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= 008173
(575 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VC9|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
In Complex With 2-Acetamido-1,2-Dideoxynojirmycin
pdb|2VCA|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
In Complex With Beta-N-Acetyl-D-Glucosamine
pdb|2VCB|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
In Complex With Pugnac
pdb|2VCC|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
Length = 891
Score = 253 bits (646), Expect = 2e-67, Method: Compositional matrix adjust.
Identities = 166/564 (29%), Positives = 277/564 (49%), Gaps = 49/564 (8%)
Query: 1 MSNLHGWGGPLPQSWLDQQLVLQKKILVRIYELGMNPVLPAFSGNVPAALQNVFPSAKIT 60
M N+ G+GGPLP W +Q+ L +K+ R+ G+NPVL +SG VP + A+
Sbjct: 344 MQNMTGFGGPLPNDWFEQRAELGRKMHDRMQSFGINPVLQGYSGMVPRDFKEKNQEAQTI 403
Query: 61 QLGNWFSVKSDPRWCCTYLLDATDPLFIEIGRAFIEQQLKEYGRTSHIYNCDTFDE--NT 118
G W P TY+ + F ++ F E+Q + +G ++ Y D F E NT
Sbjct: 404 SQGGWCGFDR-PDMLKTYVNEGEADYFQKVADVFYEKQKEVFGDVTNFYGVDPFHEGGNT 462
Query: 119 PPVDSPEYISSLGAAIYSGMQSGDSDAVWLMQGWLFSYDPFWRPPQMKALLNSVPLGKLV 178
+D+ + I + M D+DAVW++Q W + P L + +
Sbjct: 463 GDLDN----GKIYEIIQNKMIEHDNDAVWVIQNWQGN-------PSNNKLEGLTKKDQAM 511
Query: 179 VLDLFAEVKPIWSTSKQFYGVPYIWCMLHNFAGNIEMYGILDSIAFGPVEARTSENTTMV 238
VLDLF+EV P W+ ++ +P+IW MLHNF G + M + +A + + + MV
Sbjct: 512 VLDLFSEVSPDWNRLEE-RDLPWIWNMLHNFGGRMGMDAAPEKLA-TEIPKALANSEHMV 569
Query: 239 GVGMSMEGIEQNPVVYDLMSEMAFQHEKVDVKAWINQYSVRRYGRSVPAIQDAWNVLYHT 298
G+G++ E I NP+ Y+L+ +MA+ ++++ + W Y RRYG++ I +AWN++ T
Sbjct: 570 GIGITPEAINTNPLAYELLFDMAWTRDQINFRTWTEDYIERRYGKTNKEILEAWNIILDT 629
Query: 299 VYNCTDGATDKNRDVIVAFPDVDPSIISVTEGKYQNYGKPVSKEAVLKSETSSYDHPHLW 358
Y K D + SII+ G +G +KS S++ H +
Sbjct: 630 AYK-------KRNDY---YQGAAESIINARPG----FG--------IKS-ASTWGHSKIV 666
Query: 359 YSTSEVIRALELFIASGNELSASNTYRYDLIDLTRQALAKYANELFLNIIEAYQLNDAHG 418
Y SE +A+E+F + +E S+ + YD D+ +Q LA A E + + AY +
Sbjct: 667 YDKSEFEKAIEIFAKNYDEFKDSDAFLYDFADILKQLLANSAQEYYEVMCNAYNNGNGEK 726
Query: 419 VFQLSRRFLELVEDMDGLLACHDGFLLGPWLESAKQLAQNEEQ--EKQYEWNARTQITMW 476
+S +FLEL++ + +L+ FL+G W+E A+ + ++ + + +E+NAR +T W
Sbjct: 727 FKFVSGKFLELIKLQERVLSTRPEFLIGNWIEDARTMLKDSDDWTKDLFEFNARALVTTW 786
Query: 477 FDNTQEEASLLRDYGNKYWSGLLRDYYGPRAAIYFKYMIESLESGDGFRLKDWRREWIKL 536
+ L+DY N+ WSGL DYY R + + L+ G K +W K+
Sbjct: 787 GSRNNADGGGLKDYSNRQWSGLTEDYYYARWEKWINGLQAELDGG----AKAPNIDWFKM 842
Query: 537 TNDWQNGRN----VYPVESNGDAL 556
DW N ++ +YP E++ + L
Sbjct: 843 EYDWVNKKSDTDKLYPTEASNENL 866
>pdb|4A4A|A Chain A, Cpgh89 (E483q, E601q), From Clostridium Perfringens, In
Complex With Its Substrate Glcnac-Alpha-1,4-Galactose
Length = 914
Score = 250 bits (638), Expect = 2e-66, Method: Compositional matrix adjust.
