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= 007605
(596 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 = 342 bits (878), Expect = 2e-94, Method: Compositional matrix adjust.
Identities = 198/532 (37%), Positives = 300/532 (56%), Gaps = 37/532 (6%)
Query: 73 QKGLAAKVIDFVEGLIVKFMHDSSRPLHYLSGNFGPVRHETPPTADLPVIGFLHECLNGE 132
++G A V++ GL ++ P ++GNF PV E PP +LPV G + ++G
Sbjct: 24 EEGFVANVLERPHGL-----PSTADPAVQIAGNFAPV-GERPPVHELPVSGRIPPFIDGV 77
Query: 133 FIRVGPNSKFAPVAGYHWFDGDGMLHGLRIKDGKA-AYVSRYVKTSRLKQEEFFGGAKFT 191
+ R G N F PVAG+H FDGDGM+H LRI++G A +Y R+ +T+RL+QE G F
Sbjct: 78 YARNGANPCFDPVAGHHLFDGDGMVHALRIRNGAAESYACRFTETARLRQERAIGRPVFP 137
Query: 192 K-IGDVKGLFGLLMVNMTLLRESFKVLDFSYGNGAGNTALIYHHGKLLVLSEIDKPYVLK 250
K IG++ G G+ + + R + ++D S G G N L+Y +G+LL +SE D PY ++
Sbjct: 138 KAIGELHGHSGIARLALFYARAACGLVDPSAGTGVANAGLVYFNGRLLAMSEDDLPYHVR 197
Query: 251 VLKDGDLQTLGMLDYDKRLNHPFTAHPKIDPYTDEMFTFGYTQTP-PYVTYRVISKDGFM 309
V DGDL+T+G D+D +L AHPK+DP T E+ Y PY+ Y DG
Sbjct: 198 VADDGDLETVGRYDFDGQLGCAMIAHPKLDPATGELHALSYDVIKRPYLKYFYFRPDGTK 257
Query: 310 HDPVPITMSAPIMMHDFAITENYAIFLDLPMCFRQKEMVKENKLIYAFDPTIKARFGVLP 369
D V I + P M+HDFAITEN + D + F+ +EM++ + D +RFGVLP
Sbjct: 258 SDDVEIPLEQPTMIHDFAITENLVVVPDHQVVFKLQEMLRGGSPV-VLDAAKTSRFGVLP 316
Query: 370 RYARDDLQIRWFELPNCYIFHNANAWEEEEDEVVLITCRVRNPDLDMFNGPLKETLEDQT 429
++A D ++ W ++P+C+ FH NAWE+E V++ P +FN E+ E
Sbjct: 317 KHAADASEMAWVDVPDCFCFHLWNAWEDEATGEVVVIGSCMTPADSIFN----ESDERLE 372
Query: 430 TELYEMRFNMKTGLASQKKLSPAC----VDFPRINEHYMGRKQRYVYGSILENIAKVTGM 485
+ L E+R + +TG ++++ + P ++ +N + +GR+ RY Y ++ E KV+G
Sbjct: 373 SVLTEIRLDARTGRSTRRAVLPPSQQVNLEVGMVNRNLLGRETRYAYLAVAEPWPKVSGF 432
Query: 486 IKFDLRAEPETGK-TKLEVGGNVKGIFDLGPGRFGSEAVFVPREPSSTSE--EDDGYLIF 542
K DL TG+ TK F+ G GRFG E FVP +P++ EDDGY++
Sbjct: 433 AKVDL----STGELTK----------FEYGEGRFGGEPCFVPMDPAAAHPRGEDDGYVLT 478
Query: 543 HVHDENTGKSAVYVIDAKTMSADPVAVIELPHRVPYGFHGIFLSEEQLEELA 594
VHDE G S + V++A M + A ++LP RVP+GFHG F++ ++LE A
Sbjct: 479 FVHDERAGTSELLVVNAADMRLE--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 = 137 bits (345), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 128/463 (27%), Positives = 209/463 (45%), Gaps = 69/463 (14%)
Query: 149 HWFDGDGMLHGLRIK-DGKAAYVSRYVKTSRLKQEEFFGGAKFTKIGDVKGLFGLLMVNM 207
H FDGDGM+ + DG+ + S++V+T +E+ G + +G+FG
Sbjct: 67 HPFDGDGMVTAFKFPGDGRVHFQSKFVRTQGYVEEQKAGKMIY------RGVFGSQPAGG 120
Query: 208 TLLRESFKVLDFSYGNGAGNTALIYHHGKLLVLSEIDKPYVLKVLKDGDLQTLGMLDYDK 267
L + D N A NT + Y +LL L E +P+ L+ +L T+G+ D
