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= 003388
(824 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 191 bits (485), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 128/398 (32%), Positives = 210/398 (52%), Gaps = 43/398 (10%)
Query: 379 CAPSNSALDEIVLRLLNTGIRDENIRSYTPKIVRIGLKAHHSVNSVA-----------ID 427
CAPSN A+D++ ++ TG+ K+VR+ K+ +++S +D
Sbjct: 230 CAPSNIAVDQLTEKIHQTGL----------KVVRLCAKSREAIDSPVSFLALHNQIRNMD 279
Query: 428 HL-----VEQKRDD----SAADKQKHGATRKDRDSIRSAILNEAVIVCSTLSFSGSALLS 478
+ ++Q +D+ S+AD++++ A + R + R ++N VI C+ + +G L+
Sbjct: 280 SMPELQKLQQLKDETGELSSADEKRYRALK--RTAERELLMNADVICCTCVG-AGDPRLA 336
Query: 479 KLNHGFDVVIIDEAAQAVEPATLVPLATGCKQVFLVGDPVQLPATVISPVAEHLGYGTSL 538
K+ F ++IDE+ QA EP +VP+ G KQ+ LVGD QL V+ A G SL
Sbjct: 337 KMQ--FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSL 394
Query: 539 FKRLQRAGYPVKMLKTQYRMHPEVRSFPSREFYDEALEDGSDVEDYTTR--DWHEYRCFG 596
F+RL G L+ QYRMHP + +FPS FY+ +L++G D + D+ +
Sbjct: 395 FERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK 454
Query: 597 PFSFFDIHEGKESQPAGSGSWINIDEVDFVLLLFHKLISMYPQLKSSSQLAIISPYRHQV 656
P FF + +G+E + S++N E V + KL+ + Q+ II+PY Q
Sbjct: 455 PM-FFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAK---PDQIGIITPYEGQR 510
Query: 657 KQFQE--RFKETFGVESQKVVDITTVDGCQGREKDVAIFSCVRASDKKSIGFLADYRRMN 714
+ +F + + + V+I +VD QGREKD I SCVRA++ + IGFL D RR+N
Sbjct: 511 SYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLN 570
Query: 715 VGITRAKSSILVVGCASTLREDKHWNNLVKSAEKQDCL 752
V +TRA+ +++VG L + WN+L+ ++Q L
Sbjct: 571 VALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVL 608
Score = 34.7 bits (78), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 258 NASQLEAIHEGLLRKAFVLIQGPPGTGKTQT 288
N SQ+ A+ + +L++ LIQGPPGTGKT T
Sbjct: 182 NHSQVYAV-KTVLQRPLSLIQGPPGTGKTVT 211
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 191 bits (484), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 128/398 (32%), Positives = 210/398 (52%), Gaps = 43/398 (10%)
Query: 379 CAPSNSALDEIVLRLLNTGIRDENIRSYTPKIVRIGLKAHHSVNSVA-----------ID 427
CAPSN A+D++ ++ TG+ K+VR+ K+ +++S +D
Sbjct: 229 CAPSNIAVDQLTEKIHQTGL----------KVVRLCAKSREAIDSPVSFLALHNQIRNMD 278
Query: 428 HL-----VEQKRDD----SAADKQKHGATRKDRDSIRSAILNEAVIVCSTLSFSGSALLS 478
+ ++Q +D+ S+AD++++ A + R + R ++N VI C+ + +G L+
Sbjct: 279 SMPELQKLQQLKDETGELSSADEKRYRALK--RTAERELLMNADVICCTCVG-AGDPRLA 335
Query: 479 KLNHGFDVVIIDEAAQAVEPATLVPLATGCKQVFLVGDPVQLPATVISPVAEHLGYGTSL 538
K+ F ++IDE+ QA EP +VP+ G KQ+ LVGD QL V+ A G SL
Sbjct: 336 KMQ--FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSL 393
Query: 539 FKRLQRAGYPVKMLKTQYRMHPEVRSFPSREFYDEALEDGSDVEDYTTR--DWHEYRCFG 596
F+RL G L+ QYRMHP + +FPS FY+ +L++G D + D+ +
