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= 006386
(647 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 497 bits (1279), Expect = e-140, Method: Compositional matrix adjust.
Identities = 280/648 (43%), Positives = 403/648 (62%), Gaps = 17/648 (2%)
Query: 12 AVSLQEFVSVMAPLIDLEKEAEISASITSGASRNLDTAQKKGSTILNLKCVDAQTGLMGK 71
+ +++ FV+ L++LE++AE+ + + +L Q +G +L L+ +TGL G+
Sbjct: 1 SAAVESFVTKQLDLLELERDAEVEERRSWQENISLKELQSRGVCLLKLQVSSQRTGLYGR 60
Query: 72 TLLEFQSTK---GDVLPAHKFGTHDVVVLKPNKADLGSPALGQGVVYRLKDSSITVAFDD 128
L+ F+ + LP++ F + D+V L + A+ GS L G++ R+ S+TVAFD+
Sbjct: 61 LLVTFEPRRYGSAAALPSNSFTSGDIVGLY-DAANEGS-QLATGILTRVTQKSVTVAFDE 118
Query: 129 IPEEGLN----SPLRLEKLANEVTYRRMKDALIQLSKGVQNGPAAGLIPVLFGEQKPTVL 184
+ L+ + RL KLAN+VTYRR+K ALI L K +GPA+ LI VLFG P+
Sbjct: 119 SHDFQLSLDRENSYRLLKLANDVTYRRLKKALIALKK-YHSGPASSLIEVLFGRSAPSPA 177
Query: 185 KKDIAFKPFNSNLDHSQKDAISKALSSKNVFMLHXXXXXXXXXXVVEIILQEVKRGSKIL 244
+ FN+ LD SQK+A+ ALS K + ++H VVEIILQ VK+G K+L
Sbjct: 178 SEIHPLTFFNTCLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGLKVL 237
Query: 245 ACAASNIAVDNIXXXXXXXXXXXXXXGHPARLLPQVLESALDAQVLRGDNSSLASDIRKE 304
CA SNIAVDN+ GHPARLL + + +LDA + R D++ + +DIRK+
Sbjct: 238 CCAPSNIAVDNLVERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKD 297
Query: 305 MKALNGKLLKTKDKNTRREIQKELRTLSKEERKRQQLAVTDVIKNADVVLTTLTGAVS-- 362
+ + K KT+DK + + E++ L KE ++R++ A+ + + +A+VVL T TGA +
Sbjct: 298 IDQVFVKNKKTQDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADG 357
Query: 363 --RKLDNTSFDLVIIDEAAQALEIACWIALLKGSRCILAGDHLQLPPTVQSVEAEKKGLG 420
+ L + FD+V+IDE AQALE +CWI LLK +CILAGDH QLPPT S +A GL
Sbjct: 358 PLKLLPESYFDVVVIDECAQALEASCWIPLLKARKCILAGDHKQLPPTTVSHKAALAGLS 417
Query: 421 RTLFERLADLYGDEVTSMLTVQYRMHEHIMNWSSKQLYNSKIKAHPSVAAHMLFDLEGVK 480
+L ERLA+ YG V LTVQYRMH+ IM W+S +Y ++ AH SVA H+L DL GV
Sbjct: 418 LSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVA 477
Query: 481 RTSSTEPTLLLIDIAGCDMEEKKDE-EDSTMNEGEAEVAMAHAKRLIQSGVHASDIGIIT 539
T T LLL+D AGC + E ++E E S N GE + H + L+ +GV A DI +++
Sbjct: 478 ATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVS 537
Query: 540 PYAAQVVLLKILRSKDDKLKNMEVSTVDGFQGREKEAIIISMVRSNSKKEVGFLSDRRRM 599
PY QV LL+ +S + +E+ +VDGFQGREKEA+I+S VRSN K EVGFL++ RR+
Sbjct: 538 PYNLQVDLLR--QSLVHRHPELEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRI 595
Query: 600 NVAVTRARRQCCLVCDTETVSSDGFLKRLIEYFEEHAEYLSGSEYLNE 647
NVAVTRARR ++CD+ TV++ FLK L+EYF +H E + EYL++
Sbjct: 596 NVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTAFEYLDD 643
>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 = 495 bits (1275), Expect = e-140, Method: Compositional matrix adjust.
