RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5937
(201 letters)
>3qrl_A Transcription initiation factor TFIID subunit 14; yeats domain, IG
fold, nucleus, nuclear protein; HET: PGE; 1.70A
{Saccharomyces cerevisiae} PDB: 2l7e_A
Length = 140
Score = 91.2 bits (226), Expect = 6e-24
Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 3/88 (3%)
Query: 105 PEGFTHDWEVFVRGVDNA---DIHNFIDKVVFHLHETFPKPKRILKEPPYVVKESGYAGF 161
W + + +D+ DKV++HLH TF P R +PP+ ++E G+ GF
Sbjct: 28 ENFPVRQWSIEIVLLDDEGKEIPATIFDKVIYHLHPTFANPNRTFTDPPFRIEEQGWGGF 87
Query: 162 TLPIEVYLKNNNEPRKIRRKHTTPPSRH 189
L I V+L RKI +
Sbjct: 88 PLDISVFLLEKAGERKIPHDLNFLQESY 115
Score = 90.4 bits (224), Expect = 1e-23
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 5/89 (5%)
Query: 4 SNVKITLEIGHEASV--RNKRTPEGFTHDWEVFVRGVDNA---DIHNFIDKVVFHLHETF 58
+ VK T+ I + + W + + +D+ DKV++HLH TF
Sbjct: 6 ATVKRTIRIKTQQHILPEVPPVENFPVRQWSIEIVLLDDEGKEIPATIFDKVIYHLHPTF 65
Query: 59 PKPKRILKEPPYVVKESGYAGFTLPIEVY 87
P R +PP+ ++E G+ GF L I V+
Sbjct: 66 ANPNRTFTDPPFRIEEQGWGGFPLDISVF 94
>3rls_A YAF9, protein AF-9 homolog; yeats domain, histone, transcription;
1.70A {Saccharomyces cerevisiae} PDB: 3fk3_A
Length = 175
Score = 91.4 bits (226), Expect = 2e-23
Identities = 34/86 (39%), Positives = 48/86 (55%), Gaps = 4/86 (4%)
Query: 6 VKITLEIGHEASV----RNKRTPEGFTHDWEVFVRGVDNADIHNFIDKVVFHLHETFPKP 61
V + G+ A + P TH W +FVRG N DI FI KVVF LH+T+P P
Sbjct: 6 VSRPIIYGNTAKKMGSVKPPNAPAEHTHLWTIFVRGPQNEDISYFIKKVVFKLHDTYPNP 65
Query: 62 KRILKEPPYVVKESGYAGFTLPIEVY 87
R ++ PP+ + E+G+ F + I+VY
Sbjct: 66 VRSIEAPPFELTETGWGEFDINIKVY 91
Score = 91.0 bits (225), Expect = 2e-23
Identities = 32/78 (41%), Positives = 45/78 (57%)
Query: 105 PEGFTHDWEVFVRGVDNADIHNFIDKVVFHLHETFPKPKRILKEPPYVVKESGYAGFTLP 164
P TH W +FVRG N DI FI KVVF LH+T+P P R ++ PP+ + E+G+ F +
Sbjct: 28 PAEHTHLWTIFVRGPQNEDISYFIKKVVFKLHDTYPNPVRSIEAPPFELTETGWGEFDIN 87
Query: 165 IEVYLKNNNEPRKIRRKH 182
I+VY + + H
Sbjct: 88 IKVYFVEEANEKVLNFYH 105
>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 = 51.6 bits (123), Expect = 4e-08
Identities = 35/181 (19%), Positives = 58/181 (32%), Gaps = 61/181 (33%)
Query: 30 DWEVFVRGVDNADIHNFIDKVVFHL----HETFPKPKRILKEPPYVVKESGYAGFTLPIE 85
WE F V A I V+F + +E +P PP ++++S +P
Sbjct: 288 SWESFFVSVRKA-I-----TVLFFIGVRCYEAYPNTSL----PPSILEDSLENNEGVP-- 335
Query: 86 VYGDLIVPKSKRTTYIFIKPEGFTHDWEVFVRGVDNADIHNFIDKVVFHLHETFPKPKRI 145
+ + + + + ++++K HL P K++
Sbjct: 336 -------------SPMLS------------ISNLTQEQVQDYVNKTNSHL----PAGKQV 366