Sbjct: 394 FERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK 453
Query: 597 PFSFFDIHEGKESQPAGSGSWINIDEVDFVLLLFHKLISMYPQLKSSSQLAIISPYRHQV 656
P FF + +G+E + S++N E V + KL+ + Q+ II+PY Q
Sbjct: 454 PM-FFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAK---PDQIGIITPYEGQR 509
Query: 657 KQFQE--RFKETFGVESQKVVDITTVDGCQGREKDVAIFSCVRASDKKSIGFLADYRRMN 714
+ +F + + + V+I +VD QGREKD I SCVRA++ + IGFL D RR+N
Sbjct: 510 SYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLN 569
Query: 715 VGITRAKSSILVVGCASTLREDKHWNNLVKSAEKQDCL 752
V +TRA+ +++VG L + WN+L+ ++Q L
Sbjct: 570 VALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVL 607
Score = 34.7 bits (78), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 258 NASQLEAIHEGLLRKAFVLIQGPPGTGKTQT 288
N SQ+ A+ + +L++ LIQGPPGTGKT T
Sbjct: 181 NHSQVYAV-KTVLQRPLSLIQGPPGTGKTVT 210
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 190 bits (482), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 128/398 (32%), Positives = 210/398 (52%), Gaps = 43/398 (10%)
Query: 379 CAPSNSALDEIVLRLLNTGIRDENIRSYTPKIVRIGLKAHHSVNSVA-----------ID 427
CAPSN A+D++ ++ TG+ K+VR+ K+ +++S +D
Sbjct: 406 CAPSNIAVDQLTEKIHQTGL----------KVVRLCAKSREAIDSPVSFLALHNQIRNMD 455
Query: 428 HL-----VEQKRDD----SAADKQKHGATRKDRDSIRSAILNEAVIVCSTLSFSGSALLS 478
+ ++Q +D+ S+AD++++ A + R + R ++N VI C+ + +G L+
Sbjct: 456 SMPELQKLQQLKDETGELSSADEKRYRALK--RTAERELLMNADVICCTCVG-AGDPRLA 512
Query: 479 KLNHGFDVVIIDEAAQAVEPATLVPLATGCKQVFLVGDPVQLPATVISPVAEHLGYGTSL 538
K+ F ++IDE+ QA EP +VP+ G KQ+ LVGD QL V+ A G SL
Sbjct: 513 KMQ--FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSL 570
Query: 539 FKRLQRAGYPVKMLKTQYRMHPEVRSFPSREFYDEALEDGSDVEDYTTR--DWHEYRCFG 596
F+RL G L+ QYRMHP + +FPS FY+ +L++G D + D+ +
Sbjct: 571 FERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK 630
Query: 597 PFSFFDIHEGKESQPAGSGSWINIDEVDFVLLLFHKLISMYPQLKSSSQLAIISPYRHQV 656
P FF + +G+E + S++N E V + KL+ + Q+ II+PY Q
Sbjct: 631 PM-FFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAK---PDQIGIITPYEGQR 686
Query: 657 KQFQE--RFKETFGVESQKVVDITTVDGCQGREKDVAIFSCVRASDKKSIGFLADYRRMN 714
+ +F + + + V+I +VD QGREKD I SCVRA++ + IGFL D RR+N
Sbjct: 687 SYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLN 746
Query: 715 VGITRAKSSILVVGCASTLREDKHWNNLVKSAEKQDCL 752
V +TRA+ +++VG L + WN+L+ ++Q L
Sbjct: 747 VALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVL 784
Score = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 23/31 (74%), Gaps = 1/31 (3%)
Query: 258 NASQLEAIHEGLLRKAFVLIQGPPGTGKTQT 288
N SQ+ A+ + +L++ LIQGPPGTGKT T
Sbjct: 358 NHSQVYAV-KTVLQRPLSLIQGPPGTGKTVT 387
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 181 bits (460), Expect = 1e-45, Method: Compositional matrix adjust.
