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= 001266
(1112 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1MIU|A Chain A, Structure Of A Brca2-dss1 Complex
Length = 738
Score = 224 bits (570), Expect = 3e-58, Method: Compositional matrix adjust.
Identities = 160/478 (33%), Positives = 239/478 (50%), Gaps = 41/478 (8%)
Query: 514 GAEALFNMLAQS-GASTQYASKLWVSNHYKWIVWKLACYERCYLAKSAGKFLTVFNVLEE 572
G E + L + G + S +WV+NHY+WIVWKLA E + + A + L VL +
Sbjct: 140 GKEEFYRALCDTPGVDPKLISSIWVANHYRWIVWKLAAMEFAFPKEFANRCLNPERVLLQ 199
Query: 573 LKYRYEREVNNGHRSAIKRILEGDALPSSMMVLCISAIHMNCVPKIETHPEAQNGAENSY 632
LKYRY+ E++N RSA+K+ILE D + +VLCIS I ET +G + +
Sbjct: 200 LKYRYDVEIDNSRRSALKKILERDDTAAKTLVLCISDIISPSTKVSETSGGKTSGEDANK 259
Query: 633 AAKLELTDGWYSVDAFLDVLLSKHLAAGKLFVGQKLRIWGAILCGWVGPVSPLEASGSIS 692
+ELTDGWY+V A LD L + +GKL VGQK+ GA L G +PLEA S+
Sbjct: 260 VDTIELTDGWYAVRAQLDPPLMALVKSGKLTVGQKIITQGAELVGSPDACAPLEAPDSLR 319
Query: 693 LQLNINGTYRAHWADRLGFCKGFGA-PLAFRCIKSNGGPVPRTLVGVTRIYPVLYKERLS 751
L+++ N T A W RLGF + PL + S+GG V + V R+YP+ + E+
Sbjct: 320 LKISANSTRPARWHSRLGFFRDPRPFPLPLSSLFSDGGNVGCVDIIVQRVYPLQWVEKTV 379
Query: 752 DGRSIVRSERMECKVMQLYQHRQSMVVEGIV----SEFQRGNKDS--------------- 792
G I RSER E K + Q +E + +EF+ +D+
Sbjct: 380 SGLYIFRSEREEEKEALRFAEAQQKKLEALFTKVHTEFKDHEEDTTQRCVLSRTLTRQQV 439
Query: 793 HILNDSNSEGAKLFKMLETVAEPEVIMAEMSPEQLTSFATYQAKLEATRQSNMERSIEKA 852
H L D GA+L+ ++ ++P+ + A S EQL + Y+ L +Q+ ++ KA
Sbjct: 440 HALQD----GAELYAAVQYASDPDHLEACFSEEQLRALNNYRQMLNDKKQARIQSEFRKA 495
Query: 853 LENAGLRE---RDVTPFMRVRVVGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAY 909
LE+A E RDVT ++RV +Y+ K S +++IW P+ L EG+ Y
Sbjct: 496 LESAEKEEGLSRDVTTVWKLRVT-----SYKKKEKS--ALLSIWRPSSDLSSLLTEGKRY 548
Query: 910 AILGLIPMNSDSN----TLYLQARGSTTKWQPLSPLATEHFKPFFSPRRSVLISNLGE 963
I L S S ++ L A T++Q L P+++E + PR S+ S L +
Sbjct: 549 RIYHLAVSKSKSKFERPSIQLTA-TKRTQYQQL-PVSSETLLQVYQPRESLHFSRLSD 604
>pdb|1IYJ|B Chain B, Structure Of A Brca2-Dss1 Complex
pdb|1IYJ|D Chain D, Structure Of A Brca2-Dss1 Complex
Length = 817
Score = 211 bits (538), Expect = 1e-54, Method: Compositional matrix adjust.