Identities = 280/648 (43%), Positives = 404/648 (62%), Gaps = 17/648 (2%)
Query: 12 AVSLQEFVSVMAPLIDLEKEAEISASITSGASRNLDTAQKKGSTILNLKCVDAQTGLMGK 71
+ +++ FV+ L++LE++AE+ + + +L Q +G +L L+ +TGL G+
Sbjct: 1 SAAVESFVTKQLDLLELERDAEVEERRSWQENISLKELQSRGVCLLKLQVSSQRTGLYGR 60
Query: 72 TLLEFQSTK---GDVLPAHKFGTHDVVVLKPNKADLGSPALGQGVVYRLKDSSITVAFDD 128
L+ F+ + LP++ F + D+V L + A+ GS L G++ R+ S+TVAFD+
Sbjct: 61 LLVTFEPRRYGSAAALPSNSFTSGDIVGLY-DAANEGS-QLATGILTRVTQKSVTVAFDE 118
Query: 129 IP--EEGLN--SPLRLEKLANEVTYRRMKDALIQLSKGVQNGPAAGLIPVLFGEQKPTVL 184
++ L+ + RL KLAN+VTYRR+K ALI L K +GPA+ LI VLFG P+
Sbjct: 119 SHDFQQSLDRENSYRLLKLANDVTYRRLKKALIALKK-YHSGPASSLIEVLFGRSAPSPA 177
Query: 185 KKDIAFKPFNSNLDHSQKDAISKALSSKNVFMLHXXXXXXXXXXVVEIILQEVKRGSKIL 244
+ FN+ LD SQK+A+ ALS K + ++H VVEIILQ VK+G K+L
Sbjct: 178 SEIHPLTFFNTCLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGLKVL 237
Query: 245 ACAASNIAVDNIXXXXXXXXXXXXXXGHPARLLPQVLESALDAQVLRGDNSSLASDIRKE 304
CA SNIAVDN+ GHPARLL + + +LDA + R D++ + +DIRK+
Sbjct: 238 CCAPSNIAVDNLVERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKD 297
Query: 305 MKALNGKLLKTKDKNTRREIQKELRTLSKEERKRQQLAVTDVIKNADVVLTTLTGAVS-- 362
+ + K KT+DK + + E++ L KE ++R++ A+ + + +A+VVL T TGA +
Sbjct: 298 IDQVFVKNKKTQDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADG 357
Query: 363 --RKLDNTSFDLVIIDEAAQALEIACWIALLKGSRCILAGDHLQLPPTVQSVEAEKKGLG 420
+ L + FD+V+IDE AQALE +CWI LLK +CILAGDH QLPPT S +A GL
Sbjct: 358 PLKLLPESYFDVVVIDECAQALEASCWIPLLKARKCILAGDHKQLPPTTVSHKAALAGLS 417
Query: 421 RTLFERLADLYGDEVTSMLTVQYRMHEHIMNWSSKQLYNSKIKAHPSVAAHMLFDLEGVK 480
+L ERLA+ YG V LTVQYRMH+ IM W+S +Y ++ AH SVA H+L DL GV
Sbjct: 418 LSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVA 477
Query: 481 RTSSTEPTLLLIDIAGCDMEEKKDE-EDSTMNEGEAEVAMAHAKRLIQSGVHASDIGIIT 539
T T LLL+D AGC + E ++E E S N GE + H + L+ +GV A DI +++
Sbjct: 478 ATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVS 537
Query: 540 PYAAQVVLLKILRSKDDKLKNMEVSTVDGFQGREKEAIIISMVRSNSKKEVGFLSDRRRM 599
PY QV LL+ +S + +E+ +VDGFQGREKEA+I+S VRSN K EVGFL++ RR+
Sbjct: 538 PYNLQVDLLR--QSLVHRHPELEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRI 595
Query: 600 NVAVTRARRQCCLVCDTETVSSDGFLKRLIEYFEEHAEYLSGSEYLNE 647
NVAVTRARR ++CD+ TV++ FLK L+EYF +H E + EYL++
Sbjct: 596 NVAVTRARRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTAFEYLDD 643
