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= 006311
(651 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 102/474 (21%), Positives = 175/474 (36%), Gaps = 94/474 (19%)
Query: 224 KIPKDIEDLIKKDIVPKVLKKPLLPSTYKDYFAALLYAEDF---------------YEEK 268
KIP + E L + I + + K L +K+ +A L ED YE+
Sbjct: 130 KIPSEQEQLRARQITAQQINK--LEELWKENPSATL--EDLEKPGVDEEPQHVLLRYEDA 185
Query: 269 WSGFQLFNVTLELHKAAIYDKSLKNKNLEESDETDDKLFVAFEIDSVPERRPF------- 321
+ +F ++L A YDK LK +T D + V +++ +R +
Sbjct: 186 YQYQNIFGPLVKLE--ADYDKKLKE------SQTQDNITVRWDLGLNKKRIAYFTLPKTD 237
Query: 322 ----LLSRDFVYAQRSGGKSKKFQGFLYRVVK-----WTTVLVEFEEDFHSQHQPNHKYD 372
L+ D + + G + ++G + V+K + +E + + H +
Sbjct: 238 SDMRLMQGDEICLRYKGDLAPLWKGIGH-VIKVPDNYGDEIAIELRSSVGAPVEVTHNFQ 296
Query: 373 VSFSFNRVCLKRAHEAVAD--ASDSLFRNYLFPDCASRKSIPYPSLCP----YSNYKLDS 426
V F + R A+ ++ Y++ + C ++ L
Sbjct: 297 VDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPD 356
Query: 427 DSNSAVHQILSFEGQSPYLLEGPLCNNFVLSKTGNVVREAVLQIR-RRSPKSRILICAPW 485
++S V+ + + + L++GP TG V A + R +L+CAP
Sbjct: 357 LNHSQVYAVKTVLQRPLSLIQGP-------PGTGKTVTSATIVYHLARQGNGPVLVCAPS 409
Query: 486 NRTCDKLMECLMKDIPASEMFRANAAFREADGVSDEIFQVSLVERECFSCPPLEELRQYK 545
N D+L E + + ++ R A REA + R S P L++L+Q K
Sbjct: 410 NIAVDQLTEKIHQT--GLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLK 467
Query: 546 ----VISSTFVSSFR----------LHNQGIT------AG-------HFSHIFLIDASSA 578
+SS +R L N + AG F I + +++ A
Sbjct: 468 DETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQA 527
Query: 579 TEPETM--IVLGNLANENTRVIVTGAPHNSPSRVRSDIARKNGLKMSYFERLCL 630
TEPE M +VLG ++I+ G V A K GL S FERL +
Sbjct: 528 TEPECMVPVVLG-----AKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVV 576
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 64/250 (25%), Positives = 101/250 (40%), Gaps = 52/250 (20%)
Query: 411 IPYPSLCPYSNY-KLDSDSNSAVHQILSFEGQSPY-LLEGPLCNNFVLSKTGNVVREAVL 468
+P P N+ +L+S ++AV +L Q P L++GP TG V A +
Sbjct: 347 VPLPKEFSIPNFAQLNSSQSNAVSHVL----QRPLSLIQGP-------PGTGKTVTSATI 395
Query: 469 QIR-RRSPKSRILICAPWNRTCDKLMECL--------------MKDIPA--SEMFRANAA 511
+ K RIL+CAP N D L L +D+ + S + N
Sbjct: 396 VYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLV 455
Query: 512 FREADG-------VSDEIFQVSLVERECF----SCPPLEELRQYKVISSTFVSSF--RLH 558
R A G + DE+ ++S + + F E L + V+ T V + RL
Sbjct: 456 GRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLD 515
Query: 559 NQGITAGHFSHIFLIDASSATEPETMIVLGNLANENTRVIVTGAPHNSPSRVRSDIARKN 618
+ F + + +++ A+EPE +I + A + VI+ G + A
Sbjct: 516 TK------FRTVLIDESTQASEPECLIPIVKGAKQ---VILVGDHQQLGPVILERKAADA 566
Query: 619 GLKMSYFERL 628
GLK S FERL
Sbjct: 567 GLKQSLFERL 576
>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 = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 58/216 (26%), Positives = 84/216 (38%), Gaps = 44/216 (20%)
Query: 445 LLEGPLCNNFVLSKTGNVVREAVLQIR-RRSPKSRILICAPWNRTCDKLMECLMKDIPAS 503
L++GP TG V A + R +L+CAP N D+L E + +
Sbjct: 199 LIQGP-------PGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQT--GL 249