Identities = 128/396 (32%), Positives = 204/396 (51%), Gaps = 41/396 (10%)
Query: 379 CAPSNSALDEIVLRLLNTGIRDENIRSYTPKIVRIGLKAHH----SVNSVAIDHLVEQ-- 432
CAPSN A+D + +L + G+ K+VR+ K+ SV+++A+ +LV +
Sbjct: 410 CAPSNVAVDHLAAKLRDLGL----------KVVRLTAKSREDVESSVSNLALHNLVGRGA 459
Query: 433 --------KRDDSAADKQKHGATR--KDRDSIRSAILNEAVIVCSTLSFSGSALLSKLNH 482
K D + R K + ILN+A +VC T +G +L+
Sbjct: 460 KGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGD---KRLDT 516
Query: 483 GFDVVIIDEAAQAVEPATLVPLATGCKQVFLVGDPVQLPATVISPVAEHLGYGTSLFKRL 542
F V+IDE+ QA EP L+P+ G KQV LVGD QL ++ A G SLF+RL
Sbjct: 517 KFRTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERL 576
Query: 543 QRAGYPVKMLKTQYRMHPEVRSFPSREFYDEALEDGSDVEDYTTRDWH-EYRCFGPFSFF 601
G+ L+ QYRM+P + FPS FY+ +L++G +E T + + G F
Sbjct: 577 ISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMF 636
Query: 602 DIHEGKESQPAGSGSWINIDEVDFVLLLFHKLI--SMYPQLKSSSQLAIISPYRHQVKQF 659
+ G+E A S++N E + KL + P+ Q+ +I+PY Q + +
Sbjct: 637 WANYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPE-----QIGVITPYEGQ-RAY 690
Query: 660 QERFKETFGVESQKV---VDITTVDGCQGREKDVAIFSCVRASDKKSIGFLADYRRMNVG 716
++ + G + + V++ +VD QGREKD I SCVRA+++++IGFL D RR+NVG
Sbjct: 691 ILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVG 750
Query: 717 ITRAKSSILVVGCASTLREDKHWNNLVKSAEKQDCL 752
+TRAK ++++G +L + WN+L+ ++ CL
Sbjct: 751 LTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCL 786
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 258 NASQLEAIHEGLLRKAFVLIQGPPGTGKTQT 288
N+SQ A+ +L++ LIQGPPGTGKT T
Sbjct: 362 NSSQSNAVSH-VLQRPLSLIQGPPGTGKTVT 391
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 119 bits (297), Expect = 9e-27, Method: Compositional matrix adjust.
Identities = 121/413 (29%), Positives = 179/413 (43%), Gaps = 72/413 (17%)
Query: 379 CAPSNSALDEIVLRLLNTGIRDENIRSYTPKIVRIGLKAH--HSVNSVAIDHLVEQKRDD 436
CAPSN A+D +V RL R I+R+G A S+ ++D ++ R D
Sbjct: 239 CAPSNIAVDNLVERLALCKQR----------ILRLGHPARLLESIQQHSLDAVL--ARSD 286
Query: 437 SA---AD----------KQKHGATRKDRDSIRSAI------LNEAVIVCSTLSFSGSALL 477
SA AD K K ++++ + R+ I L E S + + ++
Sbjct: 287 SAQIVADIRKDIDQVFVKNKKTQDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVV 346
Query: 478 SKLNHG--------------FDVVIIDEAAQAVEPATLVPLATGCKQVFLVGDPVQLPAT 523
N G FDVV+IDE AQA+E + +PL ++ L GD QLP T
Sbjct: 347 LATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKA-RKCILAGDHKQLPPT 405
Query: 524 VISPVAEHLGYGTSLFKRL--QRAGYPVKMLKTQYRMHPEVRSFPSREFYDEALEDGSDV 581
+S A G SL +RL + V+ L QYRMH + + S Y L S V
Sbjct: 406 TVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSV 465
Query: 582 EDYTTRDWHEYRCFG----PFSFFD-----IHEGKESQPAGSGSWINIDEVDFVLLLFHK 632
+ RD P D + E +E G N EV V L
Sbjct: 466 ARHLLRDLPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKG---NPGEVRLVSLHIQA 522
Query: 633 LI-SMYPQLKSSSQLAIISPYRHQVKQFQERFKETFGVESQKVVDITTVDGCQGREKDVA 691
L+ + P + +A++SPY QV ++ V ++I +VDG QGREK+
Sbjct: 523 LVDAGVP----ARDIAVVSPYNLQVDLLRQSL-----VHRHPELEIKSVDGFQGREKEAV 573
Query: 692 IFSCVRASDKKSIGFLADYRRMNVGITRAKSSILVVGCASTLREDKHWNNLVK 744
I S VR++ K +GFLA+ RR+NV +TRA+ + V+ + T+ LV+
Sbjct: 574 ILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRTVNNHAFLKTLVE 626
Score = 37.0 bits (84), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 24/36 (66%)
Query: 258 NASQLEAIHEGLLRKAFVLIQGPPGTGKTQTILGLL 293
+ SQ EA+ L +K +I GPPGTGKT T++ ++
Sbjct: 191 DTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEII 226
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 119 bits (297), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 121/413 (29%), Positives = 179/413 (43%), Gaps = 72/413 (17%)