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 166 bits (420), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 181/650 (27%), Positives = 287/650 (44%), Gaps = 74/650 (11%)
Query: 17 EFVSVMAPLIDLE-------KEAEISASITSGASRNLDTAQKKGSTILNLKCVDAQTGLM 69
++ ++ PL+ LE KE++ +IT L+ KK L D+ LM
Sbjct: 10 QYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLN---KKRIAYFTLPKTDSDMRLM 66
Query: 70 --GKTLLEFQSTKGDVLPAHKFGTHDVVVLKPNKADLGSPALGQGVVYRLKDSSITVAFD 127
+ L + KGD+ P K G V+ + N D + L+ S
Sbjct: 67 QGDEICLRY---KGDLAPLWK-GIGHVIKVPDNYGD--------EIAIELRSSV------ 108
Query: 128 DIPEEGLNSPLRLEKLANEVTYRRMKDALIQLSKGVQNGPAAGLI-PVLFGEQKPTVLKK 186
P E + +++ + ++ RM+ AL + V +G I L G + V+ K
Sbjct: 109 GAPVE-VTHNFQVDFVWKSTSFDRMQSALKTFA--VDETSVSGYIYHKLLGHEVEDVIIK 165
Query: 187 DIAFKPFNS----NLDHSQKDAISKALSSKNVFMLHXXXXXXXXXXVVEIILQEVKRGS- 241
K F + +L+HSQ A+ L + + ++ I+ ++G+
Sbjct: 166 CQLPKRFTAQGLPDLNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSATIVYHLARQGNG 224
Query: 242 KILACAASNIAVDNIXXXXXXXXXXXXXXGHPARLLPQVLESALDAQVLRGDNSSLASDI 301
+L CA SNIAVD + RL + E A+D+ V +L + I
Sbjct: 225 PVLVCAPSNIAVDQLTEKIHQTGLKV------VRLCAKSRE-AIDSPV---SFLALHNQI 274
Query: 302 RK--EMKALNGKLLKTKDKNTRREIQKELRTLSKEERKRQQLAVTDVIKNADVVLTTLTG 359
R M L KL + KD+ E K R ++ A +++ NADV+ T G
Sbjct: 275 RNMDSMPELQ-KLQQLKDETGELSSADE-----KRYRALKRTAERELLMNADVICCTCVG 328
Query: 360 AVSRKLDNTSFDLVIIDEAAQALEIACWIALLKGSR-CILAGDHLQLPPTVQSVEAEKKG 418
A +L F ++IDE+ QA E C + ++ G++ IL GDH QL P V +A K G
Sbjct: 329 AGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAG 388
Query: 419 LGRTLFERLADLYGDEVTSMLTVQYRMHEHIMNWSSKQLYNSKIKAHPSVAAHML--FDL 476
L ++LFERL L + L VQYRMH + + S Y ++ + A + FD
Sbjct: 389 LSQSLFERLVVLGIRPIR--LQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDF 446
Query: 477 EGVKRTSSTEPTLLLIDIAGCDMEEKKDEEDSTMNEGEAEVAMAHAKRLIQSGVHASDIG 536
+ +P + EE S +N EA +L+++G IG
Sbjct: 447 QW---PQPDKPMFFYVTQG---QEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIG 500
Query: 537 IITPYAAQ----VVLLKILRSKDDKL-KNMEVSTVDGFQGREKEAIIISMVRSNSKKEVG 591
IITPY Q V ++ S KL + +E+++VD FQGREK+ II+S VR+N + +G
Sbjct: 501 IITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIG 560
Query: 592 FLSDRRRMNVAVTRARRQCCLVCDTETVSSDGFLKRLIEYFEEHAEYLSG 641
FL+D RR+NVA+TRAR +V + + +S L+ Y++E + G
Sbjct: 561 FLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEG 610
>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 = 166 bits (419), Expect = 5e-41, Method: Compositional matrix adjust.