Query: 146 ---LKEPP--YVVKESGYAGFTLPIEVY-LKNNNEPRKIRRKHTTPPSR-HLSSRDLRAV 198
L VV SG P +Y L N RK + SR S R L+
Sbjct: 367 EISLVNGAKNLVV--SGP-----PQSLYGL--NLTLRKAKAPSGLDQSRIPFSERKLKFS 417
Query: 199 W 199
Sbjct: 418 N 418
Score = 38.5 bits (89), Expect = 0.001
Identities = 38/238 (15%), Positives = 62/238 (26%), Gaps = 101/238 (42%)
Query: 3 YSNVKITLE----IG---HEASVRNKRTPEGFTHDWEVF---------VRGVDNADIHNF 46
+ +V+ + IG +EA P E + + + ++
Sbjct: 293 FVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY 352
Query: 47 IDKVVFHLHETFPKPKRI---LKEPP--YVVKESGYAGFTLPIEVYGDLI---------- 91
++K HL P K++ L VV SG P +YG L
Sbjct: 353 VNKTNSHL----PAGKQVEISLVNGAKNLVV--SGP-----PQSLYG-LNLTLRKAKAPS 400
Query: 92 ------VPKSKRTTYIFIKPEGFTHDWEVFVRGVDNADIHNF--IDKVVFH---LHETFP 140
+P S+R K F + F + FH L
Sbjct: 401 GLDQSRIPFSER------KL--------KFS--------NRFLPVA-SPFHSHLLVPASD 437
Query: 141 KPKRILKEPPYVVKESGYAGFTLPIEVYLKNNNEPRKIRRKHTTPPSRHLSSRDLRAV 198
+ L + + + I VY T DLR +
Sbjct: 438 LINKDLVK-----NNVSFNAKDIQIPVY-------------DTF------DGSDLRVL 471
Score = 35.8 bits (82), Expect = 0.007
Identities = 29/166 (17%), Positives = 47/166 (28%), Gaps = 48/166 (28%)
Query: 54 LHETF----PKPKRIL--KEPPYVVKE--SGYAGFTLPIEVYGDLIVPKSKRTTYIFIKP 105
L E F P+P + P E + G+ +V SK + +
Sbjct: 33 LQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYV-------SSLVEPSKVGQFDQVLN 85
Query: 106 EGFTHDWEVFVRGVDNADIHNFIDKVVFHLHETFPKPKRILK----------EPPYVVKE 155
T ++ G DIH K++ T K K ++K P
Sbjct: 86 LCLTEFENCYLEG---NDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSN 142
Query: 156 S--------GYAG-FTL-----PIEVYLKNNNEPRKIRRKHTTPPS 187
S G A + + Y + E R + + T
Sbjct: 143 SALFRAVGEGNAQLVAIFGGQGNTDDYFE---ELRDL---YQTYHV 182
Score = 33.9 bits (77), Expect = 0.034
Identities = 26/149 (17%), Positives = 47/149 (31%), Gaps = 52/149 (34%)
Query: 35 VRGV-DNADIH-----NF-IDKVVFH------LHETFPKPKRILKEPPYVVKESGYAGFT 81
+ V + AD H F I +V + +H K KRI + ++ E+ G
Sbjct: 1642 AQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKL 1701
Query: 82 LPIEVYGDLIVPKSKRTTYIFIKPEGFTHDWEVFVRGVDNADIHNFIDKVVFHLHET-FP 140
+++ ++ T+Y F +G L T F
Sbjct: 1702 KTEKIFKEI---NEHSTSYTFRSEKGL--------------------------LSATQFT 1732
Query: 141 KP---------KRILKEPPYVVKESGYAG 160
+P LK + ++ +AG
Sbjct: 1733 QPALTLMEKAAFEDLKSKGLIPADATFAG 1761
Score = 29.6 bits (66), Expect = 0.71
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 6/40 (15%)
Query: 27 FTHDWEVFVRGVDNADIHNFIDKVVFHLHETFPKPKRILK 66
F + ++ G DIH K++ T K K ++K
Sbjct: 91 FENC---YLEG---NDIHALAAKLLQENDTTLVKTKELIK 124