Query: 379 CAPSNSALDEIVLRLLNTGIRDENIRSYTPKIVRIGLKAH--HSVNSVAIDHLVEQKRDD 436
CAPSN A+D +V RL R I+R+G A S+ ++D ++ R D
Sbjct: 239 CAPSNIAVDNLVERLALCKQR----------ILRLGHPARLLESIQQHSLDAVL--ARSD 286
Query: 437 SA---AD----------KQKHGATRKDRDSIRSAI------LNEAVIVCSTLSFSGSALL 477
SA AD K K ++++ + R+ I L E S + + ++
Sbjct: 287 SAQIVADIRKDIDQVFVKNKKTQDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVV 346
Query: 478 SKLNHG--------------FDVVIIDEAAQAVEPATLVPLATGCKQVFLVGDPVQLPAT 523
N G FDVV+IDE AQA+E + +PL ++ L GD QLP T
Sbjct: 347 LATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKA-RKCILAGDHKQLPPT 405
Query: 524 VISPVAEHLGYGTSLFKRL--QRAGYPVKMLKTQYRMHPEVRSFPSREFYDEALEDGSDV 581
+S A G SL +RL + V+ L QYRMH + + S Y L S V
Sbjct: 406 TVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSV 465
Query: 582 EDYTTRDWHEYRCFG----PFSFFD-----IHEGKESQPAGSGSWINIDEVDFVLLLFHK 632
+ RD P D + E +E G N EV V L
Sbjct: 466 ARHLLRDLPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKG---NPGEVRLVSLHIQA 522
Query: 633 LI-SMYPQLKSSSQLAIISPYRHQVKQFQERFKETFGVESQKVVDITTVDGCQGREKDVA 691
L+ + P + +A++SPY QV ++ V ++I +VDG QGREK+
Sbjct: 523 LVDAGVP----ARDIAVVSPYNLQVDLLRQSL-----VHRHPELEIKSVDGFQGREKEAV 573
Query: 692 IFSCVRASDKKSIGFLADYRRMNVGITRAKSSILVVGCASTLREDKHWNNLVK 744
I S VR++ K +GFLA+ RR+NV +TRA+ + V+ + T+ LV+
Sbjct: 574 ILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRTVNNHAFLKTLVE 626
Score = 37.0 bits (84), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 24/36 (66%)
Query: 258 NASQLEAIHEGLLRKAFVLIQGPPGTGKTQTILGLL 293
+ SQ EA+ L +K +I GPPGTGKT T++ ++
Sbjct: 191 DTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEII 226
>pdb|3UK6|A Chain A, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|B Chain B, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|C Chain C, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|D Chain D, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|E Chain E, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|F Chain F, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|G Chain G, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|H Chain H, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|I Chain I, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|J Chain J, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|K Chain K, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|L Chain L, Crystal Structure Of The Tip48 (Tip49b) Hexamer
Length = 368
Score = 37.0 bits (84), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 27/55 (49%)
Query: 247 GLLHEYIKENHNASQLEAIHEGLLRKAFVLIQGPPGTGKTQTILGLLSAILHATP 301
G++ + LE I EG + VLI G PGTGKT +G+ A+ TP
Sbjct: 45 GMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTP 99
>pdb|2XSZ|D Chain D, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|E Chain E, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|F Chain F, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
Length = 378
Score = 33.9 bits (76), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 21/40 (52%)
Query: 262 LEAIHEGLLRKAFVLIQGPPGTGKTQTILGLLSAILHATP 301
LE I EG + VLI G PGTGKT G A+ TP
Sbjct: 75 LEXIREGKIAGRAVLIAGQPGTGKTAIAXGXAQALGPDTP 114
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 33.1 bits (74), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 12/72 (16%)
Query: 244 KIPGLLHEYIKENH----NASQLEAIHEGLLRKAFVLIQGPPGTGKTQTI-LGLLSAIL- 297
K+P + E IK+ N Q EA+ +GLL +L+ P G+GKT +G++S +L
Sbjct: 14 KLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK 73
Query: 298 ------HATPAR 303
+ TP R
Sbjct: 74 NGGKAIYVTPLR 85
>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 353
