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= 000698
(1345 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 183 bits (464), Expect = 6e-46, Method: Compositional matrix adjust.
Identities = 138/447 (30%), Positives = 220/447 (49%), Gaps = 66/447 (14%)
Query: 945 LNDDQRRAIIKVLTAKDYALILGMPGTGKTSTMVHAVKALLMRGASILLTSYTNSAVDNL 1004
L+ Q+ A++ L+ K+ A+I G PGTGKT+T+V + + +G +L + +N AVDNL
Sbjct: 190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNL 249
Query: 1005 LIKLKSQSIDFVRIGRHEVVHKEIQKHCLSAMNINS-----VEEIKKRLDQV-------- 1051
+ +L +R+G + + IQ+H L A+ S V +I+K +DQV
Sbjct: 250 VERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKTQ 309
Query: 1052 ----------------------------------KVVAVTCLGITN----PLLTDKKFDV 1073
VV T G + LL + FDV
Sbjct: 310 DKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYFDV 369
Query: 1074 CIMDEAGQTTLPVSLGPLMFASKFVLVGDHYQLPPLVQSTEARENGMEISLFRRLSEEH- 1132
++DE Q PL+ A K +L GDH QLPP S +A G+ +SL RL+EE+
Sbjct: 370 VVIDECAQALEASCWIPLLKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEEYG 429
Query: 1133 PQAISALQSQYRMCQGIMELSNALIYGDRLSCGSDEIANAKIKVSDLSSCSPWLKEALNP 1192
+ + L QYRM Q IM ++ +Y +L+ S + A+ + DL P +
Sbjct: 430 ARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHS---SVARHLLRDL----PGVAATEET 482
Query: 1193 CRPVIFVNTD--MLPAYEAKDHQTLNNPVEACLIAKITQELVKNEIEGKDIGIITPYNSQ 1250
P++ V+T L E +D Q+ NP E L++ Q LV + +DI +++PYN Q
Sbjct: 483 GVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQ 542
Query: 1251 ANLIRHSL--SVSSVEIHTIDKYQGRDKDCILVSFVRSSENPRNCTSSLLGDWHRINVAL 1308
+L+R SL +EI ++D +QGR+K+ +++SFVRS+ R L + RINVA+
Sbjct: 543 VDLLRQSLVHRHPELEIKSVDGFQGREKEAVILSFVRSN---RKGEVGFLAEDRRINVAV 599
Query: 1309 TRAKKKLIMVGSCRTLSKVPLLKLLIN 1335
TRA++ + ++ RT++ LK L+
Sbjct: 600 TRARRHVAVICDSRTVNNHAFLKTLVE 626
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 182 bits (463), Expect = 9e-46, Method: Compositional matrix adjust.
Identities = 137/447 (30%), Positives = 220/447 (49%), Gaps = 66/447 (14%)
Query: 945 LNDDQRRAIIKVLTAKDYALILGMPGTGKTSTMVHAVKALLMRGASILLTSYTNSAVDNL 1004
L+ Q+ A++ L+ K+ A+I G PGTGKT+T+V + + +G +L + +N AVDNL
Sbjct: 190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNL 249
Query: 1005 LIKLKSQSIDFVRIGRHEVVHKEIQKHCLSAMNINS-----VEEIKKRLDQV-------- 1051
+ +L +R+G + + IQ+H L A+ S V +I+K +DQV
Sbjct: 250 VERLALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKTQ 309
Query: 1052 ----------------------------------KVVAVTCLGITN----PLLTDKKFDV 1073
VV T G + LL + FDV
Sbjct: 310 DKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYFDV 369
Query: 1074 CIMDEAGQTTLPVSLGPLMFASKFVLVGDHYQLPPLVQSTEARENGMEISLFRRLSEEH- 1132
++DE Q PL+ A K +L GDH QLPP S +A G+ +SL RL+EE+
Sbjct: 370 VVIDECAQALEASCWIPLLKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEEYG 429
Query: 1133 PQAISALQSQYRMCQGIMELSNALIYGDRLSCGSDEIANAKIKVSDLSSCSPWLKEALNP 1192
+ + L QYRM Q IM ++ +Y +L+ S + A+ + DL P +
Sbjct: 430 ARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHS---SVARHLLRDL----PGVAATEET 482
