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= 019900
(334 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 = 206 bits (523), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 122/339 (35%), Positives = 182/339 (53%), Gaps = 30/339 (8%)
Query: 3 DYDKRLQHSFTAHPKVDPYTGEMFTFGY-AHTPPYITYRVISKDGFMHDPVPITVSDPIM 61
D+D +L + AHPK+DP TGE+ Y PY+ Y DG D V I + P M
Sbjct: 211 DFDGQLGCAMIAHPKLDPATGELHALSYDVIKRPYLKYFYFRPDGTKSDDVEIPLEQPTM 270
Query: 62 MHDFAITENYAIFMDLPLYFRPKEMVKENKLIFTFDDTKKARFGILPRYAKNEAQMKWFE 121
+HDFAITEN + D + F+ +EM++ + D K +RFG+LP++A + ++M W +
Sbjct: 271 IHDFAITENLVVVPDHQVVFKLQEMLRGGSPV-VLDAAKTSRFGVLPKHAADASEMAWVD 329
Query: 122 LPNCFIFHNANAWEEE--DEVVLITCRLDKPDLDMVNGAVKEKLENFSNELYEMRFNLKT 179
+P+CF FH NAWE+E EVV+I + D E E + L E+R + +T
Sbjct: 330 VPDCFCFHLWNAWEDEATGEVVVIGSCMTPAD-----SIFNESDERLESVLTEIRLDART 384
Query: 180 GLASQKRLSASA----VDFPRVNECYTGRKQRYVYGTILDSIAKVTGIIKFDLHAEPDEE 235
G ++++ + + ++ VN GR+ RY Y + + KV+G K DL E
Sbjct: 385 GRSTRRAVLPPSQQVNLEVGMVNRNLLGRETRYAYLAVAEPWPKVSGFAKVDLST---GE 441
Query: 236 KTKLEVGGNVRGIFDLGPGRFGSEAVFVPREPGTS--SEEDVGYLIFFSHDEKTGKSSVN 293
TK F+ G GRFG E FVP +P + ED GY++ F HDE+ G S +
Sbjct: 442 LTK----------FEYGEGRFGGEPCFVPMDPAAAHPRGEDDGYVLTFVHDERAGTSELL 491
Query: 294 VIDAKTMSADPVAVVELPHRVPYGFHAFFVSEEQLEEQA 332
V++A M + A V+LP RVP+GFH F++ ++LE QA
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 = 94.7 bits (234), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 84/337 (24%), Positives = 147/337 (43%), Gaps = 51/337 (15%)
Query: 12 FTAHPKVDPYTGEMFTFGYAHTPPYITYRV------------ISKDGFMHDPVPITVSDP 59
+AHP++DP + TF P Y+T+ + + G + T
Sbjct: 180 LSAHPRIDPAS----TFDGGQ-PCYVTFSIKSSLSSTLTLLELDPQGKLLRQKTETFPGF 234
Query: 60 IMMHDFAITENYAIFMD-------LPLYFRPKEMVKENKLIFTFDDTKKARFGILPRYAK 112
+HDFAIT +YAIF+ LP F ++ F K A+ ++PR
Sbjct: 235 AFIHDFAITPHYAIFLQNNVTLNGLPYLFG----LRGAGECVQFHPDKPAQIILVPR--- 287
Query: 113 NEAQMKWFELPNCFIFHNANAWEEEDEVVLIT-CRLDKPDLDMVNGAVKEKLENFS-NEL 170
+ ++K + F+FH+ANA+EE +++L + C P +D +N +L
Sbjct: 288 DGGEIKRIPVQAGFVFHHANAFEENGKIILDSICYNSLPQVDTDGDFRSTNFDNLDPGQL 347
Query: 171 YEMRFNLKTGLASQKRLSASAVDFPRVNECYTGRKQRYVY-GTILDSI--AKVTGIIKFD 227
+ + ++ + + +FP V+ GR RYVY G S A + I+K D
Sbjct: 348 WRFTIDPAAATVEKQLMVSRCCEFPVVHPQQVGRPYRYVYMGAAHHSTGNAPLQAILKVD 407
Query: 228 LHAEPDEEKTKLEVGGNVRGIFDLGPGRFGSEAVFVPREPGTSSEEDVGYLIFFSHDEKT 287
L + + ++ P F E +FVPR PG +E+D G+L+ +
Sbjct: 408 LESGTETLRS-------------FAPHGFAGEPIFVPR-PGGVAEDD-GWLLCLIYKADL 452
Query: 288 GKSSVNVIDAKTMSADPVAVVELPHRVPYGFHAFFVS 324
+S + ++DA+ ++A +A ++L H +PY H +
Sbjct: 453 HRSELVILDAQDITAPAIATLKLKHHIPYPLHGSWAQ 489
>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 = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 64/318 (20%), Positives = 115/318 (36%), Gaps = 78/318 (24%)
Query: 59 PIMMHDFAITENYAIFMDLPLYFRPKEMVKENKL-------IFTFDDTKKARFGIL---- 107
P +H F +T NY +F++ P+ + + L F ++T I
Sbjct: 237 PSYVHSFGLTPNYIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKR 296
Query: 108 PRYAKNEAQMKWFELPNCFIFHNANAWEEEDEVVLITCRLDKPD-----LDMVNGAVKEK 162
+Y N+ + F L FH+ N +E+ + +++ C + L + N ++E
Sbjct: 297 KKYINNKYRTSPFNL-----FHHINTYEDHEFLIVDLCCWKGFEFVYNYLYLAN--LREN 349
Query: 163 LENFSNEL----------YEMRFNL---KTG--LASQKRLSASAV--------------- 192
E Y + N+ TG L + +A+A+
Sbjct: 350 WEEVKKNARKAPQPEVRRYVLPLNIDKADTGKNLVTLPNTTATAILCSDETIWLEPEVLF 409
Query: 193 -------DFPRVN-ECYTGRKQRYVYGTILDSIAKVTGIIKFDLHAEPDEEKTKLEVGGN 244
+FP++N + Y G+ Y YG L+ H PD KL V
Sbjct: 410 SGPRQAFEFPQINYQKYGGKPYTYAYGLGLN-------------HFVPD-RLCKLNVKTK 455
Query: 245 VRGIFDLGPGRFGSEAVFVPREPGTSSEEDVGYLIFFSHDEKTGKSSVNVIDAKTMSADP 304
++ P + SE +FV ++ V + S + + +++AK +S
Sbjct: 456 ETWVWQ-EPDSYPSEPIFVSHPDALEEDDGVVLSVVVSPGAGQKPAYLLILNAKDLSE-- 512
Query: 305 VAVVELPHRVPYGFHAFF 322
VA E+ +P FH F
Sbjct: 513 VARAEVEINIPVTFHGLF 530