>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 = 34.1 bits (77), Expect = 0.026
Identities = 25/157 (15%), Positives = 51/157 (32%), Gaps = 34/157 (21%)
Query: 32 EVFVRGVDNADIHNFIDKVVFHLHETFPKPKRILKEPPYVVKESGYAGFTLPIEVYGDLI 91
+ FV D D+ + K + E I+ F + + +
Sbjct: 27 DAFVDNFDCKDVQDMP-KSILSKEEI----DHIIMSKD--AVSGTLRLFWT-LLSKQEEM 78
Query: 92 VPK----SKRTTYIFI------KPEGFTHDWEVFVRGVDNADIHNFIDKVVF-HLHETFP 140
V K R Y F+ + + +++ D ++N D VF + +
Sbjct: 79 VQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDR--LYN--DNQVFAKYNVSRL 134
Query: 141 KPKRILKE------P-PYVVKESGYAGF---TLPIEV 167
+P L++ P V+ + G G + ++V
Sbjct: 135 QPYLKLRQALLELRPAKNVLID-GVLGSGKTWVALDV 170
Score = 27.1 bits (59), Expect = 4.4
Identities = 40/228 (17%), Positives = 72/228 (31%), Gaps = 64/228 (28%)
Query: 17 SVRNKRTPEGFTHDWEVFVRGVDN--ADIHNFIDKVVFHLHETFPKPKRILKEPPYV--- 71
+++N +PE + + +D + + +H + +R+LK PY
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL 247
Query: 72 -----VKESG-YAGF---------TLPIEVYGDLIVPKSKRTTYIFIK--PEGFTHD--W 112
V+ + + F T +V L + TT+I + T D
Sbjct: 248 LVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFL---SAATTTHISLDHHSMTLTPDEVK 304
Query: 113 EVFVRGVDNADIHNFIDKVVFHLHETFPKPKRILKEPPYVV-----------------KE 155
+ + ++D L P+ +L P + K
Sbjct: 305 SLLL---------KYLDCRPQDL------PREVLTTNPRRLSIIAESIRDGLATWDNWKH 349
Query: 156 SGYAGFTLPIEVYLKNNNEPRKIRRKHTT----PPSRHLSSRDLRAVW 199
T IE L N EP + R+ PPS H+ + L +W
Sbjct: 350 VNCDKLTTIIESSL-NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW 396
>3h99_A Methionyl-tRNA synthetase; rossmann fold, aminoacyl-tRNA
synthetase, ATP-binding, ligas binding,
nucleotide-binding, protein biosynthesis; HET: CIT;
1.40A {Escherichia coli} PDB: 3h97_A* 3h9b_A* 1f4l_A
3h9c_A* 1pfv_A* 1pfu_A 1p7p_A* 1pfw_A* 1pfy_A* 1pg0_A*
1pg2_A* 1qqt_A 1mea_A 1med_A
Length = 560
Score = 28.7 bits (65), Expect = 1.4
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 12 IGHEASVRNKRTPEGFTHDWEVFVRGVDNADIHNFI--DKVVFH 53
IG S +N G + ++ + + A++++FI D V F
Sbjct: 271 IGLMGSFKNLCDKRGDSVSFDEYWKKDSTAELYHFIGKDIVYFL 314
Score = 27.6 bits (62), Expect = 3.6
Identities = 7/31 (22%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 106 EGFTHDWEVFVRGVDNADIHNFI--DKVVFH 134
G + ++ + + A++++FI D V F
Sbjct: 284 RGDSVSFDEYWKKDSTAELYHFIGKDIVYFL 314
>4fbk_A DNA repair and telomere maintenance protein NBS1, protein RAD32
chimeric protein; DNA double-strand break repair,
nuclease; HET: DNA; 2.38A {Schizosaccharomyces pombe}
PDB: 4fbq_A*
