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= psy9269
(148 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 66.6 bits (161), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 41/125 (32%), Positives = 64/125 (51%), Gaps = 5/125 (4%)
Query: 3 YEKLVEGREPVESSLHRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGF 62
++K + PVES L + +H N+EIV KTI + AV++L TF + R+ NP +Y
Sbjct: 1313 FKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNL 1372
Query: 63 PAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNT 122
G+S L L S L + L+ L + I++ D D+ P G I A + I + T
Sbjct: 1373 -QGISHRHLSDHL----SELVEQTLSDLEQSKCISIEDEMDVAPLNLGMIAAYYYINYTT 1427
Query: 123 MVAFT 127
+ F+
Sbjct: 1428 IELFS 1432
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 38/129 (29%), Positives = 64/129 (49%), Gaps = 7/129 (5%)
Query: 1 ERYEKLVEGREPVESSLHRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHY 60
+ Y L+ + P+ES + L + LN+EIVL + + AV WL + ++R+L +P Y
Sbjct: 476 QYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLY 535
Query: 61 GFP-AGLSSEEL--QSRLQGKNSGLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117
G L + L Q RL ++ M + N L +Y+ T N F + T G I + +
Sbjct: 536 GISHDDLKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKTGN--FQV--TELGRIASHYY 591
Query: 118 IGFNTMVAF 126
I +T+ +
Sbjct: 592 ITNDTVQTY 600
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 66.6 bits (161), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 41/125 (32%), Positives = 64/125 (51%), Gaps = 5/125 (4%)
Query: 3 YEKLVEGREPVESSLHRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGF 62
++K + PVES L + +H N+EIV KTI + AV++L TF + R+ NP +Y
Sbjct: 1313 FKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNL 1372
Query: 63 PAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNT 122
G+S L L S L + L+ L + I++ D D+ P G I A + I + T
Sbjct: 1373 -QGISHRHLSDHL----SELVEQTLSDLEQSKCISIEDEMDVAPLNLGMIAAYYYINYTT 1427
Query: 123 MVAFT 127
+ F+
Sbjct: 1428 IELFS 1432
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 38/129 (29%), Positives = 64/129 (49%), Gaps = 7/129 (5%)
Query: 1 ERYEKLVEGREPVESSLHRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHY 60
+ Y L+ + P+ES + L + LN+EIVL + + AV WL + ++R+L +P Y
Sbjct: 476 QYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLY 535
Query: 61 GFP-AGLSSEEL--QSRLQGKNSGLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117
G L + L Q RL ++ M + N L +Y+ T N F + T G I + +
Sbjct: 536 GISHDDLKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKTGN--FQV--TELGRIASHYY 591
Query: 118 IGFNTMVAF 126
I +T+ +
Sbjct: 592 ITNDTVQTY 600
>pdb|3TQK|A Chain A, Structure Of Phospho-2-Dehydro-3-Deoxyheptonate Aldolase
From Francisella Tularensis Schu S4
Length = 346
Score = 28.9 bits (63), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 9 GREPVESSLHRHLVEHLNSEIVLK--TISDVSVAVEWLRSTFF 49
G VES +HR L L++ I K T DV VAV+ ++S +
Sbjct: 160 GARTVESQVHRELASGLSASIGFKNATNGDVQVAVDAVKSATY 202
>pdb|1W79|A Chain A, Crystal Structure Of The
Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39
pdb|1W79|B Chain B, Crystal Structure Of The
Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39
pdb|1W79|C Chain C, Crystal Structure Of The
Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39
pdb|1W79|D Chain D, Crystal Structure Of The
Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39
pdb|1W8Q|A Chain A, Crystal Structure Of The
Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39
pdb|1W8Q|B Chain B, Crystal Structure Of The
Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39
pdb|1W8Q|C Chain C, Crystal Structure Of The
Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39
pdb|1W8Q|D Chain D, Crystal Structure Of The
Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39
pdb|1W8Y|A Chain A, Crystal Structure Of The Nitrocefin Acyl-Dd-Peptidase From
Actinomadura R39.
pdb|1W8Y|B Chain B, Crystal Structure Of The Nitrocefin Acyl-Dd-Peptidase From
Actinomadura R39.
pdb|1W8Y|C Chain C, Crystal Structure Of The Nitrocefin Acyl-Dd-Peptidase From
Actinomadura R39.
pdb|1W8Y|D Chain D, Crystal Structure Of The Nitrocefin Acyl-Dd-Peptidase From
Actinomadura R39.