Query: 1193 CRPVIFVNTDMLPAY--EAKDHQTLNNPVEACLIAKITQELVKNEIEGKDIGIITPYNSQ 1250
P++ V+T + E +D Q+ NP E L++ Q LV + +DI +++PYN Q
Sbjct: 483 GVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQ 542
Query: 1251 ANLIRHSL--SVSSVEIHTIDKYQGRDKDCILVSFVRSSENPRNCTSSLLGDWHRINVAL 1308
+L+R SL +EI ++D +QGR+K+ +++SFVRS+ R L + RINVA+
Sbjct: 543 VDLLRQSLVHRHPELEIKSVDGFQGREKEAVILSFVRSN---RKGEVGFLAEDRRINVAV 599
Query: 1309 TRAKKKLIMVGSCRTLSKVPLLKLLIN 1335
TRA++ + ++ RT++ LK L+
Sbjct: 600 TRARRHVAVICDSRTVNNHAFLKTLVE 626
>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 = 155 bits (392), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 139/441 (31%), Positives = 205/441 (46%), Gaps = 61/441 (13%)
Query: 945 LNDDQRRAIIKVLTAKDYALILGMPGTGKTSTMVHAVKALLMRG-ASILLTSYTNSAVDN 1003
LN Q A+ VL + +LI G PGTGKT T V L +G +L+ + +N AVD
Sbjct: 181 LNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQ 239
Query: 1004 LLIKLKSQSIDFVRI--GRHEVVHKEIQKHCL--SAMNINSVEEIKKRLDQVK------- 1052
L K+ + VR+ E + + L N++S+ E++K L Q+K
Sbjct: 240 LTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQK-LQQLKDETGELS 298
Query: 1053 -----------------------VVAVTCLGITNPLLTDKKFDVCIMDEAGQTTLPVSLG 1089
V+ TC+G +P L +F ++DE+ Q T P +
Sbjct: 299 SADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMV 358
Query: 1090 PLMFASK-FVLVGDHYQLPPLVQSTEARENGMEISLFRRLSEEHPQAISALQSQYRMCQG 1148
P++ +K +LVGDH QL P+V +A + G+ SLF RL + I LQ QYRM
Sbjct: 359 PVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIR-LQVQYRMHPA 417
Query: 1149 IMELSNALIYGDRLSCGSDEIANAKIKVSDLSSCSPWLKEALNPCRPVIFVNTDMLPAYE 1208
+ + + Y L G K K D W + P +P+ F T
Sbjct: 418 LSAFPSNIFYEGSLQNGVTAADRVK-KGFDFQ----WPQ----PDKPMFFYVTQGQEEIA 468
Query: 1209 AKDHQTLNNPVEACLIAKITQELVKNEIEGKDIGIITPYNSQANLIRHSLSVSS------ 1262
+ LN EA + KIT +L+K + IGIITPY Q + + + S
Sbjct: 469 SSGTSYLNR-TEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKL 527
Query: 1263 ---VEIHTIDKYQGRDKDCILVSFVRSSENPRNCTSSLLGDWHRINVALTRAKKKLIMVG 1319
VEI ++D +QGR+KD I++S VR++E+ L D R+NVALTRA+ +I+VG
Sbjct: 528 YQEVEIASVDAFQGREKDFIILSCVRANEHQ---GIGFLNDPRRLNVALTRARYGVIIVG 584
Query: 1320 SCRTLSKVPLLKLLINKVGEQ 1340
+ + LSK PL L+N EQ
Sbjct: 585 NPKALSKQPLWNHLLNYYKEQ 605
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 155 bits (392), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 139/441 (31%), Positives = 205/441 (46%), Gaps = 61/441 (13%)
Query: 945 LNDDQRRAIIKVLTAKDYALILGMPGTGKTSTMVHAVKALLMRG-ASILLTSYTNSAVDN 1003
LN Q A+ VL + +LI G PGTGKT T V L +G +L+ + +N AVD
Sbjct: 180 LNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQ 238
Query: 1004 LLIKLKSQSIDFVRI--GRHEVVHKEIQKHCL--SAMNINSVEEIKKRLDQVK------- 1052
L K+ + VR+ E + + L N++S+ E++K L Q+K
Sbjct: 239 LTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQK-LQQLKDETGELS 297
Query: 1053 -----------------------VVAVTCLGITNPLLTDKKFDVCIMDEAGQTTLPVSLG 1089
V+ TC+G +P L +F ++DE+ Q T P +
Sbjct: 298 SADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMV 357
