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= 009062
(545 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 = 215 bits (548), Expect = 5e-56, Method: Compositional matrix adjust.
Identities = 150/527 (28%), Positives = 253/527 (48%), Gaps = 49/527 (9%)
Query: 8 VLPAFSGNVPAALQNVFPSAKITQLGNWFSVKSDPRWCCTYLLDATDPLFIEIGRAFIEQ 67
VL +SG VP + A+ G W P TY+ + F ++ F E+
Sbjct: 381 VLQGYSGMVPRDFKEKNQEAQTISQGGWCGFDR-PDMLKTYVNEGEADYFQKVADVFYEK 439
Query: 68 QLKEYGRTSHIYNCDTFDE--NTPPVDSPEYISSLGAAIYSGMQSGDSDAVWLMQGWLFS 125
Q + +G ++ Y D F E NT +D+ + I + M D+DAVW++Q W +
Sbjct: 440 QKEVFGDVTNFYGVDPFHEGGNTGDLDN----GKIYEIIQNKMIEHDNDAVWVIQNWQGN 495
Query: 126 YDPFWRPPQMKALLNSVPLGKLVVLDLFAEVKPIWSTSKQFYGVPYIWCMLHNFAGNIEM 185
P L + +VLDLF+EV P W+ ++ +P+IW MLHNF G + M
Sbjct: 496 -------PSNNKLEGLTKKDQAMVLDLFSEVSPDWNRLEE-RDLPWIWNMLHNFGGRMGM 547
Query: 186 YGILDSIAFGPVEARTSENTTMVGVGMSMEGIEQNPVVYDLMSEMAFQHEKVDVKAWINQ 245
+ +A + + + MVG+G++ E I NP+ Y+L+ +MA+ ++++ + W
Sbjct: 548 DAAPEKLA-TEIPKALANSEHMVGIGITPEAINTNPLAYELLFDMAWTRDQINFRTWTED 606
Query: 246 YSVRRYGRSVPAIQDAWNVLYHTVYNCTDGATDKNRDVIVAFPDVDPSIISVTEGKYQNY 305
Y RRYG++ I +AWN++ T Y K D + SII+ G +
Sbjct: 607 YIERRYGKTNKEILEAWNIILDTAYK-------KRNDY---YQGAAESIINARPG----F 652
Query: 306 GKPVSKEAVLKSETSSYDHPHLWYSTSEVIRALELFIASGNELSASNTYRYDLIDLTRQA 365
G +KS S++ H + Y SE +A+E+F + +E S+ + YD D+ +Q
Sbjct: 653 G--------IKS-ASTWGHSKIVYDKSEFEKAIEIFAKNYDEFKDSDAFLYDFADILKQL 703
Query: 366 LAKYANELFLNIIEAYQLNDAHGVFQLSRRFLELVEDMDGLLACHDGFLLGPWLESAKQL 425
LA A E + + AY + +S +FLEL++ + +L+ FL+G W+E A+ +
Sbjct: 704 LANSAQEYYEVMCNAYNNGNGEKFKFVSGKFLELIKLQERVLSTRPEFLIGNWIEDARTM 763
Query: 426 AQNEEQ--EKQYEWNARTQITMWFDNTQEEASLLRDYGNKYWSGLLRDYYGPRAAIYFKY 483
++ + + +E+NAR +T W + L+DY N+ WSGL DYY R +
Sbjct: 764 LKDSDDWTKDLFEFNARALVTTWGSRNNADGGGLKDYSNRQWSGLTEDYYYARWEKWING 823
Query: 484 MIESLESGDGFRLKDWRREWIKLTNDWQNGRN----VYPVESNGDAL 526
+ L+ G K +W K+ DW N ++ +YP E++ + L
Sbjct: 824 LQAELDGG----AKAPNIDWFKMEYDWVNKKSDTDKLYPTEASNENL 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 = 213 bits (541), Expect = 3e-55, Method: Compositional matrix adjust.