>pdb|1X9D|A Chain A, Crystal Structure Of Human Class I Alpha-1,2-Mannosidase
In Complex With Thio-Disaccharide Substrate Analogue
Length = 538
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 139 EVVLITCRLDKPDLDMVNGAVKE 161
E L+TCRLD P D+ +G +E
Sbjct: 1 EFALLTCRLDPPSQDLKDGTQEE 23
>pdb|3H41|A Chain A, Crystal Structure Of A NlpcP60 FAMILY PROTEIN (BCE_2878)
FROM Bacillus Cereus Atcc 10987 At 1.79 A Resolution
Length = 311
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 11/47 (23%)
Query: 256 FGSEAVFVPREPGTSSEEDV---------GYLIFFSHDEKTGKSSVN 293
+ S + +PR+ G S V G LIFF+HD+ GK SV+
Sbjct: 224 YKSHGITIPRDSGPQSRNGVAVDKEHLQKGDLIFFAHDQ--GKGSVH 268
>pdb|1QF6|A Chain A, Structure Of E. Coli Threonyl-Trna Synthetase Complexed
With Its Cognate Trna
Length = 642
Score = 28.1 bits (61), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 214 LDSIAKVTGIIKFDLHAEPDEEKTKLEVGGNVRGIFDLGPGRFGSEAVFVPREPGTSSEE 273
L + +V G + D H EE+ + EV G +R ++D+ FG E + V + T E+
Sbjct: 370 LHGLMRVRGFTQDDAHIFCTEEQIRDEVNGCIRLVYDM-YSTFGFEKIVV--KLSTRPEK 426
Query: 274 DVG 276
+G
Sbjct: 427 RIG 429
>pdb|1EVK|A Chain A, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With The Ligand Threonine
pdb|1EVK|B Chain B, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With The Ligand Threonine
pdb|1EVL|A Chain A, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With A Threonyl Adenylate Analog
pdb|1EVL|B Chain B, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With A Threonyl Adenylate Analog
pdb|1EVL|C Chain C, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With A Threonyl Adenylate Analog
pdb|1EVL|D Chain D, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase With A Threonyl Adenylate Analog
pdb|1FYF|A Chain A, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase Complexed With A Seryl Adenylate Analog
pdb|1FYF|B Chain B, Crystal Structure Of A Truncated Form Of Threonyl-Trna
Synthetase Complexed With A Seryl Adenylate Analog
pdb|1KOG|A Chain A, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|B Chain B, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|C Chain C, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|D Chain D, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|E Chain E, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|F Chain F, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|G Chain G, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
pdb|1KOG|H Chain H, Crystal Structure Of E. Coli Threonyl-Trna Synthetase
Interacting With The Essential Domain Of Its Mrna
Operator
Length = 401
Score = 28.1 bits (61), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 214 LDSIAKVTGIIKFDLHAEPDEEKTKLEVGGNVRGIFDLGPGRFGSEAVFVPREPGTSSEE 273
L + +V G + D H EE+ + EV G +R ++D+ FG E + V + T E+
Sbjct: 129 LHGLMRVRGFTQDDAHIFCTEEQIRDEVNGCIRLVYDM-YSTFGFEKIVV--KLSTRPEK 185
Query: 274 DVG 276
+G
Sbjct: 186 RIG 188
>pdb|2PFJ|A Chain A, Crystal Structure Of T7 Endo I Resolvase In Complex With A
Holliday Junction
pdb|2PFJ|B Chain B, Crystal Structure Of T7 Endo I Resolvase In Complex With A
Holliday Junction
Length = 149
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 120 FELPNCFIFHNANAWEEEDEVVLITCRLDKPDLDM 154
F LPN A WE +D + R P+LD+
Sbjct: 56 FLLPNGIFVETAGLWESDDRKKHLLIREQHPELDI 90
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
0.320 0.138 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,536,661
Number of Sequences: 62578
Number of extensions: 453840
Number of successful extensions: 849
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 835
Number of HSP's gapped (non-prelim): 11
length of query: 334
length of database: 14,973,337
effective HSP length: 99
effective length of query: 235
effective length of database: 8,778,115
effective search space: 2062857025
effective search space used: 2062857025
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)