Query: 1090 PLMFASK-FVLVGDHYQLPPLVQSTEARENGMEISLFRRLSEEHPQAISALQSQYRMCQG 1148
P++ +K +LVGDH QL P+V +A + G+ SLF RL + I LQ QYRM
Sbjct: 358 PVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIR-LQVQYRMHPA 416
Query: 1149 IMELSNALIYGDRLSCGSDEIANAKIKVSDLSSCSPWLKEALNPCRPVIFVNTDMLPAYE 1208
+ + + Y L G K K D W + P +P+ F T
Sbjct: 417 LSAFPSNIFYEGSLQNGVTAADRVK-KGFDFQ----WPQ----PDKPMFFYVTQGQEEIA 467
Query: 1209 AKDHQTLNNPVEACLIAKITQELVKNEIEGKDIGIITPYNSQANLIRHSLSVSS------ 1262
+ LN EA + KIT +L+K + IGIITPY Q + + + S
Sbjct: 468 SSGTSYLNR-TEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKL 526
Query: 1263 ---VEIHTIDKYQGRDKDCILVSFVRSSENPRNCTSSLLGDWHRINVALTRAKKKLIMVG 1319
VEI ++D +QGR+KD I++S VR++E+ L D R+NVALTRA+ +I+VG
Sbjct: 527 YQEVEIASVDAFQGREKDFIILSCVRANEHQ---GIGFLNDPRRLNVALTRARYGVIIVG 583
Query: 1320 SCRTLSKVPLLKLLINKVGEQ 1340
+ + LSK PL L+N EQ
Sbjct: 584 NPKALSKQPLWNHLLNYYKEQ 604
>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 = 155 bits (392), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 139/441 (31%), Positives = 205/441 (46%), Gaps = 61/441 (13%)
Query: 945 LNDDQRRAIIKVLTAKDYALILGMPGTGKTSTMVHAVKALLMRG-ASILLTSYTNSAVDN 1003
LN Q A+ VL + +LI G PGTGKT T V L +G +L+ + +N AVD
Sbjct: 357 LNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQ 415
Query: 1004 LLIKLKSQSIDFVRI--GRHEVVHKEIQKHCL--SAMNINSVEEIKKRLDQVK------- 1052
L K+ + VR+ E + + L N++S+ E++K L Q+K
Sbjct: 416 LTEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQK-LQQLKDETGELS 474
Query: 1053 -----------------------VVAVTCLGITNPLLTDKKFDVCIMDEAGQTTLPVSLG 1089
V+ TC+G +P L +F ++DE+ Q T P +
Sbjct: 475 SADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMV 534
Query: 1090 PLMFASK-FVLVGDHYQLPPLVQSTEARENGMEISLFRRLSEEHPQAISALQSQYRMCQG 1148
P++ +K +LVGDH QL P+V +A + G+ SLF RL + I LQ QYRM
Sbjct: 535 PVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIR-LQVQYRMHPA 593
Query: 1149 IMELSNALIYGDRLSCGSDEIANAKIKVSDLSSCSPWLKEALNPCRPVIFVNTDMLPAYE 1208
+ + + Y L G K K D W + P +P+ F T
Sbjct: 594 LSAFPSNIFYEGSLQNGVTAADRVK-KGFDFQ----WPQ----PDKPMFFYVTQGQEEIA 644
Query: 1209 AKDHQTLNNPVEACLIAKITQELVKNEIEGKDIGIITPYNSQANLIRHSLSVSS------ 1262
+ LN EA + KIT +L+K + IGIITPY Q + + + S
Sbjct: 645 SSGTSYLNR-TEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKL 703
Query: 1263 ---VEIHTIDKYQGRDKDCILVSFVRSSENPRNCTSSLLGDWHRINVALTRAKKKLIMVG 1319
VEI ++D +QGR+KD I++S VR++E+ L D R+NVALTRA+ +I+VG
Sbjct: 704 YQEVEIASVDAFQGREKDFIILSCVRANEHQ---GIGFLNDPRRLNVALTRARYGVIIVG 760
Query: 1320 SCRTLSKVPLLKLLINKVGEQ 1340
+ + LSK PL L+N EQ
Sbjct: 761 NPKALSKQPLWNHLLNYYKEQ 781
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 134 bits (338), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 128/439 (29%), Positives = 203/439 (46%), Gaps = 71/439 (16%)
Query: 945 LNDDQRRAIIKVLTAKDYALILGMPGTGKTSTMVHAVKAL-LMRGASILLTSYTNSAVDN 1003
LN Q A+ VL + +LI G PGTGKT T V L + IL+ + +N AVD+
Sbjct: 361 LNSSQSNAVSHVLQ-RPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDH 419
Query: 1004 LLIKLKSQSIDFVRI---------------GRHEVVHKEIQKHC------------LSAM 1036