Identities = 139/457 (30%), Positives = 216/457 (47%), Gaps = 36/457 (7%)
Query: 196 NLDHSQKDAISKALSSKNVFMLHXXXXXXXXXXVVEIILQEVKRGS-KILACAASNIAVD 254
+L+HSQ A+ K + + + ++ I+ ++G+ +L CA SNIAVD
Sbjct: 180 DLNHSQVYAV-KTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVD 238
Query: 255 NIXXXXXXXXXXXXXXGHPARLLPQVLESALDAQVLRGDNSSLASDIRK--EMKALNGKL 312
+ RL + E A+D+ V +L + IR M L KL
Sbjct: 239 QLTEKIHQTGLKV------VRLCAKSRE-AIDSPV---SFLALHNQIRNMDSMPELQ-KL 287
Query: 313 LKTKDKNTRREIQKELRTLSKEERKRQQLAVTDVIKNADVVLTTLTGAVSRKLDNTSFDL 372
+ KD+ E K R ++ A +++ NADV+ T GA +L F
Sbjct: 288 QQLKDETGELSSADE-----KRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRS 342
Query: 373 VIIDEAAQALEIACWIALLKGSR-CILAGDHLQLPPTVQSVEAEKKGLGRTLFERLADLY 431
++IDE+ QA E C + ++ G++ IL GDH QL P V +A K GL ++LFERL L
Sbjct: 343 ILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLG 402
Query: 432 GDEVTSMLTVQYRMHEHIMNWSSKQLYNSKIKAHPSVAAHML--FDLEGVKRTSSTEPTL 489
+ L VQYRMH + + S Y ++ + A + FD + +P
Sbjct: 403 IRPIR--LQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQW---PQPDKPMF 457
Query: 490 LLIDIAGCDMEEKKDEEDSTMNEGEAEVAMAHAKRLIQSGVHASDIGIITPYAAQ----V 545
+ EE S +N EA +L+++G IGIITPY Q V
Sbjct: 458 FYVTQG---QEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLV 514
Query: 546 VLLKILRSKDDKL-KNMEVSTVDGFQGREKEAIIISMVRSNSKKEVGFLSDRRRMNVAVT 604
++ S KL + +E+++VD FQGREK+ II+S VR+N + +GFL+D RR+NVA+T
Sbjct: 515 QYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALT 574
Query: 605 RARRQCCLVCDTETVSSDGFLKRLIEYFEEHAEYLSG 641
RAR +V + + +S L+ Y++E + G
Sbjct: 575 RARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEG 611
>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 = 166 bits (419), Expect = 5e-41, Method: Compositional matrix adjust.
Identities = 180/650 (27%), Positives = 289/650 (44%), Gaps = 74/650 (11%)
Query: 17 EFVSVMAPLIDLE-------KEAEISASITSGASRNLDTAQKKGSTILNLKCVDAQTGLM 69
++ ++ PL+ LE KE++ +IT L+ KK L D+ LM
Sbjct: 187 QYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLN---KKRIAYFTLPKTDSDMRLM 243
Query: 70 --GKTLLEFQSTKGDVLPAHKFGTHDVVVLKPNKADLGSPALGQGVVYRLKDSSITVAFD 127
+ L + KGD+ P K G V+ + N D + L+ SS+ +
Sbjct: 244 QGDEICLRY---KGDLAPLWK-GIGHVIKVPDNYGD--------EIAIELR-SSVGAPVE 290
Query: 128 DIPEEGLNSPLRLEKLANEVTYRRMKDALIQLSKGVQNGPAAGLI-PVLFGEQKPTVLKK 186
+ +++ + ++ RM+ AL + V +G I L G + V+ K
Sbjct: 291 ------VTHNFQVDFVWKSTSFDRMQSALKTFA--VDETSVSGYIYHKLLGHEVEDVIIK 342
Query: 187 DIAFKPFNS----NLDHSQKDAISKALSSKNVFMLHXXXXXXXXXXVVEIILQEVKRGS- 241
K F + +L+HSQ A+ K + + + ++ I+ ++G+
Sbjct: 343 CQLPKRFTAQGLPDLNHSQVYAV-KTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNG 401
Query: 242 KILACAASNIAVDNIXXXXXXXXXXXXXXGHPARLLPQVLESALDAQVLRGDNSSLASDI 301
+L CA SNIAVD + RL + E A+D+ V +L + I
Sbjct: 402 PVLVCAPSNIAVDQLTEKIHQTGLKV------VRLCAKSRE-AIDSPV---SFLALHNQI 451
Query: 302 RK--EMKALNGKLLKTKDKNTRREIQKELRTLSKEERKRQQLAVTDVIKNADVVLTTLTG 359
R M L KL + KD+ E K R ++ A +++ NADV+ T G
Sbjct: 452 RNMDSMPELQ-KLQQLKDETGELSSADE-----KRYRALKRTAERELLMNADVICCTCVG 505
Query: 360 AVSRKLDNTSFDLVIIDEAAQALEIACWIALLKGSR-CILAGDHLQLPPTVQSVEAEKKG 418
A +L F ++IDE+ QA E C + ++ G++ IL GDH QL P V +A K G
Sbjct: 506 AGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAG 565
