RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5982
(102 letters)
>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA
complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP:
d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A*
1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A*
1lpq_A* 1rr8_C* 1ej9_A*
Length = 591
Score = 58.2 bits (140), Expect = 1e-11
Identities = 37/48 (77%), Positives = 43/48 (89%)
Query: 3 DKKKTALGRLKEQLLKLEVQETDKEENKTIALGTSKLNYLDPRISVAW 50
+ KK A+ RL+EQL+KLEVQ TD+EENK IALGTSKLNYLDPRI+VAW
Sbjct: 511 ESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAW 558
>2b9s_B DNA topoisomerase I-like protein; vanadate complex, isomerase/DNA
complex; HET: DNA; 2.27A {Leishmania donovani}
Length = 62
Score = 48.9 bits (116), Expect = 1e-09
Identities = 16/31 (51%), Positives = 23/31 (74%)
Query: 20 EVQETDKEENKTIALGTSKLNYLDPRISVAW 50
E K++NK ++LGTSK+NY+DPRI +W
Sbjct: 1 ENIIRIKDDNKAVSLGTSKINYIDPRIICSW 31
>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 = 30.7 bits (68), Expect = 0.047
Identities = 7/29 (24%), Positives = 17/29 (58%), Gaps = 7/29 (24%)
Query: 65 KKVIK-VES----F--NSLPSQAIKRRID 86
K+ +K +++ + +S P+ AIK ++
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATME 47
>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 = 27.7 bits (61), Expect = 0.73
Identities = 14/115 (12%), Positives = 39/115 (33%), Gaps = 38/115 (33%)
Query: 8 ALGRLKEQLLKLEVQETDKEENKT------IALGTSKL--------NYLDP--------- 44
+L L L K + + ++++ + L + L P
Sbjct: 385 SLYGLNLTLRKAKA-PSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDL 443
Query: 45 -RISVAW--YNLG---FDFYNWSGKTKKVIKVESFNSLPS---QAIKRRIDWDLS 90
+ +V++ ++ +D ++ S ++V S + I+ + W+ +
Sbjct: 444 VKNNVSFNAKDIQIPVYDTFDGS-----DLRVLSGSISERIVDCIIRLPVKWETT 493
Score = 27.3 bits (60), Expect = 1.1
Identities = 11/70 (15%), Positives = 21/70 (30%), Gaps = 11/70 (15%)
Query: 32 IALGTSKLNYL--DPRISVAWYNLGFDFYNWSGKTKKVIKVESFNSLPSQAIKRRIDWDL 89
I L+ L + + G + W + S+P I L
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIP-------ISCPL 240
Query: 90 SGLPNTRIAN 99
G+ ++A+
Sbjct: 241 IGV--IQLAH 248
>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR,
tetratricopeptide repeat like, TPR-like, transport
protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1
Length = 158
Score = 26.3 bits (57), Expect = 1.9
Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 3/84 (3%)
Query: 8 ALGRLKEQLLKLEVQETDKEENKTIALGTSKLNY---LDPRISVAWYNLGFDFYNWSGKT 64
L R LL+L + + + I +K +DP+ A + +G + +++ T
Sbjct: 38 NLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFLT 97
Query: 65 KKVIKVESFNSLPSQAIKRRIDWD 88
+ + L +Q ++ +D
Sbjct: 98 PDETEAKHNFDLATQFFQQAVDEQ 121
>3qq2_A BRKA autotransporter; beta barrel, transmembrane, membrane
protein-protein transpo complex; 3.00A {Bordetella
pertussis}
Length = 284
Score = 26.0 bits (57), Expect = 2.4
Identities = 6/36 (16%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 41 YLDPRISVAWYNLGFDFYNWSGKTKKVIKVESFNSL 76
+ +P+ V + Y S + +KV++ +
Sbjct: 155 FAEPQAEVMLWRTSGKRYRASNGLR--VKVDANTAT 188
>2kat_A Uncharacterized protein; NESG, structure, structural genomics,
PSI-2, protein structure initiative; NMR {Bordetella
parapertussis}
Length = 115
Score = 25.0 bits (55), Expect = 3.4
Identities = 8/13 (61%), Positives = 8/13 (61%)
Query: 42 LDPRISVAWYNLG 54
DP SVAW LG
Sbjct: 48 FDPTYSVAWKWLG 60
>3i1k_A Hemagglutinin-esterase protein; SGNH-hydrolase fold, swiss roll,
envelope protein, glycoprot hemagglutinin, membrane,
transmembrane, virion; HET: NAG; 2.10A {Porcine
torovirus} PDB: 3i1l_A*
Length = 377
Score = 25.5 bits (55), Expect = 3.6
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 46 ISVAWYN-LGFDFYNWSGKTKKVIKVESFNSLPSQAIK 82