Identities = 164/564 (29%), Positives = 277/564 (49%), Gaps = 49/564 (8%)
Query: 1 MSNLHGWGGPLPQSWLDQQLVLQKKILVRIYELGMNPVLPAFSGNVPAALQNVFPSAKIT 60
M N+ G+GGPLP W +Q+ L +K+ R+ G+NPVL +SG VP + A+
Sbjct: 367 MQNMTGFGGPLPNDWFEQRAELGRKMHDRMQSFGINPVLQGYSGMVPRDFKEKNQEAQTI 426
Query: 61 QLGNWFSVKSDPRWCCTYLLDATDPLFIEIGRAFIEQQLKEYGRTSHIYNCDTFDE--NT 118
G W P TY+ + F ++ F E+Q + +G ++ Y D F + NT
Sbjct: 427 SQGGWCGFDR-PDMLKTYVNEGEADYFQKVADVFYEKQKEVFGDVTNFYGVDPFHQGGNT 485
Query: 119 PPVDSPEYISSLGAAIYSGMQSGDSDAVWLMQGWLFSYDPFWRPPQMKALLNSVPLGKLV 178
+D+ + I + M D+DAVW++Q W + P L + +
Sbjct: 486 GDLDN----GKIYEIIQNKMIEHDNDAVWVIQNWQGN-------PSNNKLEGLTKKDQAM 534
Query: 179 VLDLFAEVKPIWSTSKQFYGVPYIWCMLHNFAGNIEMYGILDSIAFGPVEARTSENTTMV 238
VLDLF+EV P W+ ++ +P+IW MLHNF G + M + +A + + + MV
Sbjct: 535 VLDLFSEVSPDWNRLEE-RDLPWIWNMLHNFGGRMGMDAAPEKLA-TEIPKALANSEHMV 592
Query: 239 GVGMSMEGIEQNPVVYDLMSEMAFQHEKVDVKAWINQYSVRRYGRSVPAIQDAWNVLYHT 298
G+G++ + I NP+ Y+L+ +MA+ ++++ + W Y RRYG++ I +AWN++ T
Sbjct: 593 GIGITPQAINTNPLAYELLFDMAWTRDQINFRTWTEDYIERRYGKTNKEILEAWNIILDT 652
Query: 299 VYNCTDGATDKNRDVIVAFPDVDPSIISVTEGKYQNYGKPVSKEAVLKSETSSYDHPHLW 358
Y K D + SII+ G +G +KS S++ H +
Sbjct: 653 AYK-------KRNDY---YQGAAESIINARPG----FG--------IKS-ASTWGHSKIV 689
Query: 359 YSTSEVIRALELFIASGNELSASNTYRYDLIDLTRQALAKYANELFLNIIEAYQLNDAHG 418
Y SE +A+E+F + +E S+ + YD D+ +Q LA A E + + AY +
Sbjct: 690 YDKSEFEKAIEIFAKNYDEFKDSDAFLYDFADILKQLLANSAQEYYEVMCNAYNNGNGEK 749
Query: 419 VFQLSRRFLELVEDMDGLLACHDGFLLGPWLESAKQLAQNEEQ--EKQYEWNARTQITMW 476
+S +FLEL++ + +L+ FL+G W+E A+ + ++ + + +E+NAR +T W
Sbjct: 750 FKFVSGKFLELIKLQERVLSTRPEFLIGNWIEDARTMLKDSDDWTKDLFEFNARALVTTW 809
Query: 477 FDNTQEEASLLRDYGNKYWSGLLRDYYGPRAAIYFKYMIESLESGDGFRLKDWRREWIKL 536
+ L+DY N+ WSGL DYY R + + L+ G K +W K+
Sbjct: 810 GSRNNADGGGLKDYSNRQWSGLTEDYYYARWEKWINGLQAELDGG----AKAPNIDWFKM 865
Query: 537 TNDWQNGRN----VYPVESNGDAL 556
DW N ++ +YP E++ + L
Sbjct: 866 EYDWVNKKSDTDKLYPTEASNENL 889
>pdb|3IZR|N Chain N, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 134
Score = 31.2 bits (69), Expect = 1.5, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 87 FIEIGRAFIEQQLKEYGRTSHIYNCDTFDENTPPVDSPEYI 127
F+EIGR + K+YGR I D D+N VD+P+ +
Sbjct: 6 FVEIGRVALVNYGKDYGRLVVI--VDVVDQNRALVDAPDMV 44
>pdb|2Z13|A Chain A, Crystal Structure Of The N-Terminal Duf1126 In Human Ef-
Hand Domain
Length = 133
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 102 YGRTSHIYNCDTFDENTPPVDSPEYISSLGAAIYSGMQSGDSDA 145