Sbjct: 121 WLK----TIFDLRLKNIA-NTNITYWGDRLLALWEGGQPHRLE---PSNLATIGLDDLGG 172
Query: 268 RL--NHPFTAHPKIDPYTDEMFTFGYTQTPPYVTYRV------------ISKDGFMHDPV 313
L P +AHP+IDP + TF Q P YVT+ + + G +
Sbjct: 173 ILAEGQPLSAHPRIDPAS----TFDGGQ-PCYVTFSIKSSLSSTLTLLELDPQGKLLRQK 227
Query: 314 PITMSAPIMMHDFAITENYAIFLD-------LPMCFRQKEMVKENKLIYAFDPTIKARFG 366
T +HDFAIT +YAIFL LP F ++ F P A+
Sbjct: 228 TETFPGFAFIHDFAITPHYAIFLQNNVTLNGLPYLFG----LRGAGECVQFHPDKPAQII 283
Query: 367 VLPRYARDDLQIRWFELPNCYIFHNANAWEEEEDEVVLITCRVRNPDLDMFNGPLKETLE 426
++PR D +I+ + ++FH+ANA+EE ++ C P +D +G + T
Sbjct: 284 LVPR---DGGEIKRIPVQAGFVFHHANAFEENGKIILDSICYNSLPQVDT-DGDFRSTNF 339
Query: 427 DQTTELYEMRFNMKTGLASQKK--LSPACVDFPRINEHYMGRKQRYVYGSILENI---AK 481
D RF + A+ +K + C +FP ++ +GR RYVY + A
Sbjct: 340 DNLDPGQLWRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAP 399
Query: 482 VTGMIKFDLRAEPETGKTKLEVGGNVKGIFDLGPGRFGSEAVFVPREPSSTSEEDDGYLI 541
+ ++K DL + ET ++ P F E +FVPR P +E DDG+L+
Sbjct: 400 LQAILKVDLESGTETLRS-------------FAPHGFAGEPIFVPR-PGGVAE-DDGWLL 444
Query: 542 FHVHDENTGKSAVYVIDAKTMSADPVAVIELPHRVPYGFHGIF 584
++ + +S + ++DA+ ++A +A ++L H +PY HG +
Sbjct: 445 CLIYKADLHRSELVILDAQDITAPAIATLKLKHHIPYPLHGSW 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 = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 114/540 (21%), Positives = 196/540 (36%), Gaps = 115/540 (21%)
Query: 121 VIGFLHECLNGEFIRVGPNS-KFAPVAGYHWFDGDGMLHGLRIKDGKAAYVSRYVKT--- 176
V G + L G +R GP + YH FDG +LH K+G Y R+++T
Sbjct: 30 VTGRIPLWLTGSLLRCGPGLFEVGSEPFYHLFDGQALLHKFDFKEGHVTYHRRFIRTDAY 89
Query: 177 ------SRLKQEEFFGGAKFTKIGDVKGLFGLLMVNMTLLRESFKVLDFSYGNGAGNT-- 228
R+ EF G F K +F FSY G T
Sbjct: 90 VRAMTEKRIVITEF-GTCAFPD--PCKNIFSRF---------------FSYFRGVEVTDN 131
Query: 229 AL--IYHHGK-LLVLSEIDKPYVLKVLKDGDLQTLGMLDYDKRLN-HPFTAHPKID---P 281
AL IY G+ +E + ++ KV + L+T+ +D ++ + TAHP I+
Sbjct: 132 ALVNIYPVGEDYYACTETN--FITKVNPE-TLETIKQVDLCNYVSVNGATAHPHIENDGT 188
Query: 282 YTDEMFTFGYTQTPPYVTYRVISKDGFMHDPVP---ITMSAPI-------MMHDFAITEN 331
+ FG + Y ++ DP+ I + P +H F +T N
Sbjct: 189 VYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPN 248
Query: 332 YAIFLDLPMCFRQKEMVKENKL-------IYAFDPTIKARFGVLPRYARDDLQIRWFELP 384
Y +F++ P+ + + L + + T+ + + + + ++ P
Sbjct: 249 YIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSP 308
Query: 385 NCYIFHNANAWEEEEDEVVLITC----------------------------RVRNPDLDM 416
+FH+ N +E+ E +V + C + P++
Sbjct: 309 -FNLFHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLANLRENWEEVKKNARKAPQPEVRR 367
Query: 417 FNGPLKETLEDQTTELYEMRFNMKTGLASQKK---LSPACV--------DFPRIN-EHYM 464
+ PL D L + T + + L P + +FP+IN + Y