Identities = 151/477 (31%), Positives = 229/477 (48%), Gaps = 39/477 (8%)
Query: 514 GAEALFNMLAQS-GASTQYASKLWVSNHYKWIVWKLACYERCYLAKSAGKFLTVFNVLEE 572
G E + L + G + S +WVSNHY+WIVWKLA E + + A + L VL +
Sbjct: 192 GKEEFYRALCDTPGVDPKLISSVWVSNHYRWIVWKLAAMEFAFPKEFANRCLNPERVLLQ 251
Query: 573 LKYRYEREVNNGHRSAIKRILEGDALPSSMMVLCISAIHMNCVPKIETHPEAQNGAENSY 632
LKYRY+ E++N RSA+K+ILE D + +VLC+S I ET + +++
Sbjct: 252 LKYRYDVEIDNSSRSALKKILERDDTAAKTLVLCVSDIISLSTNVSETSGSKASSEDSNK 311
Query: 633 AAKLELTDGWYSVDAFLDVLLSKHLAAGKLFVGQKLRIWGAILCGWVGPVSPLEASGSIS 692
+ELTDGWY+V A LD L + +G+L VGQK+ GA L G +PLEA S+
Sbjct: 312 VDTIELTDGWYAVKAQLDPPLLALVKSGRLTVGQKIITQGAELVGSPDACAPLEAPDSLR 371
Query: 693 LQLNINGTYRAHWADRLGFCKGFGA-PLAFRCIKSNGGPVPRTLVGVTRIYPVLYKERLS 751
L+++ N T A W +LGF PL + S+GG V V V R+YP+ + E+
Sbjct: 372 LKISANSTRPARWHSKLGFFHDPRPFPLPLSSLFSDGGNVGCVDVIVQRVYPLQWVEKTV 431
Query: 752 DGRSIVRSERMECKVMQLYQHRQSMVVEGIV----SEFQRGNKD---------------S 792
G I R+ER E K + Q +E + +E + +D
Sbjct: 432 SGSYIFRNEREEEKEALRFAEAQQKKLEALFTKVHTELKEHEEDIAQRRVLSRALTRQQV 491
Query: 793 HILNDSNSEGAKLFKMLETVAEPEVIMAEMSPEQLTSFATYQAKLEATRQSNMERSIEKA 852
H L D GA+L+ ++ ++PE + S EQL + Y+ L +Q+ ++ KA
Sbjct: 492 HALQD----GAELYAAVQDASDPEHLETCFSEEQLRALNNYRQMLSDKKQARIQSEFRKA 547
Query: 853 LENAGLRE---RDVTPFMRVRVVGLTGKNYQGKGSSREGIITIWNPAEKQQCELVEGQAY 909
LE A E RDV+ ++RV K + +++IW P+ L EGQ Y
Sbjct: 548 LEAAEKEEGLSRDVSTVWKLRVTSY-------KKREKSALLSIWRPSSDLPSLLTEGQRY 600
Query: 910 AILGLIPMNSDSNTLYLQARGSTTK---WQPLSPLATEHFKPFFSPRRSVLISNLGE 963
I L S + + + + TK +Q L P+++E + PR + S L +
Sbjct: 601 RIYHLSVSKSKNKFEWPSIQLTATKRTQYQQL-PVSSETLLQLYQPRELLPFSKLSD 656
>pdb|1MJE|A Chain A, Structure Of A Brca2-Dss1-Ssdna Complex
Length = 649
Score = 173 bits (438), Expect = 5e-43, Method: Compositional matrix adjust.
Identities = 104/273 (38%), Positives = 147/273 (53%), Gaps = 2/273 (0%)
Query: 514 GAEALFNMLAQS-GASTQYASKLWVSNHYKWIVWKLACYERCYLAKSAGKFLTVFNVLEE 572
G E + L + G + S +WV+NHY+WIVWKLA E + + A + L VL +
Sbjct: 140 GKEEFYRALCDTPGVDPKLISSIWVANHYRWIVWKLAAMEFAFPKEFANRCLNPERVLLQ 199
Query: 573 LKYRYEREVNNGHRSAIKRILEGDALPSSMMVLCISAIHMNCVPKIETHPEAQNGAENSY 632
LKYRY+ E++N RSA+K+ILE D + +VLCIS I ET +G + +
Sbjct: 200 LKYRYDVEIDNSRRSALKKILERDDTAAKTLVLCISDIISPSTKVSETSGGKTSGEDANK 259
Query: 633 AAKLELTDGWYSVDAFLDVLLSKHLAAGKLFVGQKLRIWGAILCGWVGPVSPLEASGSIS 692
+ELTDGWY+V A LD L + +GKL VGQK+ GA L G +PLEA S+
Sbjct: 260 VDTIELTDGWYAVRAQLDPPLMALVKSGKLTVGQKIITQGAELVGSPDACAPLEAPDSLR 319
Query: 693 LQLNINGTYRAHWADRLGFCKGFGA-PLAFRCIKSNGGPVPRTLVGVTRIYPVLYKERLS 751
L+++ N T A W RLGF + PL + S+GG V + V R+YP+ + E+
Sbjct: 320 LKISANSTRPARWHSRLGFFRDPRPFPLPLSSLFSDGGNVGCVDIIVQRVYPLQWVEKTV 379
Query: 752 DGRSIVRSERMECKVMQLYQHRQSMVVEGIVSE 784
G I RSER E K + Q +E + ++
Sbjct: 380 SGLYIFRSEREEEKEALRFAEAQQKKLEALFTK 412
>pdb|3YPI|A Chain A, Electrophilic Catalysis In Triosephosphase Isomerase: The
Role Of Histidine-95
pdb|3YPI|B Chain B, Electrophilic Catalysis In Triosephosphase Isomerase: The
Role Of Histidine-95
Length = 247
Score = 31.6 bits (70), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 583 NGHRSAIKRILE---GDALPSSM-MVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLEL 638
NG + +IK I+E ++P ++ +V+C A +++ + P+ GA+N+Y
Sbjct: 13 NGSKQSIKEIVERLNTASIPENVEVVICPPATYLDYSVSLVKKPQVTVGAQNAYLKASGA 72
Query: 639 TDGWYSVDAFLDV 651
G SVD DV
Sbjct: 73 FTGENSVDQIKDV 85
>pdb|1I45|A Chain A, Yeast Triosephosphate Isomerase (Mutant)