Query: 504 EMFRANAAFREADGVSDEIFQVSLVERECFSCPPLEELRQYK----VISSTFVSSFR--- 556
++ R A REA + R S P L++L+Q K +SS +R
Sbjct: 250 KVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALK 309
Query: 557 -------LHNQGIT------AG-------HFSHIFLIDASSATEPETM--IVLGNLANEN 594
L N + AG F I + +++ ATEPE M +VLG
Sbjct: 310 RTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLG-----A 364
Query: 595 TRVIVTGAPHNSPSRVRSDIARKNGLKMSYFERLCL 630
++I+ G V A K GL S FERL +
Sbjct: 365 KQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVV 400
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 58/216 (26%), Positives = 84/216 (38%), Gaps = 44/216 (20%)
Query: 445 LLEGPLCNNFVLSKTGNVVREAVLQIR-RRSPKSRILICAPWNRTCDKLMECLMKDIPAS 503
L++GP TG V A + R +L+CAP N D+L E + +
Sbjct: 198 LIQGP-------PGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQT--GL 248
Query: 504 EMFRANAAFREADGVSDEIFQVSLVERECFSCPPLEELRQYK----VISSTFVSSFR--- 556
++ R A REA + R S P L++L+Q K +SS +R
Sbjct: 249 KVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALK 308
Query: 557 -------LHNQGIT------AG-------HFSHIFLIDASSATEPETM--IVLGNLANEN 594
L N + AG F I + +++ ATEPE M +VLG
Sbjct: 309 RTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLG-----A 363
Query: 595 TRVIVTGAPHNSPSRVRSDIARKNGLKMSYFERLCL 630
++I+ G V A K GL S FERL +
Sbjct: 364 KQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVV 399
>pdb|1TU5|A Chain A, Crystal Structure Of Bovine Plasma Copper-Containing Amine
Oxidase
pdb|1TU5|B Chain B, Crystal Structure Of Bovine Plasma Copper-Containing Amine
Oxidase
pdb|2PNC|A Chain A, Crystal Structure Of Bovine Plasma Copper-Containing Amine
Oxidase In Complex With Clonidine
pdb|2PNC|B Chain B, Crystal Structure Of Bovine Plasma Copper-Containing Amine
Oxidase In Complex With Clonidine
Length = 746
Score = 33.1 bits (74), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 1/88 (1%)
Query: 564 AGHFSHIFLIDASSATEPETMIVLGNLANENTRVIVTGAPHNSPSRVRSDIARKNGLKMS 623
A +H+ A E ++ G N +V G P PS +R ++G +
Sbjct: 90 AAALAHLDRGSPPPAREALAIVFFGGQPQPNVTELVVG-PLPQPSYMRDVTVERHGGPLP 148
Query: 624 YFERLCLTEAYRSCNSMFFSQLFTEEVG 651
Y+ R L Y + M F++ + G
Sbjct: 149 YYRRPVLLREYLDIDQMIFNRELPQAAG 176
>pdb|1BDM|A Chain A, The Structure At 1.8 Angstroms Resolution Of A Single Site
Mutant (T189i) Of Malate Dehydrogenase From Thermus
Flavus With Increased Enzymatic Activity
pdb|1BDM|B Chain B, The Structure At 1.8 Angstroms Resolution Of A Single Site
Mutant (T189i) Of Malate Dehydrogenase From Thermus
Flavus With Increased Enzymatic Activity
Length = 327
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 14/78 (17%)
Query: 584 MIVLGNLANENTRVIVTGAPHNSP-----------SRVRSDIARKNGLKMSYFERLCLTE 632
++V+GN AN N + AP +P +R ++ +A+K G + R+ +
Sbjct: 126 VLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTV-- 183
Query: 633 AYRSCNSMFFSQLFTEEV 650
+ + +S+ F LF EV
Sbjct: 184 -WGNHSSIMFPDLFHAEV 200
>pdb|1BMD|A Chain A, Determinants Of Protein Thermostability Observed In The
1.9 Angstroms Crystal Structure Of Malate Dehydrogenase
