BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 004706
(734 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2Y35|A Chain A, Crystal Structure Of Xrn1-Substrate Complex
Length = 1140
Score = 391 bits (1004), Expect = e-109, Method: Compositional matrix adjust.
Identities = 231/637 (36%), Positives = 334/637 (52%), Gaps = 88/637 (13%)
Query: 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGII 60
MGVP F+R++++RYP +AR + EFDNLYLDMNGI+
Sbjct: 1 MGVPKFFRYISERYPCL-------------SELAREHCIP-------EFDNLYLDMNGIV 40
Query: 61 HPCFHPDGKPAPTSYDD--VFKSIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTX 118
H C HPD ++ +F+ IF+Y+D +F L++P++L +L++DGVAPRAKMNQQR+
Sbjct: 41 HNCSHPDDNNIHFHLEEEQIFQEIFNYVDKLFYLIKPQRLFFLSVDGVAPRAKMNQQRSR 100
Query: 119 XXXXXXXXXXXXXXXXXXXXXXXXXGKLLSAKEKPETCDSNVITPGTQFMAVLSAALQYF 178
G+L + E DSN ITPGT+FM L L+ F
Sbjct: 101 RFRTAREAEQQEAKAAQR-------GEL----REHERFDSNCITPGTEFMVRLQEGLRAF 149
Query: 179 IQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLI 238
++ +++ P WQ VILS PGEGEHKIM YIR + P +DPNTRHCLYGLDA LI
Sbjct: 150 LKTKISTDPLWQRCTVILSGQEAPGEGEHKIMDYIRYMKTQPDYDPNTRHCLYGLDAALI 209
Query: 239 MLSLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIH 298
+L L THE+HF +LRE + K G N V T +
Sbjct: 210 ILGLCTHELHFVVLREEV------------------------KFGRN------VKRTSVE 239
Query: 299 KKKYQFLNIWVLREYLQYELD-IPNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIR 357
+ ++ L++ +LREYL+ E D + ++ +++DD+V + F VGNDF+PH+P L I
Sbjct: 240 ETRFFLLHLGLLREYLELEFDALRTDEHKLDIAQLIDDWVLMGFLVGNDFIPHLPCLHIS 299
Query: 358 EGAINLLMHVYRREFTAMGGYLTDAGEVLLDRVEKFIQSVAVYE-DQIFQKRTRIQQAYE 416
A+ LL Y + +GG + + G++ L R++ FI ++ E D + ++
Sbjct: 300 SNALPLLYRTYIGIYPTLGGNINENGKLNLRRLQIFISALTEVELDHFKEHADDLKYMNN 359
Query: 417 YNEAMKLNARRESSEELLQAPVAV-------------------ADTVKLGE-PGYKERYY 456
+EA ++ + + L + + + V L E YK +Y
Sbjct: 360 KSEAFDMDVGEITESQNLDSDLGALINKSMLLYDDDSEEDCSDENAVLLKEFQNYKRNFY 419
Query: 457 ADKFEISNPEEIXXXXXXXXXXXXEGLCWVCRYYYQDVCSWQWFYPYHYAPFASDLKDLS 516
+KF+ +E+ L WV YYY+ V SW W+YP+HY PF SDLK++
Sbjct: 420 RNKFKRDPNDELIEELCHHYV---NALQWVLDYYYRGVQSWDWYYPFHYTPFISDLKNIE 476
Query: 517 DLEITFFLGEPFRPFDQLMGTLPAASSSALPEKYRNLMTDPSSPIYKFYPPDFQIDMNGK 576
+EI F +G PF PF QL+ LPAAS+ LP Y +LM P+SP+ +FYP +F+ D+NGK
Sbjct: 477 QVEIAFHMGTPFLPFQQLLAVLPAASAKLLPVAYHDLMLLPTSPLAEFYPLEFESDLNGK 536
Query: 577 RFAWQGVVKLPFIDEKLLLRQTKKLEVFLTEEELFRN 613
+ W+ VV +PFIDE LL E L+ EE RN
Sbjct: 537 KHDWEAVVLIPFIDEGRLLAAMLPCEAQLSLEERERN 573
>pdb|3FQD|A Chain A, Crystal Structure Of The S. Pombe Rat1-Rai1 Complex
Length = 899
Score = 351 bits (900), Expect = 9e-97, Method: Compositional matrix adjust.
