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= 019836
(335 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NPE|A Chain A, Structure Of Vp14 In Complex With Oxygen
Length = 529
Score = 209 bits (532), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 121/339 (35%), Positives = 185/339 (54%), Gaps = 29/339 (8%)
Query: 3 DYDKRLNHPFTAHPKIDPYTDEMFTFGYTQTP-PYVTYRVISKDGFMHDPVPITMSAPIM 61
D+D +L AHPK+DP T E+ Y PY+ Y DG D V I + P M
Sbjct: 211 DFDGQLGCAMIAHPKLDPATGELHALSYDVIKRPYLKYFYFRPDGTKSDDVEIPLEQPTM 270
Query: 62 MHDFAITENYAIFLDLPMCFRQKEMVKENKLIYAFDPTIKARFGVLPRYARDDLQIRWFE 121
+HDFAITEN + D + F+ +EM++ + D +RFGVLP++A D ++ W +
Sbjct: 271 IHDFAITENLVVVPDHQVVFKLQEMLRGGSPV-VLDAAKTSRFGVLPKHAADASEMAWVD 329
Query: 122 LPNCYIFHNANAWEEEEDEVVLITCRVRNPDLDMFNGPLKETLEDQTTELYEMRFNMKTG 181
+P+C+ FH NAWE+E V++ P +FN E+ E + L E+R + +TG
Sbjct: 330 VPDCFCFHLWNAWEDEATGEVVVIGSCMTPADSIFN----ESDERLESVLTEIRLDARTG 385
Query: 182 LASQKKLSPAC----VDFPRINEHYMGRKQRYVYGSILENIAKVTGMIKFDLRAEPETGK 237
++++ + P ++ +N + +GR+ RY Y ++ E KV+G K DL TG+
Sbjct: 386 RSTRRAVLPPSQQVNLEVGMVNRNLLGRETRYAYLAVAEPWPKVSGFAKVDL----STGE 441
Query: 238 -TKLEVGGNVKGIFDLGPGRFGSEAVFVPREPSST--SEEDDGYLIFHVHDENTGKSAVY 294
TK F+ G GRFG E FVP +P++ EDDGY++ VHDE G S +
Sbjct: 442 LTK----------FEYGEGRFGGEPCFVPMDPAAAHPRGEDDGYVLTFVHDERAGTSELL 491
Query: 295 VIDAKTMSADPVAVIELPHRVPYGFHGIFLSEEQLEELA 333
V++A M + A ++LP RVP+GFHG F++ ++LE A
Sbjct: 492 VVNAADMRLE--ATVQLPSRVPFGFHGTFITGQELEAQA 528
>pdb|2BIW|A Chain A, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIW|B Chain B, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIW|C Chain C, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIW|D Chain D, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Native Enzyme
pdb|2BIX|A Chain A, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Fe-Free Apoenzyme
pdb|2BIX|B Chain B, Crystal Structure Of Apocarotenoid Cleavage Oxygenase From
Synechocystis, Fe-Free Apoenzyme
Length = 490
Score = 109 bits (272), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 93/339 (27%), Positives = 153/339 (45%), Gaps = 52/339 (15%)
Query: 9 NHPFTAHPKIDPYTDEMFTFGYTQTPPYVTYRV------------ISKDGFMHDPVPITM 56
P +AHP+IDP + TF Q P YVT+ + + G + T
Sbjct: 177 GQPLSAHPRIDPAS----TFDGGQ-PCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETF 231
Query: 57 SAPIMMHDFAITENYAIFLD-------LPMCFRQKEMVKENKLIYAFDPTIKARFGVLPR 109
+HDFAIT +YAIFL LP F ++ F P A+ ++PR
Sbjct: 232 PGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFG----LRGAGECVQFHPDKPAQIILVPR 287
Query: 110 YARDDLQIRWFELPNCYIFHNANAWEEEEDEVVLITCRVRNPDLDMFNGPLKETLEDQTT 169
D +I+ + ++FH+ANA+EE ++ C P +D +G + T D
Sbjct: 288 ---DGGEIKRIPVQAGFVFHHANAFEENGKIILDSICYNSLPQVDT-DGDFRSTNFDNLD 343