Query: 419 LGRTLFERLADLYGDEVTSMLTVQYRMHEHIMNWSSKQLYNSKIKAHPSVAAHML--FDL 476
L ++LFERL L + L VQYRMH + + S Y ++ + A + FD
Sbjct: 566 LSQSLFERLVVLGIRPIR--LQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDF 623
Query: 477 EGVKRTSSTEPTLLLIDIAGCDMEEKKDEEDSTMNEGEAEVAMAHAKRLIQSGVHASDIG 536
+ +P + EE S +N EA +L+++G IG
Sbjct: 624 QW---PQPDKPMFFYVTQG---QEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIG 677
Query: 537 IITPYAAQ----VVLLKILRSKDDKL-KNMEVSTVDGFQGREKEAIIISMVRSNSKKEVG 591
IITPY Q V ++ S KL + +E+++VD FQGREK+ II+S VR+N + +G
Sbjct: 678 IITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIG 737
Query: 592 FLSDRRRMNVAVTRARRQCCLVCDTETVSSDGFLKRLIEYFEEHAEYLSG 641
FL+D RR+NVA+TRAR +V + + +S L+ Y++E + G
Sbjct: 738 FLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVEG 787
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 162 bits (409), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 158/564 (28%), Positives = 258/564 (45%), Gaps = 69/564 (12%)
Query: 110 GQGVVYRLKDSSITVAFDDI-----------PEEGLNSPLRLEKLANEVTYRRMKDALIQ 158
G+G + RL +S F D P L + E + +Y RM+DAL +
Sbjct: 265 GRGYIVRLPNS-----FQDTFTLELKPSKTPPPTHLTTGFTAEFIWKGTSYDRMQDALKK 319
Query: 159 LSKGVQNGPAAGLIPV-LFGEQKPTV-----LKKDIAFKPFNSNLDHSQKDAISKALSSK 212
+ + +G + + G Q + L K+ + F + L+ SQ +A+S L +
Sbjct: 320 FA--IDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNF-AQLNSSQSNAVSHVLQ-R 375
Query: 213 NVFMLHXXXXXXXXXXVVEIILQEVK-RGSKILACAASNIAVDNIXXXXXXXXXXXXXXG 271
+ ++ I+ K +IL CA SN+AVD++
Sbjct: 376 PLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLT 435
Query: 272 HPARLLPQVLESALDAQVLRGDNSSLASDIRKEMKALNGKLLKTKDKNTRREIQKELRTL 331
+R + +ES++ N +L + + + K LLK KD E+ L
Sbjct: 436 AKSR---EDVESSVS-------NLALHNLVGRGAKGELKNLLKLKD---------EVGEL 476
Query: 332 SKEERKRQQLAV----TDVIKNADVVLTTLTGAVSRKLDNTSFDLVIIDEAAQALEIACW 387
S + KR V +++ ADVV T GA ++LD T F V+IDE+ QA E C
Sbjct: 477 SASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLD-TKFRTVLIDESTQASEPECL 535
Query: 388 IALLKGSR-CILAGDHLQLPPTVQSVEAEKKGLGRTLFERLADLYGDEVTSMLTVQYRMH 446
I ++KG++ IL GDH QL P + +A GL ++LFERL L V L VQYRM+
Sbjct: 536 IPIVKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISL--GHVPIRLEVQYRMN 593
Query: 447 EHIMNWSSKQLYNSKIKAHPSVAAHMLFDLEGVKRTSSTEPT--LLLIDIAGCDMEEKKD 504
++ + S Y ++ ++ + V + P + ++ A EE
Sbjct: 594 PYLSEFPSNMFYEGSLQNGVTI------EQRTVPNSKFPWPIRGIPMMFWANYGREEISA 647
Query: 505 EEDSTMNEGEAEVAMAHAKRLIQSGVHASDIGIITPYAAQ-VVLLKILR-----SKDDKL 558
S +N EA +L + GV IG+ITPY Q +L+ ++ KD +
Sbjct: 648 NGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYI 707
Query: 559 KNMEVSTVDGFQGREKEAIIISMVRSNSKKEVGFLSDRRRMNVAVTRARRQCCLVCDTET 618
K +EV++VD FQGREK+ II+S VR+N ++ +GFL D RR+NV +TRA+ ++ + +
Sbjct: 708 K-VEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRS 766
Query: 619 VSSDGFLKRLIEYFEEHAEYLSGS 642
++ + L+ +F E + G+
Sbjct: 767 LARNTLWNHLLIHFREKGCLVEGT 790
>pdb|3E1S|A Chain A, Structure Of An N-Terminal Truncation Of Deinococcus
Radiodurans Recd2
pdb|3GP8|A Chain A, Crystal Structure Of The Binary Complex Of Recd2 With Dna
pdb|3GPL|A Chain A, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
pdb|3GPL|B Chain B, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