Sbjct: 368 YVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLFSGPRQAFEFPQINYQKYG 427
Query: 465 GRKQRYVYGSILENIAKVTGMIKFDLRAEPETGKTKLEVGGNVKGIFDLGPGRFGSEAVF 524
G+ Y YG L + + K +++ + ET + P + SE +F
Sbjct: 428 GKPYTYAYGLGLNHFVP-DRLCKLNVKTK-ETWVWQ-------------EPDSYPSEPIF 472
Query: 525 VPREPSSTSEEDDGYLIFHVHDENTGKSAVYVIDAKTMSADPVAVIELPHRVPYGFHGIF 584
V P + EEDDG ++ V G+ Y++ VA E+ +P FHG+F
Sbjct: 473 V-SHPDAL-EEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSEVARAEVEINIPVTFHGLF 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 = 32.0 bits (71), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 465 GRKQRYVYGSILENIAKVTG----MIKFDLRA--EPETGKTKLEVGGNVKGIFDLGP 515
G Q YV G +L I TG IK D+ A + TG ++ +GGN+ G D G
Sbjct: 82 GNDQLYVAGDVLGKIDAGTGNDEIYIKGDVSAAVDAGTGNDEVYIGGNLSGDLDAGT 138
>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 = 28.9 bits (63), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 54/120 (45%), Gaps = 17/120 (14%)
Query: 257 LQTLGMLDYDKRL-----NHPFTAHPKIDPYTDEMFTFGYTQTPPYVTYRVISKDGFMHD 311
L L +++ D+ L HPF PK+ Y + TF + + + ++ +
Sbjct: 59 LDQLTVIELDRDLAARLQTHPFLG-PKLTIYQQDAMTFNFGE----LAEKMGQPLRVFGN 113
Query: 312 PVPITMSAPIMMHDFAITENYAIFLDLPMCFRQKEMVKENKLIYAFDPTIKARFGVLPRY 371
P P +S P+M H F+ T+ A D+ QKE+V N+L+ + R V+ +Y
Sbjct: 114 P-PYNISTPLMFHLFSYTDAIA---DMHFML-QKEVV--NRLVAGPNSKAYGRLSVMAQY 166
>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 = 8.7, Method: Compositional matrix adjust.
Identities = 32/122 (26%), Positives = 53/122 (43%), Gaps = 21/122 (17%)
Query: 257 LQTLGMLDYDKRL-----NHPFTAHPKIDPYTDEMFTFGYTQTPPYV--TYRVISKDGFM 309
L L +++ D+ L HPF PK+ Y + TF + + + RV
Sbjct: 43 LDQLTVIELDRDLAARLQTHPFLG-PKLTIYQQDAMTFNFGELAEKMGQPLRVFGN---- 97
Query: 310 HDPVPITMSAPIMMHDFAITENYAIFLDLPMCFRQKEMVKENKLIYAFDPTIKARFGVLP 369
+P +S P+M H F+ T+ A D+ QKE+V N+L+ + R V+
Sbjct: 98 ---LPYNISTPLMFHLFSYTDAIA---DMHFML-QKEVV--NRLVAGPNSKAYGRLSVMA 148
Query: 370 RY 371
+Y
Sbjct: 149 QY 150
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 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,503,634
Number of Sequences: 62578
Number of extensions: 892695
Number of successful extensions: 1699
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1679
Number of HSP's gapped (non-prelim): 11
length of query: 596
length of database: 14,973,337
effective HSP length: 104
effective length of query: 492
effective length of database: 8,465,225
effective search space: 4164890700
effective search space used: 4164890700
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)