L KL+ + VR+ H +V + + LSA
Sbjct: 420 LAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELKNLLKLKDEVGELSAS 479
Query: 1037 NINSVEEIKKR-----LDQVKVVAVTCLGITNPLLTDKKFDVCIMDEAGQTTLPVSLGPL 1091
+ ++ ++ L++ VV TC+G + L D KF ++DE+ Q + P L P+
Sbjct: 480 DTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRL-DTKFRTVLIDESTQASEPECLIPI 538
Query: 1092 MFASK-FVLVGDHYQLPPLVQSTEARENGMEISLFRRLSEEHPQAISALQSQYRMCQGIM 1150
+ +K +LVGDH QL P++ +A + G++ SLF RL I L+ QYRM +
Sbjct: 539 VKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISLGHVPIR-LEVQYRMNPYLS 597
Query: 1151 ELSNALIYGDRLSCG----SDEIANAKIKVSDLSSCSPWLKEALNPCR--PVIFVNTDML 1204
E + + Y L G + N+K PW P R P++F
Sbjct: 598 EFPSNMFYEGSLQNGVTIEQRTVPNSKF---------PW------PIRGIPMMFWANYGR 642
Query: 1205 PAYEAKDHQTLNNPVEACLIAKITQELVKNEIEGKDIGIITPYNSQANLIRHSLSVSS-- 1262
A LN +EA +I +L ++ ++ + IG+ITPY Q I + ++
Sbjct: 643 EEISANGTSFLNR-IEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGSL 701
Query: 1263 -------VEIHTIDKYQGRDKDCILVSFVRSSENPRNCTSSLLGDWHRINVALTRAKKKL 1315
VE+ ++D +QGR+KD I++S VR++E L D R+NV LTRAK L
Sbjct: 702 DKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQ---AIGFLRDPRRLNVGLTRAKYGL 758
Query: 1316 IMVGSCRTLSKVPLLKLLI 1334
+++G+ R+L++ L L+
Sbjct: 759 VILGNPRSLARNTLWNHLL 777
>pdb|3LFU|A Chain A, Crystal Structure Of E. Coli Uvrd
Length = 647
Score = 36.2 bits (82), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 12/119 (10%)
Query: 944 SLNDDQRRAIIKVLTAKDYALILGMPGTGKTSTMVHAVKALL----MRGASILLTSYTNS 999
SLND QR A V + L+L G+GKT +VH + L+ SI+ ++TN
Sbjct: 9 SLNDKQREA---VAAPRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNK 65
Query: 1000 AVDNL---LIKLKSQSIDFVRIGR-HEVVHKEIQKHCLSAMNINSVEEIKKRLDQVKVV 1054
A + + +L S + +G H + H+ ++ H + A N+ +I DQ++++
Sbjct: 66 AAAEMRHRIGQLMGTSQGGMWVGTFHGLAHRLLRAHHMDA-NLPQDFQILDSEDQLRLL 123
>pdb|2IS1|A Chain A, Crystal Structure Of Uvrd-Dna-So4 Complex
pdb|2IS1|B Chain B, Crystal Structure Of Uvrd-Dna-So4 Complex
pdb|2IS2|A Chain A, Crystal Structure Of Uvrd-Dna Binary Complex
pdb|2IS2|B Chain B, Crystal Structure Of Uvrd-Dna Binary Complex
pdb|2IS4|A Chain A, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
pdb|2IS4|B Chain B, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
pdb|2IS6|A Chain A, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
pdb|2IS6|B Chain B, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
Length = 680
Score = 36.2 bits (82), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 12/119 (10%)
Query: 944 SLNDDQRRAIIKVLTAKDYALILGMPGTGKTSTMVHAVKALL----MRGASILLTSYTNS 999
SLND QR A V + L+L G+GKT +VH + L+ SI+ ++TN
Sbjct: 9 SLNDKQREA---VAAPRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNK 65
Query: 1000 AVDNL---LIKLKSQSIDFVRIGR-HEVVHKEIQKHCLSAMNINSVEEIKKRLDQVKVV 1054
A + + +L S + +G H + H+ ++ H + A N+ +I DQ++++
Sbjct: 66 AAAEMRHRIGQLMGTSQGGMWVGTFHGLAHRLLRAHHMDA-NLPQDFQILDSEDQLRLL 123
>pdb|1UJ3|A Chain A, Crystal Structure Of A Humanized Fab Fragment Of Anti-