Length = 574
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 365 LDNTSFDLVIIDEAAQ---ALEIACWIALLKGSRCILAGDHLQLPP 407
L+ +DL+I+DE + AL ++ A+ G+R +L GD QLPP
Sbjct: 275 LEPAPYDLLIVDEVSMMGDALMLSLLAAVPPGARVLLVGDTDQLPP 320
>pdb|3P2Y|A Chain A, Crystal Structure Of Alanine DehydrogenasePYRIDINE
NUCLEOTIDE Transhydrogenase From Mycobacterium Smegmatis
Length = 381
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 38/137 (27%), Positives = 57/137 (41%), Gaps = 33/137 (24%)
Query: 329 RTLSKEERKRQQLAVTDVIKNADVVLTTLTGAVSRKLDNTSFDLVIIDEAAQALEIACWI 388
R LS+ ER +QQ A+ D I D+V+TT LV A + + A
Sbjct: 245 RELSEAERAQQQQALEDAITKFDIVITTA--------------LVPGRPAPRLVTAAAAT 290
Query: 389 ALLKGSRCI-LAGDHLQLPPTVQSVEAEKKGLGRTLFERLADLYGDEVTSMLTVQYRMHE 447
+ GS + LAG+ T + E + GRT+ +G +TS L + M E
Sbjct: 291 GMQPGSVVVDLAGE------TGGNCELTEP--GRTIVH-----HGVTITSPLNLPATMPE 337
Query: 448 HIMNWSSKQLYNSKIKA 464
H + +LY + A
Sbjct: 338 H-----ASELYAKNVTA 349
>pdb|3SK3|A Chain A, Crystal Structure Of Salmonella Typhimurium Acetate Kinase
(Acka) With Citrate Bound At The Dimeric Interface
pdb|3SK3|B Chain B, Crystal Structure Of Salmonella Typhimurium Acetate Kinase
(Acka) With Citrate Bound At The Dimeric Interface
pdb|3SLC|A Chain A, Crystal Structure Of Apo Form Of Acetate Kinase (Acka)
From Salmonella Typhimurium
pdb|3SLC|B Chain B, Crystal Structure Of Apo Form Of Acetate Kinase (Acka)
From Salmonella Typhimurium
pdb|3SLC|C Chain C, Crystal Structure Of Apo Form Of Acetate Kinase (Acka)
From Salmonella Typhimurium
pdb|3SLC|D Chain D, Crystal Structure Of Apo Form Of Acetate Kinase (Acka)
From Salmonella Typhimurium
Length = 415
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 20/42 (47%)
Query: 54 STILNLKCVDAQTGLMGKTLLEFQSTKGDVLPAHKFGTHDVV 95
S I N KCVD GL L + GD+ PA F HD +
Sbjct: 233 SAIRNGKCVDTSMGLTPLEGLVMGTRSGDIDPAIIFHLHDTL 274
>pdb|2ZXH|A Chain A, Structure Of Aquifex Aeolicus Gida In The Form I Crystal
pdb|2ZXH|B Chain B, Structure Of Aquifex Aeolicus Gida In The Form I Crystal
pdb|2ZXI|A Chain A, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
pdb|2ZXI|B Chain B, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
pdb|2ZXI|C Chain C, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
pdb|2ZXI|D Chain D, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
Length = 637
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 108 ALGQGVVY-RLKDSSITVAFDDIPEEGLNSPLRLEKLANEVT-YRRMKDALIQLSK 161
A G+ +Y R +S I V DD+ +G+ P RL +E Y R +A+++L+K
Sbjct: 422 AFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAK 477
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
0.315 0.131 0.356
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,336,535
Number of Sequences: 62578
Number of extensions: 626270
Number of successful extensions: 1616
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1569
Number of HSP's gapped (non-prelim): 20
length of query: 647
length of database: 14,973,337
effective HSP length: 105
effective length of query: 542
effective length of database: 8,402,647
effective search space: 4554234674
effective search space used: 4554234674
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)