Identities = 194/433 (44%), Positives = 259/433 (59%), Gaps = 16/433 (3%)
Query: 2 GVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIH 61
GVPA +R L+ ++ I V+E + +G D+S PNPNG+E DNLYLD NGI+H
Sbjct: 5 GVPALFRLLSRKFAKVITPVIEAPTEKLPDGTEIEPDLSLPNPNGVECDNLYLDXNGIVH 64
Query: 62 PCFHPDGKPAPTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTXXXX 121
PC HP+ +PAP + D+ ++F+Y D I VRPR+LL++AIDGVAPRAK NQQR+
Sbjct: 65 PCSHPEDRPAPETEDEXXVAVFEYTDRILAXVRPRQLLFIAIDGVAPRAKXNQQRSRRFR 124
Query: 122 XXXXXXXXXXXXXXXXXXXXXXGKLLSAK-EKPETCDSNVITPGTQFMAVLSAALQYFIQ 180
G + K ++ DSN ITPGT F L+ +L+Y+I
Sbjct: 125 SSREAALKEEELQAFIEEAKQQGIPIDENATKKKSWDSNCITPGTPFXDTLAKSLRYYII 184
Query: 181 ARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIML 240
+LN P W+ + ILSDA+VPGEGEHKI +IR QR P +DPNT H +YGLDADLI L
Sbjct: 185 NKLNSDPCWRNVRFILSDASVPGEGEHKIXEFIRSQRVKPEYDPNTHHVVYGLDADLIXL 244
Query: 241 SLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHG-KPGDNPADWNGVDDTPIHK 299
LATHE HF +LRE + F G E G K D+ ++ N V P+ K
Sbjct: 245 GLATHEPHFRVLREDV--------FFQQGSTKKTKEERLGIKRLDDVSETNKV---PV-K 292
Query: 300 KKYQFLNIWVLREYLQYELDIPNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIREG 359
K + +LN+ +LREYL+ EL +PN PFP + ER +DD+VF FFVGNDFLPH+P+L+IR+G
Sbjct: 293 KPFIWLNVSILREYLEVELYVPNLPFPFDLERAIDDWVFFIFFVGNDFLPHLPSLDIRDG 352
Query: 360 AINLLMHVYRREFTAMGGYLTDAGEVLLDRVEKFIQSVAVYEDQIFQKRTRIQQAYEYNE 419
A+ L ++R GGYLT G V L R E + +V ED IF++ QQ NE
Sbjct: 353 AVERLTEIWRASLPHXGGYLTLDGSVNLARAEVILSAVGNQEDDIFKRLK--QQEDRRNE 410
Query: 420 AMKLNARRESSEE 432
+ +RES++E
Sbjct: 411 NYRRRQQRESNQE 423
Score = 207 bits (527), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 117/277 (42%), Positives = 157/277 (56%), Gaps = 28/277 (10%)
Query: 441 ADTVKLGEPGYKERYYADKFEIS--NPEEIXXXXXXXXXXXXEGLCWVCRYYYQDVCSWQ 498
DTV+L EPGY+ERYY KF IS PE+I GLCWV YYYQ SW
Sbjct: 584 TDTVRLYEPGYRERYYEQKFHISPDEPEKIREAVKHYV----HGLCWVLLYYYQGCPSWT 639
Query: 499 WFYPYHYAPFASDLKDLSDLEITFFLGEPFRPFDQLMGTLPAASSSALPEKYRNLMTDPS 558
W+YPYHYAPFA+D KDL+ +++ F L +PF+P++QL+G LPAAS + LPEK + L TD +
Sbjct: 640 WYYPYHYAPFAADFKDLASIDVKFELNQPFKPYEQLLGVLPAASKNNLPEKLQTLXTDEN 699
Query: 559 SPIYKFYPPDFQIDMNGKRFAWQGVVKLPFIDEKLLLRQTKKLEVFLTEEELFRNSVMLD 618
S I FYP +F ID+NGK+F WQGV LPFIDE LL K+ LTEEE RN
Sbjct: 700 SEIIDFYPENFTIDLNGKKFEWQGVALLPFIDENRLLNAVSKIYPQLTEEESKRNEDGST 759
Query: 619 LLYVHPQHPLYQQITLYCQLYHQLPPQDRFAWEIDVNASGGMNGYIWLCERNGLRSIIPS 678
LL++ HP + + L QLY + + ++ + G+ G + N S+IP+
Sbjct: 760 LLFISEHHPXFSE--LVKQLYSK--KRQGKPLKLSGKXAHGLFGKV-----NTNDSVIPN 810
Query: 679 PVKGLP-------------DIERNQAINVTYLNPQKH 702
P I+ NQ+I++ + P+ H
Sbjct: 811 VSVQCPIDVTSADALQKYGSIDDNQSISLVFEVPKSH 847
>pdb|3PIE|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIF|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
Length = 1155
Score = 270 bits (689), Expect = 3e-72, Method: Compositional matrix adjust.