Identities = 148/527 (28%), Positives = 253/527 (48%), Gaps = 49/527 (9%)
Query: 8 VLPAFSGNVPAALQNVFPSAKITQLGNWFSVKSDPRWCCTYLLDATDPLFIEIGRAFIEQ 67
VL +SG VP + A+ G W P TY+ + F ++ F E+
Sbjct: 404 VLQGYSGMVPRDFKEKNQEAQTISQGGWCGFDR-PDMLKTYVNEGEADYFQKVADVFYEK 462
Query: 68 QLKEYGRTSHIYNCDTFDE--NTPPVDSPEYISSLGAAIYSGMQSGDSDAVWLMQGWLFS 125
Q + +G ++ Y D F + NT +D+ + I + M D+DAVW++Q W +
Sbjct: 463 QKEVFGDVTNFYGVDPFHQGGNTGDLDN----GKIYEIIQNKMIEHDNDAVWVIQNWQGN 518
Query: 126 YDPFWRPPQMKALLNSVPLGKLVVLDLFAEVKPIWSTSKQFYGVPYIWCMLHNFAGNIEM 185
P L + +VLDLF+EV P W+ ++ +P+IW MLHNF G + M
Sbjct: 519 -------PSNNKLEGLTKKDQAMVLDLFSEVSPDWNRLEE-RDLPWIWNMLHNFGGRMGM 570
Query: 186 YGILDSIAFGPVEARTSENTTMVGVGMSMEGIEQNPVVYDLMSEMAFQHEKVDVKAWINQ 245
+ +A + + + MVG+G++ + I NP+ Y+L+ +MA+ ++++ + W
Sbjct: 571 DAAPEKLA-TEIPKALANSEHMVGIGITPQAINTNPLAYELLFDMAWTRDQINFRTWTED 629
Query: 246 YSVRRYGRSVPAIQDAWNVLYHTVYNCTDGATDKNRDVIVAFPDVDPSIISVTEGKYQNY 305
Y RRYG++ I +AWN++ T Y K D + SII+ G +
Sbjct: 630 YIERRYGKTNKEILEAWNIILDTAYK-------KRNDY---YQGAAESIINARPG----F 675
Query: 306 GKPVSKEAVLKSETSSYDHPHLWYSTSEVIRALELFIASGNELSASNTYRYDLIDLTRQA 365
G +KS S++ H + Y SE +A+E+F + +E S+ + YD D+ +Q
Sbjct: 676 G--------IKS-ASTWGHSKIVYDKSEFEKAIEIFAKNYDEFKDSDAFLYDFADILKQL 726
Query: 366 LAKYANELFLNIIEAYQLNDAHGVFQLSRRFLELVEDMDGLLACHDGFLLGPWLESAKQL 425
LA A E + + AY + +S +FLEL++ + +L+ FL+G W+E A+ +
Sbjct: 727 LANSAQEYYEVMCNAYNNGNGEKFKFVSGKFLELIKLQERVLSTRPEFLIGNWIEDARTM 786
Query: 426 AQNEEQ--EKQYEWNARTQITMWFDNTQEEASLLRDYGNKYWSGLLRDYYGPRAAIYFKY 483
++ + + +E+NAR +T W + L+DY N+ WSGL DYY R +
Sbjct: 787 LKDSDDWTKDLFEFNARALVTTWGSRNNADGGGLKDYSNRQWSGLTEDYYYARWEKWING 846
Query: 484 MIESLESGDGFRLKDWRREWIKLTNDWQNGRN----VYPVESNGDAL 526
+ L+ G K +W K+ DW N ++ +YP E++ + L
Sbjct: 847 LQAELDGG----AKAPNIDWFKMEYDWVNKKSDTDKLYPTEASNENL 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 = 1.4, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 57 FIEIGRAFIEQQLKEYGRTSHIYNCDTFDENTPPVDSPEYI 97
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 = 2.0, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 72 YGRTSHIYNCDTFDENTPPVDSPEYISSLGAAIYSGMQSGDSDA 115
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 = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 72 YGRTSHIYNCDTFDENTPPVDSPEYISSLGAAIYSGMQSGDSDA 115
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 = 3.4, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 14 GNVPAALQNVFPSAKITQLGNWFSVKSDPRWCCTYLLDATDPL 56
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 = 3.9, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 313 AVLKSETSSYDHPHLWYSTSEVIRALELFIASGNELSASNTYRYDLIDLTRQALAK 368
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 = 7.3, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 363 RQALAKYANELFLNIIEAYQLNDAHGVFQLSRRFLELVEDMDGLLACHDGFLLGPWLESA 422
R Y E ++ +I+ Y LN+A F L F+EL +D + + +G L L
Sbjct: 226 RNGFQAYLREKYVPLIQKY-LNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGG 284
Query: 423 KQLA 426
+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 0.135 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,548,712
Number of Sequences: 62578
Number of extensions: 763554
Number of successful extensions: 1874
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1855
Number of HSP's gapped (non-prelim): 11
length of query: 545
length of database: 14,973,337
effective HSP length: 104
effective length of query: 441
effective length of database: 8,465,225
effective search space: 3733164225
effective search space used: 3733164225
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)