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= 001642
(1039 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/209 (22%), Positives = 93/209 (44%), Gaps = 34/209 (16%)
Query: 763 SRRGDVI--LQMHERLVDMGVRLNQAYYNSLITILCRLGMTRKATSVLEDMRGRGIMMDT 820
S++GDV+ L++++ GV+L+Q +YN L+ + C L A + E G
Sbjct: 37 SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYV-CSL-----AEAATESSPNPG----- 85
Query: 821 ITYNALMRGYWVSSHINKALATYTQMINEGVSPNTATYNILLGIFLGTGSTKEVDDLFGE 880
L RG+ + QMI + V PN AT+ + + + D+ +
Sbjct: 86 -----LSRGF----------DIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQ 130
Query: 881 MKKRGLKPDASTYDTLISGHAKIGNKKESIQIYCEMITKGYVPKTSTYNVLIG---DFAK 937
MK G++P +Y + G + G+ ++ ++ M+ VP+ L+ D
Sbjct: 131 MKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKN 190
Query: 938 EGKMHQARELLKEMQARGRNPNSSTYDIL 966
K+++ + L+++ R + ST+D++
Sbjct: 191 ADKVYKTLQRLRDLV---RQVSKSTFDMI 216
Score = 34.3 bits (77), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 33/150 (22%), Positives = 62/150 (41%), Gaps = 9/150 (6%)
Query: 408 IDSLFKAGCAMEAFALQSQMMVRGVA-----FDVVVYTTLMDGLFKAGRP----SEAEDT 458
+D K G +EA L + GV ++V++Y + P S D
Sbjct: 33 LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 459 FNLILKHNLVSNHVTYSSLIDGCCKLGDMSAAESILQEMEEKHVVPNVITYSSIINGYVK 518
F ++ +V N T+++ D A ++++M+ + P + +Y + G+ +
Sbjct: 93 FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCR 152
Query: 519 KGMLDEAANVMRKMKSQNIMPNVFIFAALI 548
KG D+A V M ++P AAL+
Sbjct: 153 KGDADKAYEVDAHMVESEVVPEEPELAALL 182
Score = 34.3 bits (77), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 24/114 (21%), Positives = 54/114 (47%)
Query: 676 LTPDLATYNIMISASCKQGNLEIAFKLWDEMRRNGIMPNSVTCNVLVGGLVGFGEIEKAM 735
+ P+ AT+ + + + E+AF + +M+ GI P + + G G+ +KA
Sbjct: 101 VVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAY 160
Query: 736 DVLNDMLVWGFSPTSTTIKILLDTSSKSRRGDVILQMHERLVDMGVRLNQAYYN 789
+V M+ P + LL S ++ D + + +RL D+ +++++ ++
Sbjct: 161 EVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFD 214
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 255 DLSSALKLMEGMRREGVIPDIVSYNTLISGFCKRGDFVKA 294
D A +++ M+ G+ P + SY + GFC++GD KA
Sbjct: 120 DPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKA 159
Score = 30.8 bits (68), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 40/77 (51%)
Query: 487 MSAAESILQEMEEKHVVPNVITYSSIINGYVKKGMLDEAANVMRKMKSQNIMPNVFIFAA 546
+S I ++M VVPN T+++ V K + A +++++MK+ I P + +
Sbjct: 86 LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGP 145
Query: 547 LIDGYFKAGKQEVAFDL 563
+ G+ + G + A+++
Sbjct: 146 ALFGFCRKGDADKAYEV 162
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 35.8 bits (81), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 70/162 (43%), Gaps = 30/162 (18%)
Query: 753 IKILLDTSSKSRRGDVI--LQMHERLVDMGVRLNQAYYNSLITILCRLGMTRKATSVLED 810
+K LD SK +GDV+ L++++ GV+L+Q +YN L+ + C L A + E
Sbjct: 29 LKQKLDXCSK--KGDVLEALRLYDEARRNGVQLSQYHYNVLLYV-CSL-----AEAATES 80
Query: 811 MRGRGIMMDTITYNALMRGYWVSSHINKALATYTQMINEGVSPNTATYNILLGIFLGTGS 870
G L RG+ + + Q I + V PN AT+ + +
Sbjct: 81 SPNPG----------LSRGFDI----------FKQXIVDKVVPNEATFTNGARLAVAKDD 120
Query: 871 TKEVDDLFGEMKKRGLKPDASTYDTLISGHAKIGNKKESIQI 912
+ D + K G++P +Y + G + G+ ++ ++
Sbjct: 121 PEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162
Score = 30.0 bits (66), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 27/130 (20%), Positives = 51/130 (39%), Gaps = 9/130 (6%)
Query: 408 IDSLFKAGCAMEAFALQSQMMVRGVA-----FDVVVYTTLMDGLFKAGRP----SEAEDT 458
+D K G +EA L + GV ++V++Y + P S D
Sbjct: 33 LDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92
Query: 459 FNLILKHNLVSNHVTYSSLIDGCCKLGDMSAAESILQEMEEKHVVPNVITYSSIINGYVK 518
F + +V N T+++ D A +++ + + P + +Y + G+ +
Sbjct: 93 FKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCR 152
Query: 519 KGMLDEAANV 528
KG D+A V
Sbjct: 153 KGDADKAYEV 162
>pdb|3HHD|A Chain A, Structure Of The Human Fatty Acid Synthase Ks-Mat Didomain
As A Framework For Inhibitor Design.