IS+ W N GFD +++S + + E N P +
Sbjct: 56 ISMHWNNGSGFDAFDYSNCGVEKVFYEGVNFSPHRNYT 93
>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein
structure initiative, northeast structural genomics
consortium, NESG; 2.28A {Cytophaga hutchinsonii}
Length = 272
Score = 25.3 bits (56), Expect = 4.1
Identities = 4/54 (7%), Positives = 13/54 (24%), Gaps = 7/54 (12%)
Query: 29 NKTIALGTSKLNYLDPRISVAWYNLGFDFYNWSGKTKKVIKVESFNSLPSQAIK 82
K I + + A + + + + K ++ +
Sbjct: 203 EKLIEVCAPGGAKYKDELIEANEYIAYYYTI-NRDKVKAD--AAWK----NILA 249
>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C
biogenesis, O157:H7 EDL933, formate- nitrite reductase
complex, lyase; 2.05A {Escherichia coli}
Length = 177
Score = 24.8 bits (54), Expect = 5.2
Identities = 5/18 (27%), Positives = 6/18 (33%)
Query: 42 LDPRISVAWYNLGFDFYN 59
LD A L D +
Sbjct: 110 LDSNEITALMLLASDAFM 127
>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial
toxin, type III secretion, protein binding; 1.85A
{Pseudomonas aeruginosa} PDB: 2xcc_A
Length = 142
Score = 24.7 bits (54), Expect = 5.8
Identities = 6/18 (33%), Positives = 7/18 (38%)
Query: 42 LDPRISVAWYNLGFDFYN 59
L Y LGF+ Y
Sbjct: 13 LSEDTLEQLYALGFNQYQ 30
>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A
{Saccharomyces cerevisiae}
Length = 258
Score = 24.8 bits (55), Expect = 5.9
Identities = 6/43 (13%), Positives = 17/43 (39%), Gaps = 7/43 (16%)
Query: 41 YLDPRISVAWYNLGFDFYNWSGKTKKVIKVESFNSLPSQAIKR 83
Y++P + G +++ + +++ + IKR
Sbjct: 133 YVNPEKAEEARLEGKEYFT-KSDWPNAV--KAYT----EMIKR 168
>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle,
phagocyte oxidase factor, SH3 domain, repeat, TPR
repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP:
a.118.8.1 PDB: 1wm5_A 1e96_B*
Length = 213
Score = 24.3 bits (53), Expect = 7.7
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 42 LDPRISVAWYNLGFDFYN 59
D ++VA++ G +Y
Sbjct: 66 RDKHLAVAYFQRGMLYYQ 83
>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing
protein, structur genomics, joint center for structural
genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}
Length = 208
Score = 24.3 bits (53), Expect = 7.9
Identities = 7/28 (25%), Positives = 13/28 (46%)
Query: 42 LDPRISVAWYNLGFDFYNWSGKTKKVIK 69
L+ A LG +Y + + KK ++
Sbjct: 117 LEADNLAANIFLGNYYYLTAEQEKKKLE 144
>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria
translocation, allosteric REG phosphoprotein, TPR
repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae}
PDB: 3fp3_A 3fp4_A 3lca_A
Length = 537
Score = 24.3 bits (53), Expect = 9.6
Identities = 8/42 (19%), Positives = 13/42 (30%), Gaps = 7/42 (16%)
Query: 42 LDPRISVAWYNLGFDFYNWSGKTKKVIKVESFNSLPSQAIKR 83
L+P + L Y GK + FN + +
Sbjct: 339 LNPENVYPYIQLACLLYK-QGKFTESE--AFFN----ETKLK 373
>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide
repeat, type III secretion; HET: MLY; 1.95A {Yersinia
enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*
Length = 148
Score = 24.1 bits (52), Expect = 9.9
Identities = 4/18 (22%), Positives = 7/18 (38%)
Query: 42 LDPRISVAWYNLGFDFYN 59
+ Y+L F+ Y
Sbjct: 16 ISSDTLEQLYSLAFNQYQ 33
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
0.313 0.131 0.380
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,523,112
Number of extensions: 76337
Number of successful extensions: 267
Number of sequences better than 10.0: 1
Number of HSP's gapped: 267
Number of HSP's successfully gapped: 95
Length of query: 102
Length of database: 6,701,793
Length adjustment: 67
Effective length of query: 35
Effective length of database: 4,831,086
Effective search space: 169088010
Effective search space used: 169088010
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (23.7 bits)