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/18 (72%), Positives = 14/18 (77%)
Query: 275 VLIQGPPGTGKTQTILGL 292
+L GPPGTGKT TIL L
Sbjct: 61 MLFYGPPGTGKTSTILAL 78
>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 405
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 240 DQSWKIPGLLHEYIKENHNASQLEAIHE------GLLRKAFVLIQGPPGTGKTQTILGLL 293
D ++ + G L + IKE +L H G+ + V++ GPPGTGKT L
Sbjct: 144 DSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTL----LA 199
Query: 294 SAILHAT 300
A+ H T
Sbjct: 200 RAVAHHT 206
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 31.2 bits (69), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 275 VLIQGPPGTGKTQTILGLLSAI 296
+L GPPGTGKT TI+ L I
Sbjct: 49 LLFYGPPGTGKTSTIVALAREI 70
>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C-
Terminal Aaa-Atpase Domain
Length = 274
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 33/64 (51%), Gaps = 15/64 (23%)
Query: 257 HNASQLEAIHEGLLRKAFVLIQGPPGTGKTQTILGLLSAILHATPARVHSKGGLREIK-R 315
N Q +A+ GL+ A VL+ GPPG GKT LL+ V ++ GL I +
Sbjct: 31 RNPDQFKAL--GLVTPAGVLLAGPPGCGKT-----LLAKA-------VANESGLNFISVK 76
Query: 316 GPEL 319
GPEL
Sbjct: 77 GPEL 80
>pdb|3HYT|A Chain A, Structural Basis Of Gdp Release And Gating In G Protein
Coupled Fe2+ Transport
pdb|3HYT|B Chain B, Structural Basis Of Gdp Release And Gating In G Protein
Coupled Fe2+ Transport
pdb|3HYT|C Chain C, Structural Basis Of Gdp Release And Gating In G Protein
Coupled Fe2+ Transport
Length = 270
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 6/88 (6%)
Query: 114 EADEVESISPNDLLLLSKE----EFKEGSTFPTTYAFALVEHCQANLLRLRMYLAGEVIH 169
EAD + + P+D+ L + + EG + YA +H A L RLR + +H
Sbjct: 184 EADSLAKVMPSDIPLKQRRWLGLQMLEGDIYSRAYAGEASQHLDAALARLRNEMDDPALH 243
Query: 170 INKDAVKSQRLLNIHSLITSSVSAVEKR 197
I DA + Q + I +++++++A R
Sbjct: 244 I-ADA-RYQCIAAICDVVSNTLTAEPSR 269
>pdb|3I8S|A Chain A, Structure Of The Cytosolic Domain Of E. Coli Feob,
Nucleotide-Free Form
pdb|3I8S|B Chain B, Structure Of The Cytosolic Domain Of E. Coli Feob,
Nucleotide-Free Form
pdb|3I8S|C Chain C, Structure Of The Cytosolic Domain Of E. Coli Feob,
Nucleotide-Free Form
pdb|3I8X|A Chain A, Structure Of The Cytosolic Domain Of E. Coli Feob,
Gdp-Bound Form
pdb|3I8X|B Chain B, Structure Of The Cytosolic Domain Of E. Coli Feob,
Gdp-Bound Form
pdb|3I8X|C Chain C, Structure Of The Cytosolic Domain Of E. Coli Feob,
Gdp-Bound Form
pdb|3I92|A Chain A, Structure Of The Cytosolic Domain Of E. Coli Feob,
Gppch2p- Bound Form
pdb|3I92|B Chain B, Structure Of The Cytosolic Domain Of E. Coli Feob,
Gppch2p- Bound Form
pdb|3I92|C Chain C, Structure Of The Cytosolic Domain Of E. Coli Feob,
Gppch2p- Bound Form
Length = 274
Score = 30.8 bits (68), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 114 EADEVESISPNDLLLLSKE----EFKEGSTFPTTYAFALVEHCQANLLRLRMYLAGEVIH 169
EAD + + P+D+ L + + EG + YA +H A L RLR + +H
Sbjct: 184 EADSLAKVMPSDIPLKQRRWLGLQMLEGDIYSRAYAGEASQHLDAALARLRNEMDDPALH 243
Query: 170 INKDAVKSQRLLNIHSLITSSVSAVEKRLFS 200
I DA + Q + I +++++++A R +
Sbjct: 244 I-ADA-RYQCIAAICDVVSNTLTAEPSRFTT 272
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
0.318 0.134 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,702,654
Number of Sequences: 62578
Number of extensions: 985985
Number of successful extensions: 2329
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2287
Number of HSP's gapped (non-prelim): 35
length of query: 824
length of database: 14,973,337
effective HSP length: 107
effective length of query: 717
effective length of database: 8,277,491
effective search space: 5934961047
effective search space used: 5934961047
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)