Query: 170 ELYEMRFNMKTGLASQKK--LSPACVDFPRINEHYMGRKQRYVYGSILENI---AKVTGM 224
RF + A+ +K + C +FP ++ +GR RYVY + A + +
Sbjct: 344 PGQLWRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAI 403
Query: 225 IKFDLRAEPETGKTKLEVGGNVKGIFDLGPGRFGSEAVFVPREPSSTSEEDDGYLIFHVH 284
+K DL + ET ++ P F E +FVPR P +E DDG+L+ ++
Sbjct: 404 LKVDLESGTETLRS-------------FAPHGFAGEPIFVPR-PGGVAE-DDGWLLCLIY 448
Query: 285 DENTGKSAVYVIDAKTMSADPVAVIELPHRVPYGFHGIF 323
+ +S + ++DA+ ++A +A ++L H +PY HG +
Sbjct: 449 KADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSW 487
>pdb|3FSN|A Chain A, Crystal Structure Of Rpe65 At 2.14 Angstrom Resolution
pdb|3FSN|B Chain B, Crystal Structure Of Rpe65 At 2.14 Angstrom Resolution
pdb|3KVC|A Chain A, Crystal Structure Of Bovine Rpe65 At 1.9 Angstrom
Resolution
pdb|3KVC|B Chain B, Crystal Structure Of Bovine Rpe65 At 1.9 Angstrom
Resolution
pdb|4F2Z|A Chain A, Crystal Structure Of Rpe65 In A Lipid Environment
pdb|4F2Z|E Chain E, Crystal Structure Of Rpe65 In A Lipid Environment
pdb|4F30|A Chain A, Structure Of Rpe65: P6522 Crystal Form Grown In Ammonium
Phosphate Solution
pdb|4F3A|A Chain A, Structure Of Rpe65: P6522 Crystal Form, Iridium Derivative
pdb|4F3D|A Chain A, Structure Of Rpe65: P65 Crystal Form Grown In
Fos-Choline-10
pdb|4F3D|B Chain B, Structure Of Rpe65: P65 Crystal Form Grown In
Fos-Choline-10
Length = 533
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 61/312 (19%), Positives = 114/312 (36%), Gaps = 65/312 (20%)
Query: 59 PIMMHDFAITENYAIFLDLPMCFRQKEMVKENKL-------IYAFDPTIKARFGVLPRYA 111
P +H F +T NY +F++ P+ + + L + + T+ + +
Sbjct: 237 PSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKR 296
Query: 112 RDDLQIRWFELPNCYIFHNANAWEEEEDEVVLITC------------------------- 146
+ + ++ P +FH+ N +E+ E +V + C
Sbjct: 297 KKYINNKYRTSP-FNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKK 355
Query: 147 ---RVRNPDLDMFNGPLKETLEDQTTELYEMRFNMKTGLASQKK---LSPACV------- 193
+ P++ + PL D L + T + + L P +
Sbjct: 356 NARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQA 415
Query: 194 -DFPRIN-EHYMGRKQRYVYGSILENIAKVTGMIKFDLRAEPETGKTKLEVGGNVKGIFD 251
+FP+IN + Y G+ Y YG L + + K +++ + ET +
Sbjct: 416 FEFPQINYQKYGGKPYTYAYGLGLNHFVP-DRLCKLNVKTK-ETWVWQ------------ 461
Query: 252 LGPGRFGSEAVFVPREPSSTSEEDDGYLIFHVHDENTGKSAVYVIDAKTMSADPVAVIEL 311
P + SE +FV P + EEDDG ++ V G+ Y++ VA E+
Sbjct: 462 -EPDSYPSEPIFV-SHPDAL-EEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEV 518
Query: 312 PHRVPYGFHGIF 323
+P FHG+F
Sbjct: 519 EINIPVTFHGLF 530
>pdb|3P4G|A Chain A, X-Ray Crystal Structure Of A Hyperactive, Ca2+-Dependent,
Beta-Helical Antifreeze Protein From An Antarctic
Bacterium