pdb|1I45|B Chain B, Yeast Triosephosphate Isomerase (Mutant)
Length = 248
Score = 31.6 bits (70), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 583 NGHRSAIKRILE---GDALPSSM-MVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLEL 638
NG + +IK I+E ++P ++ +V+C A +++ + P+ GA+N+Y
Sbjct: 14 NGSKQSIKEIVERLNTASIPENVEVVICPPATYLDYSVSLVKKPQVTVGAQNAYLKASGA 73
Query: 639 TDGWYSVDAFLDV 651
G SVD DV
Sbjct: 74 FTGENSVDQIKDV 86
>pdb|1YPI|A Chain A, Structure Of Yeast Triosephosphate Isomerase At 1.9-
Angstroms Resolution
pdb|1YPI|B Chain B, Structure Of Yeast Triosephosphate Isomerase At 1.9-
Angstroms Resolution
pdb|2YPI|A Chain A, Crystallographic Analysis Of The Complex Between
Triosephosphate Isomerase And 2-Phosphoglycolate At 2.5-
Angstroms Resolution. Implications For Catalysis
pdb|2YPI|B Chain B, Crystallographic Analysis Of The Complex Between
Triosephosphate Isomerase And 2-Phosphoglycolate At 2.5-
Angstroms Resolution. Implications For Catalysis
pdb|7TIM|A Chain A, Structure Of The Triosephosphate Isomerase-
Phosphoglycolohydroxamate Complex: An Analogue Of The
Intermediate On The Reaction Pathway
pdb|7TIM|B Chain B, Structure Of The Triosephosphate Isomerase-
Phosphoglycolohydroxamate Complex: An Analogue Of The
Intermediate On The Reaction Pathway
Length = 247
Score = 31.2 bits (69), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 583 NGHRSAIKRILE---GDALPSSM-MVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLEL 638
NG + +IK I+E ++P ++ +V+C A +++ + P+ GA+N+Y
Sbjct: 13 NGSKQSIKEIVERLNTASIPENVEVVICPPATYLDYSVSLVKKPQVTVGAQNAYLKASGA 72
Query: 639 TDGWYSVDAFLDV 651
G SVD DV
Sbjct: 73 FTGENSVDQIKDV 85
>pdb|4FF7|A Chain A, Structure Of C126s Mutant Of Saccharomyces Cerevisiae
Triosephosphate Isomerase
pdb|4FF7|B Chain B, Structure Of C126s Mutant Of Saccharomyces Cerevisiae
Triosephosphate Isomerase
Length = 248
Score = 31.2 bits (69), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 583 NGHRSAIKRILE---GDALPSSM-MVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLEL 638
NG + +IK I+E ++P ++ +V+C A +++ + P+ GA+N+Y
Sbjct: 14 NGSKQSIKEIVERLNTASIPENVEVVICPPATYLDYSVSLVKKPQVTVGAQNAYLKASGA 73
Query: 639 TDGWYSVDAFLDV 651
G SVD DV
Sbjct: 74 FTGENSVDQIKDV 86
>pdb|1NF0|A Chain A, Triosephosphate Isomerase In Complex With Dhap
pdb|1NF0|B Chain B, Triosephosphate Isomerase In Complex With Dhap
pdb|1NEY|A Chain A, Triosephosphate Isomerase In Complex With Dhap
pdb|1NEY|B Chain B, Triosephosphate Isomerase In Complex With Dhap
Length = 247
Score = 31.2 bits (69), Expect = 3.8, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 583 NGHRSAIKRILE---GDALPSSM-MVLCISAIHMNCVPKIETHPEAQNGAENSYAAKLEL 638
NG + +IK I+E ++P ++ +V+C A +++ + P+ GA+N+Y
Sbjct: 13 NGSKQSIKEIVERLNTASIPENVEVVICPPATYLDYSVSLVKKPQVTVGAQNAYLKASGA 72
Query: 639 TDGWYSVDAFLDV 651
G SVD DV
Sbjct: 73 FTGENSVDQIKDV 85
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
0.316 0.131 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,424,931
Number of Sequences: 62578
Number of extensions: 1350435
Number of successful extensions: 2917
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2900
Number of HSP's gapped (non-prelim): 20
length of query: 1112
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1003
effective length of database: 8,152,335
effective search space: 8176792005
effective search space used: 8176792005
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: 57 (26.6 bits)