Identities = 149/412 (36%), Positives = 220/412 (53%), Gaps = 63/412 (15%)
Query: 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGII 60
MG+P F+ ++++R+P + +DG + EFDNLYLDMN I+
Sbjct: 1 MGIPKFFHFISERWP-------QISQLIDGSQIP-------------EFDNLYLDMNSIL 40
Query: 61 HPCFHPDGKPAPT--SYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTX 118
H C H DG + S ++V+ IF YIDH+F ++P++ Y+AIDGVAPRAKMNQQR
Sbjct: 41 HNCTHGDGSEVNSRLSEEEVYSKIFSYIDHLFHTIKPKQTFYMAIDGVAPRAKMNQQRAR 100
Query: 119 XXXXXXXXXXXXXXXXXXXXXXXXXGKLLSAKEKPETCDSNVITPGTQFMAVLSAALQYF 178
G L K E DSN ITPGT+FMA L+ L+YF
Sbjct: 101 RFRTAMDAEKALQKAIEN-------GDELP---KGEPFDSNAITPGTEFMAKLTENLKYF 150
Query: 179 IQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLI 238
I ++ WQ KVI S VPGEG+HKIM YIR R ++PNTRHC+YGLDADLI
Sbjct: 151 IHDKITNDTRWQNVKVIFSGHEVPGEGQHKIMDYIRAIRAQEDYNPNTRHCIYGLDADLI 210
Query: 239 MLSLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIH 298
+L L+TH+ HF +LRE +T + +
Sbjct: 211 ILGLSTHDHHFCLLREEVTFGKRSSSV-----------------------------KTLE 241
Query: 299 KKKYQFLNIWVLREYLQYELD--IPNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEI 356
+ + L++ +LREYL E + + F +FER++DDF+F+ F +GNDFLP++P L +
Sbjct: 242 TQNFFLLHLSILREYLALEFEEITDSVQFEYDFERVLDDFIFVLFTIGNDFLPNLPDLHL 301
Query: 357 REGAINLLMHVYRREFTAMGGYLTDAGEVLLDRVEKFIQSVAVYEDQIFQKR 408
++GA +L+ ++ M GY+ + G++ L R +++ ++ +E F+K+
Sbjct: 302 KKGAFPVLLQTFKEALQHMDGYINEQGKINLARFSIWLKYLSDFEYLNFEKK 353
Score = 135 bits (339), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 72/178 (40%), Positives = 102/178 (57%), Gaps = 7/178 (3%)
Query: 451 YKERYYADK--FEISNPEEIXXXXXXXXXXXXEGLCWVCRYYYQDVCSWQWFYPYHYAPF 508
+K++YY DK F I++ + + GL WV YYY+ SW W+Y YHYAP
Sbjct: 491 WKDQYYKDKLDFSINDTDSLKEMTENYVG----GLQWVLYYYYRGCPSWSWYYRYHYAPR 546
Query: 509 ASDLKDLSDLEITFFLGEPFRPFDQLMGTLPAASSSALPEKYRNLMTDPSSPIYKFYPPD 568
SD+ D I F G+PF+PF QLM LP S + +P YR LM D SPI FYP +
Sbjct: 547 ISDVIKGIDQNIEFHKGQPFKPFQQLMAVLPERSKNLIPVVYRPLMYDEHSPILDFYPNE 606
Query: 569 FQIDMNGKRFAWQGVVKLPFIDEKLLLRQTKKLEVFLTEEELFRNSVMLDLLYV-HPQ 625
++D+NGK W+ VVK+ F+D+K L+ + L+ +E RNS DL+++ +PQ
Sbjct: 607 VELDLNGKTADWEAVVKISFVDQKRLVEAMAPYDAKLSPDEKKRNSFGTDLIFIFNPQ 664
>pdb|2L93|A Chain A, Solution Structure Of The C-Terminal Domain Of Salmonella
H-Ns
Length = 55
Score = 30.0 bits (66), Expect = 4.3, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 571 IDMNGKRFAWQGVVKLPFIDEKLLLRQTKKLEVFLTEE 608
+D NG+ W G + P + +K + Q K+LE FL +E
Sbjct: 10 VDENGETKTWTGQGRTPAVIKKAMEEQGKQLEDFLIKE 47
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.141 0.443
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,077,082
Number of Sequences: 62578
Number of extensions: 1018884
Number of successful extensions: 1953
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1932
Number of HSP's gapped (non-prelim): 16
length of query: 734
length of database: 14,973,337
effective HSP length: 106
effective length of query: 628
effective length of database: 8,340,069
effective search space: 5237563332
effective search space used: 5237563332
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)