pdb|3P4G|B Chain B, X-Ray Crystal Structure Of A Hyperactive, Ca2+-Dependent,
Beta-Helical Antifreeze Protein From An Antarctic
Bacterium
pdb|3P4G|C Chain C, X-Ray Crystal Structure Of A Hyperactive, Ca2+-Dependent,
Beta-Helical Antifreeze Protein From An Antarctic
Bacterium
pdb|3P4G|D Chain D, X-Ray Crystal Structure Of A Hyperactive, Ca2+-Dependent,
Beta-Helical Antifreeze Protein From An Antarctic
Bacterium
Length = 323
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 204 GRKQRYVYGSILENIAKVTGM----IKFDLRA--EPETGKTKLEVGGNVKGIFDLGP 254
G Q YV G +L I TG IK D+ A + TG ++ +GGN+ G D G
Sbjct: 82 GNDQLYVAGDVLGKIDAGTGNDEIYIKGDVSAAVDAGTGNDEVYIGGNLSGDLDAGT 138
>pdb|1QYR|A Chain A, 2.1 Angstrom Crystal Structure Of Ksga: A Universally
Conserved Adenosine Dimethyltransferase
pdb|1QYR|B Chain B, 2.1 Angstrom Crystal Structure Of Ksga: A Universally
Conserved Adenosine Dimethyltransferase
pdb|4ADV|V Chain V, Structure Of The E. Coli Methyltransferase Ksga Bound To
The E. Coli 30s Ribosomal Subunit
Length = 252
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 48/111 (43%), Gaps = 17/111 (15%)
Query: 3 DYDKRLN-HPFTAHPKIDPYTDEMFTFGYTQTPPYVT--YRVISKDGFMHDPVPITMSAP 59
D RL HPF PK+ Y + TF + + + RV +P +S P
Sbjct: 54 DLAARLQTHPFLG-PKLTIYQQDAMTFNFGELAEKMGQPLRVFGN-------LPYNISTP 105
Query: 60 IMMHDFAITENYAIFLDLPMCFRQKEMVKENKLIYAFDPTIKARFGVLPRY 110
+M H F+ T+ A D+ QKE+V N+L+ + R V+ +Y
Sbjct: 106 LMFHLFSYTDAIA---DMHFML-QKEVV--NRLVAGPNSKAYGRLSVMAQY 150
>pdb|3TPZ|A Chain A, 2.1 Angstrom Crystal Structure Of The L114p Mutant Of E.
Coli Ksga
pdb|3TPZ|B Chain B, 2.1 Angstrom Crystal Structure Of The L114p Mutant Of E.
Coli Ksga
Length = 273
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 49/109 (44%), Gaps = 13/109 (11%)
Query: 3 DYDKRLN-HPFTAHPKIDPYTDEMFTFGYTQTPPYVTYRVISKDGFMHDPVPITMSAPIM 61
D RL HPF PK+ Y + TF + + + ++ +P P +S P+M
Sbjct: 70 DLAARLQTHPFLG-PKLTIYQQDAMTFNFGE----LAEKMGQPLRVFGNP-PYNISTPLM 123
Query: 62 MHDFAITENYAIFLDLPMCFRQKEMVKENKLIYAFDPTIKARFGVLPRY 110
H F+ T+ A D+ QKE+V N+L+ + R V+ +Y
Sbjct: 124 FHLFSYTDAIA---DMHFML-QKEVV--NRLVAGPNSKAYGRLSVMAQY 166
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
0.321 0.139 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,859,996
Number of Sequences: 62578
Number of extensions: 474109
Number of successful extensions: 836
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: 819
Number of HSP's gapped (non-prelim): 10
length of query: 335
length of database: 14,973,337
effective HSP length: 99
effective length of query: 236
effective length of database: 8,778,115
effective search space: 2071635140
effective search space used: 2071635140
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: 52 (24.6 bits)