YGRT IY+CD F N ++ +G + +QSG S
Sbjct: 98 YGRTFKIYDCDAFTRN--------FLRKMGVKVNPPVQSGPSSG 133
>pdb|2Z14|A Chain A, Crystal Structure Of The N-Terminal Duf1126 In Human Ef-
Hand Domain Containing 2 Protein
Length = 133
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 102 YGRTSHIYNCDTFDENTPPVDSPEYISSLGAAIYSGMQSGDSDA 145
YGRT IY+CD F N ++ +G + +QSG S
Sbjct: 98 YGRTFKIYDCDAFTRN--------FLRKIGVKVNPPVQSGPSSG 133
>pdb|1YR2|A Chain A, Structural And Mechanistic Analysis Of Two Prolyl
Endopeptidases: Role Of Inter-Domain Dynamics In
Catalysis And Specificity
Length = 741
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 44 GNVPAALQNVFPSAKITQLGNWFSVKSDPRWCCTYLLDATDPL 86
G +A Q VF + ++ + G+ SV SD RW + TDP+
Sbjct: 251 GTPQSADQPVFATPELPKRGHGASVSSDGRWVVITSSEGTDPV 293
>pdb|1L1J|A Chain A, Crystal Structure Of The Protease Domain Of An Atp-
Independent Heat Shock Protease Htra
pdb|1L1J|B Chain B, Crystal Structure Of The Protease Domain Of An Atp-
Independent Heat Shock Protease Htra
Length = 239
Score = 29.6 bits (65), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 343 AVLKSETSSYDHPHLWYSTSEVIRALELFIASGNELSASNTYRYDLIDLTRQALAK 398
AV+K + S P+L + S+ ++ E IA GN L +T ++ T + + K
Sbjct: 106 AVIKIKASDKKFPYLEFGDSDKVKIGEWAIAIGNPLGFQHTVTVGVVSATNRRIPK 161
>pdb|3AUX|A Chain A, Crystal Structure Of Rad50 Bound To Adp
pdb|3AUY|A Chain A, Crystal Structure Of Rad50 Bound To Adp
pdb|3AUY|B Chain B, Crystal Structure Of Rad50 Bound To Adp
pdb|3AV0|B Chain B, Crystal Structure Of Mre11-Rad50 Bound To Atp S
Length = 371
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 393 RQALAKYANELFLNIIEAYQLNDAHGVFQLSRRFLELVEDMDGLLACHDGFLLGPWLESA 452
R Y E ++ +I+ Y LN+A F L F+EL +D + + +G L L
Sbjct: 226 RNGFQAYLREKYVPLIQKY-LNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGG 284
Query: 453 KQLA 456
+Q+A
Sbjct: 285 EQIA 288
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
0.319 0.136 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,694,966
Number of Sequences: 62578
Number of extensions: 815789
Number of successful extensions: 1954
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1934
Number of HSP's gapped (non-prelim): 10
length of query: 575
length of database: 14,973,337
effective HSP length: 104
effective length of query: 471
effective length of database: 8,465,225
effective search space: 3987120975
effective search space used: 3987120975
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)