From The Thermophilic Bacterium Thermus Flavus
pdb|1BMD|B Chain B, Determinants Of Protein Thermostability Observed In The
1.9 Angstroms Crystal Structure Of Malate Dehydrogenase
From The Thermophilic Bacterium Thermus Flavus
Length = 327
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 14/78 (17%)
Query: 584 MIVLGNLANENTRVIVTGAPHNSP-----------SRVRSDIARKNGLKMSYFERLCLTE 632
++V+GN AN N + AP +P +R ++ +A+K G + R+ +
Sbjct: 126 VLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTV-- 183
Query: 633 AYRSCNSMFFSQLFTEEV 650
+ + +S F LF EV
Sbjct: 184 -WGNHSSTMFPDLFHAEV 200
>pdb|1IZ9|A Chain A, Crystal Structure Of Malate Dehydrogenase From Thermus
Thermophilus Hb8
pdb|1IZ9|B Chain B, Crystal Structure Of Malate Dehydrogenase From Thermus
Thermophilus Hb8
pdb|1Y7T|A Chain A, Crystal Structure Of Nad(H)-Depenent Malate Dehydrogenase
Complexed With Nadph
pdb|1Y7T|B Chain B, Crystal Structure Of Nad(H)-Depenent Malate Dehydrogenase
Complexed With Nadph
pdb|2CVQ|A Chain A, Crystal Structure Of Nad(H)-Dependent Malate Dehydrogenase
Complexed With Nadph
pdb|2CVQ|B Chain B, Crystal Structure Of Nad(H)-Dependent Malate Dehydrogenase
Complexed With Nadph
Length = 327
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 14/78 (17%)
Query: 584 MIVLGNLANENTRVIVTGAPHNSP-----------SRVRSDIARKNGLKMSYFERLCLTE 632
++V+GN AN N + AP +P +R ++ +A+K G + R+ +
Sbjct: 126 VLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTV-- 183
Query: 633 AYRSCNSMFFSQLFTEEV 650
+ + +S F LF EV
Sbjct: 184 -WGNHSSTMFPDLFHAEV 200
>pdb|1WZE|A Chain A, Structural Basis For Alteration Of Cofactor Specificity Of
Malate Dehydrogenase From Thermus Flavus
pdb|1WZE|B Chain B, Structural Basis For Alteration Of Cofactor Specificity Of
Malate Dehydrogenase From Thermus Flavus
pdb|1WZI|A Chain A, Structural Basis For Alteration Of Cofactor Specificity Of
Malate Dehydrogenase From Thermus Flavus
pdb|1WZI|B Chain B, Structural Basis For Alteration Of Cofactor Specificity Of
Malate Dehydrogenase From Thermus Flavus
Length = 327
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 14/78 (17%)
Query: 584 MIVLGNLANENTRVIVTGAPHNSP-----------SRVRSDIARKNGLKMSYFERLCLTE 632
++V+GN AN N + AP +P +R ++ +A+K G + R+ +
Sbjct: 126 VLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTV-- 183
Query: 633 AYRSCNSMFFSQLFTEEV 650
+ + +S F LF EV
Sbjct: 184 -WGNHSSTMFPDLFHAEV 200
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 0.133 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,662,745
Number of Sequences: 62578
Number of extensions: 670323
Number of successful extensions: 1463
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1460
Number of HSP's gapped (non-prelim): 13
length of query: 651
length of database: 14,973,337
effective HSP length: 105
effective length of query: 546
effective length of database: 8,402,647
effective search space: 4587845262
effective search space used: 4587845262
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: 55 (25.8 bits)