Length = 472
Score = 26.4 bits (57), Expect = 6.9
Identities = 14/87 (16%), Positives = 25/87 (28%), Gaps = 5/87 (5%)
Query: 89 DLIVPKSKRTTYIFIKPEGFTHDWEVFVRGVDNADIHNFIDKVVF-HLHETFPKPKRILK 147
+ P R + + H + + I +F D V++ H HE
Sbjct: 263 KFLRPDLYRDEWFNLLTVHQNHSAHTPTSYLPESFIQDFYDFVLWGHEHECLIDGSYNPT 322
Query: 148 EPPYVVKESGYAGFTLPIEVYLKNNNE 174
+ VV G T+ +
Sbjct: 323 QKFTVV----QPGSTIATSLSPGETAP 345
>2ycd_A Glutathione S-transferase; SOIL bacteria, herbicide detoxification;
HET: GTB; 1.40A {Agrobacterium tumefaciens} PDB: 3lq7_A
Length = 230
Score = 26.1 bits (58), Expect = 7.8
Identities = 4/19 (21%), Positives = 7/19 (36%)
Query: 182 HTTPPSRHLSSRDLRAVWL 200
+P +RD+ W
Sbjct: 23 ERSPDGGRGLARDMPVRWA 41
>4fbw_A DNA repair protein RAD32; DNA double-strand break repair, nuclease,
hydrolase; HET: DNA; 2.20A {Schizosaccharomyces pombe}
PDB: 4fcx_B*
Length = 417
Score = 26.4 bits (57), Expect = 8.1
Identities = 14/88 (15%), Positives = 25/88 (28%), Gaps = 5/88 (5%)
Query: 89 DLIVPKSKRTTYIFIKPEGFTHDWEVFVRGVDNADIHNFIDKVVF-HLHETFPKPKRILK 147
+ P R + + H + + I +F D V++ H HE
Sbjct: 200 KFLRPDLYRDEWFNLLTVHQNHSAHTPTSYLPESFIQDFYDFVLWGHEHECLIDGSYNPT 259
Query: 148 EPPYVVKESGYAGFTLPIEVYLKNNNEP 175
+ VV G T+ +
Sbjct: 260 QKFTVV----QPGSTIATSLSPGETAPK 283
>2nvu_B Maltose binding protein/NEDD8-activating enzyme E1 catalytic
subunit chimera; multifunction macromolecular complex,
ubiquitin, ATP, conformational change, thioester,
switch, adenylation, protein turnover, ligase; HET: ATP;
2.80A {Homo sapiens} SCOP: c.111.1.2 c.94.1.1
Length = 805
Score = 26.4 bits (58), Expect = 9.1
Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 5/74 (6%)
Query: 91 IVPKSKRTTY---IFIKPEGFTHDWEVFVRGVDNADIHNFIDKVVFHLHETFPKPKRILK 147
VP + I + F + + V G+D+ +I+ ++ L
Sbjct: 477 RVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSS 536
Query: 148 EPPYVVKESGYAGF 161
P + + G GF
Sbjct: 537 IVPLI--DGGTEGF 548
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
0.321 0.140 0.435
Gapped
Lambda K H
0.267 0.0450 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,348,289
Number of extensions: 205432
Number of successful extensions: 380
Number of sequences better than 10.0: 1
Number of HSP's gapped: 371
Number of HSP's successfully gapped: 26
Length of query: 201
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 112
Effective length of database: 4,216,824
Effective search space: 472284288
Effective search space used: 472284288
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)