyridoxal phosphate; HET: LLP;
2.00A {Saccharomyces cerevisiae}
Length = 447
Score = 25.0 bits (55), Expect = 9.3
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 84 KDDEVINLAKTLIKNWKKFI 103
KDD + A +K K ++
Sbjct: 428 KDDAYLENAVERLKLLKDYL 447
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
0.317 0.131 0.373
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,804,547
Number of extensions: 94624
Number of successful extensions: 491
Number of sequences better than 10.0: 1
Number of HSP's gapped: 487
Number of HSP's successfully gapped: 159
Length of query: 125
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 43
Effective length of database: 4,412,271
Effective search space: 189727653
Effective search space used: 189727653
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 (21.7 bits)
S2: 51 (23.3 bits)