Tissue-Factor Antibody In Complex With Tissue Factor
Length = 215
Score = 34.3 bits (77), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 221 QQSPFRTPPSLSYYHDKLANGVACNGASDHLGLRHTKKV-LLQTYDFDDIHCL 272
QQ P + P SL YY LA+GV + G +T + LQ DF +CL
Sbjct: 37 QQKPEKAPKSLIYYATSLADGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCL 89
>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
Length = 1232
Score = 32.3 bits (72), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 18/23 (78%)
Query: 1304 INVALTRAKKKLIMVGSCRTLSK 1326
+ VALTRAK+KL ++GSC+ K
Sbjct: 867 LYVALTRAKEKLFLIGSCKDHQK 889
>pdb|1PG7|L Chain L, Murine 6a6 Fab In Complex With Humanized Anti-Tissue
Factor D3h44 Fab
pdb|1PG7|M Chain M, Murine 6a6 Fab In Complex With Humanized Anti-Tissue
Factor D3h44 Fab
Length = 213
Score = 32.0 bits (71), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 221 QQSPFRTPPSLSYYHDKLANGVACNGASDHLGLRHTKKV-LLQTYDFDDIHCL 272
QQ P + P L YY LA GV + G +T + LQ DF +CL
Sbjct: 37 QQKPGKAPKVLIYYATSLAEGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCL 89
>pdb|1JPS|L Chain L, Crystal Structure Of Tissue Factor In Complex With
Humanized Fab D3h44
pdb|1JPT|L Chain L, Crystal Structure Of Fab D3h44
Length = 214
Score = 31.6 bits (70), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 221 QQSPFRTPPSLSYYHDKLANGVACNGASDHLGLRHTKKV-LLQTYDFDDIHCL 272
QQ P + P L YY LA GV + G +T + LQ DF +CL
Sbjct: 37 QQKPGKAPKVLIYYATSLAEGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCL 89
>pdb|3CZX|A Chain A, The Crystal Structure Of The Putative N-Acetylmuramoyl-L-
Alanine Amidase From Neisseria Meningitidis
pdb|3CZX|B Chain B, The Crystal Structure Of The Putative N-Acetylmuramoyl-L-
Alanine Amidase From Neisseria Meningitidis
pdb|3CZX|C Chain C, The Crystal Structure Of The Putative N-Acetylmuramoyl-L-
Alanine Amidase From Neisseria Meningitidis
pdb|3CZX|D Chain D, The Crystal Structure Of The Putative N-Acetylmuramoyl-L-
Alanine Amidase From Neisseria Meningitidis
Length = 182
Score = 31.6 bits (70), Expect = 3.3, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 11/89 (12%)
Query: 925 DSGSVFSQDPALSYIWSEKSLNDDQRRAIIKVLTAKDYALILGMPGTGKTST-MVHAVKA 983
D G+V D E L D R + +L DY L + GTGK + + AVK
Sbjct: 16 DPGAVNGSD-------READLAQDXRNIVASILR-NDYGLTVKTDGTGKGNXPLRDAVK- 66
Query: 984 LLMRGASILLTSYTNSAVDNLLIKLKSQS 1012
L+RG+ + + +TN+A + +++ S
Sbjct: 67 -LIRGSDVAIEFHTNAAANKTATGIEALS 94
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
0.317 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 37,411,182
Number of Sequences: 62578
Number of extensions: 1508155
Number of successful extensions: 3543
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 3501
Number of HSP's gapped (non-prelim): 31
length of query: 1345
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1234
effective length of database: 8,027,179
effective search space: 9905538886
effective search space used: 9905538886
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: 57 (26.6 bits)