pdb|3HHD|B Chain B, Structure Of The Human Fatty Acid Synthase Ks-Mat Didomain
As A Framework For Inhibitor Design.
pdb|3HHD|C Chain C, Structure Of The Human Fatty Acid Synthase Ks-Mat Didomain
As A Framework For Inhibitor Design.
pdb|3HHD|D Chain D, Structure Of The Human Fatty Acid Synthase Ks-Mat Didomain
As A Framework For Inhibitor Design
Length = 965
Score = 33.1 bits (74), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 2/82 (2%)
Query: 796 CRLGMTRKATSVLEDMRGRGIMMDTITYNALM--RGYWVSSHINKALATYTQMINEGVSP 853
C+ M S D RG I +DT ++LM + + + H + A IN + P
Sbjct: 137 CQRAMMANRLSFFFDFRGPSIALDTACSSSLMALQNAYQAIHSGQCPAAIVGGINVLLKP 196
Query: 854 NTATYNILLGIFLGTGSTKEVD 875
NT+ + LG+ G+ K D
Sbjct: 197 NTSVQFLRLGMLSPEGTCKAFD 218
>pdb|2G8Y|A Chain A, The Structure Of A Putative MalateLACTATE DEHYDROGENASE
FROM E. COLI.
pdb|2G8Y|B Chain B, The Structure Of A Putative MalateLACTATE DEHYDROGENASE
FROM E. COLI
Length = 385
Score = 33.1 bits (74), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 24/41 (58%)
Query: 880 EMKKRGLKPDASTYDTLISGHAKIGNKKESIQIYCEMITKG 920
E +K+G+ DA ++ + +IG +E++Q +C+ + G
Sbjct: 344 ERQKQGIPLDAGSWQAICDAARQIGXPEETLQAFCQQLASG 384
>pdb|4HS7|A Chain A, 2.6 Angstrom Structure Of The Extracellular Solute-Binding
Protein From Staphylococcus Aureus In Complex With Peg.
pdb|4HS7|B Chain B, 2.6 Angstrom Structure Of The Extracellular Solute-Binding
Protein From Staphylococcus Aureus In Complex With Peg.
pdb|4HW8|A Chain A, 2.25 Angstrom Structure Of The Extracellular
Solute-Binding Protein From Staphylococcus Aureus In
Complex With Maltose.
pdb|4HW8|B Chain B, 2.25 Angstrom Structure Of The Extracellular
Solute-Binding Protein From Staphylococcus Aureus In
Complex With Maltose
Length = 420
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 21/25 (84%), Gaps = 1/25 (4%)
Query: 919 KGYVPKTSTYNVLIGDFAKEGKMHQ 943
KGY+PK +T++V+IG F KEGK+ Q
Sbjct: 241 KGYLPKAATHDVMIGLF-KEGKVGQ 264
>pdb|2UY1|B Chain B, Crystal Structure Of Cstf-77
Length = 493
Score = 30.4 bits (67), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 58/300 (19%), Positives = 128/300 (42%), Gaps = 48/300 (16%)
Query: 385 AKMLFREME---KMGVDPN----HVSYTTLIDSLFKAGCAMEAFALQSQMMVRGVAFDVV 437
A+++ EME K+G P+ H + ++DS F A E + S+ ++ G+
Sbjct: 176 ARLIDLEMENGMKLGGRPHESRMHFIHNYILDSFF---YAEEVYFFYSEYLI-GIGQKEK 231
Query: 438 VYTTLMDGLFKAGRPSEAEDTFNLILKHNLVSNHVTYSSLIDGCCKLGDMSAAESIL-QE 496
+ G+ E D L L + LV + + +G+ +AE + +E
Sbjct: 232 AKKVVERGI-------EMSDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKE 284
Query: 497 MEEKHVVPNVITYSSIINGYVKKGMLDEAANVMRKMKSQNIMPNVFIFAALIDGYFKAGK 556
++ + + +N +KK L+ + ++ ++ + P+VFI+ A I+ Y+ G
Sbjct: 285 LDLLRI--------NHLNYVLKKRGLELFRKLFIELGNEGVGPHVFIYCAFIE-YYATGS 335
Query: 557 QEVAFDLYNDLKLVGMEENNYILDIFVNYLKRHGKMKEANGLVVDMMSRGLVPDRVNYTS 616
+ +++++ L+ ++ + + F +L R G + A L + + D S
Sbjct: 336 RATPYNIFSS-GLLKHPDSTLLKEEFFLFLLRIGDEENARALFKRLEKTSRMWD-----S 389
Query: 617 LMDGFFKVGKETAALNIAQEMTEKNI----------PFDVTAYNVLINGLLRHGKCEVQS 666
+++ F VG ++ + +E+ ++ + P +NV + G+L C + S
Sbjct: 390 MIEYEFMVG----SMELFRELVDQKMDAIKADAILPPLPPREHNVQMEGILGRYHCFLDS 445
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 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,293,510
Number of Sequences: 62578
Number of extensions: 1203036
Number of successful extensions: 2882
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2851
Number of HSP's gapped (non-prelim): 36
length of query: 1039
length of database: 14,973,337
effective HSP length: 109
effective length of query: 930
effective length of database: 8,152,335
effective search space: 7581671550
effective search space used: 7581671550
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)