pdb|2VGJ|A Chain A, Crystal Structure Of Actinomadura R39 Dd-Peptidase
Complexed With A Peptidoglycan-Mimetic Cephalosporin
pdb|2VGJ|B Chain B, Crystal Structure Of Actinomadura R39 Dd-Peptidase
Complexed With A Peptidoglycan-Mimetic Cephalosporin
pdb|2VGJ|C Chain C, Crystal Structure Of Actinomadura R39 Dd-Peptidase
Complexed With A Peptidoglycan-Mimetic Cephalosporin
pdb|2VGJ|D Chain D, Crystal Structure Of Actinomadura R39 Dd-Peptidase
Complexed With A Peptidoglycan-Mimetic Cephalosporin
pdb|2VGK|A Chain A, Crystal Structure Of Actinomadura R39 Dd-Peptidase
Complexed With A Peptidoglycan-Mimetic Cephalosporin
pdb|2VGK|B Chain B, Crystal Structure Of Actinomadura R39 Dd-Peptidase
Complexed With A Peptidoglycan-Mimetic Cephalosporin
pdb|2VGK|C Chain C, Crystal Structure Of Actinomadura R39 Dd-Peptidase
Complexed With A Peptidoglycan-Mimetic Cephalosporin
pdb|2VGK|D Chain D, Crystal Structure Of Actinomadura R39 Dd-Peptidase
Complexed With A Peptidoglycan-Mimetic Cephalosporin
pdb|2XLN|A Chain A, Crystal Structure Of A Complex Between Actinomadura R39
Dd-Peptidase And A Boronate Inhibitor
pdb|2XLN|B Chain B, Crystal Structure Of A Complex Between Actinomadura R39
Dd-Peptidase And A Boronate Inhibitor
pdb|2XLN|C Chain C, Crystal Structure Of A Complex Between Actinomadura R39
Dd-Peptidase And A Boronate Inhibitor
pdb|2XLN|D Chain D, Crystal Structure Of A Complex Between Actinomadura R39
Dd-Peptidase And A Boronate Inhibitor
Length = 489
Score = 27.7 bits (60), Expect = 2.6, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 64 AGLSS-EELQSRLQGKNSGLCMRELNGLSRYNLITMNDGFDIL 105
AGL EE S L +GL + + +GLSR NL+T + D+L
Sbjct: 322 AGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLL 364
>pdb|2WKE|A Chain A, Crystal Structure Of The Actinomadura R39 Dd-Peptidase
Inhibited By 6-Beta-Iodopenicillanate.
pdb|2WKE|B Chain B, Crystal Structure Of The Actinomadura R39 Dd-Peptidase
Inhibited By 6-Beta-Iodopenicillanate.
pdb|2WKE|C Chain C, Crystal Structure Of The Actinomadura R39 Dd-Peptidase
Inhibited By 6-Beta-Iodopenicillanate.
pdb|2WKE|D Chain D, Crystal Structure Of The Actinomadura R39 Dd-Peptidase
Inhibited By 6-Beta-Iodopenicillanate.
pdb|2XDM|A Chain A, Crystal Structure Of A Complex Between Actinomadura R39 Dd
Peptidase And A Peptidoglycan Mimetic Boronate Inhibitor
pdb|2XDM|B Chain B, Crystal Structure Of A Complex Between Actinomadura R39 Dd
Peptidase And A Peptidoglycan Mimetic Boronate Inhibitor
pdb|2XDM|C Chain C, Crystal Structure Of A Complex Between Actinomadura R39 Dd
Peptidase And A Peptidoglycan Mimetic Boronate Inhibitor
pdb|2XDM|D Chain D, Crystal Structure Of A Complex Between Actinomadura R39 Dd
Peptidase And A Peptidoglycan Mimetic Boronate Inhibitor
pdb|2XK1|A Chain A, Crystal Structure Of A Complex Between Actinomadura R39
Dd- Peptidase And A Boronate Inhibitor
pdb|2XK1|B Chain B, Crystal Structure Of A Complex Between Actinomadura R39
Dd- Peptidase And A Boronate Inhibitor
pdb|2XK1|C Chain C, Crystal Structure Of A Complex Between Actinomadura R39
Dd- Peptidase And A Boronate Inhibitor
pdb|2XK1|D Chain D, Crystal Structure Of A Complex Between Actinomadura R39
Dd- Peptidase And A Boronate Inhibitor
pdb|2Y4A|A Chain A, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y4A|B Chain B, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y4A|C Chain C, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y4A|D Chain D, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y55|A Chain A, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y55|B Chain B, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y55|C Chain C, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y55|D Chain D, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y59|A Chain A, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y59|B Chain B, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y59|C Chain C, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|2Y59|D Chain D, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|3ZVT|A Chain A, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|3ZVT|B Chain B, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|3ZVT|C Chain C, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|3ZVT|D Chain D, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|3ZVW|A Chain A, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|3ZVW|B Chain B, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|3ZVW|C Chain C, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
pdb|3ZVW|D Chain D, Unexpected Tricovalent Binding Mode Of Boronic Acids
Within The Active Site Of A Penicillin Binding Protein
Length = 466
Score = 27.7 bits (60), Expect = 2.6, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 64 AGLSS-EELQSRLQGKNSGLCMRELNGLSRYNLITMNDGFDIL 105
AGL EE S L +GL + + +GLSR NL+T + D+L
Sbjct: 322 AGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLL 364
>pdb|1MKP|A Chain A, Crystal Structure Of Pyst1 (Mkp3)
Length = 144
Score = 27.3 bits (59), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 14/66 (21%)
Query: 62 FPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLIT-----------MNDGFDILPTVTG 110
FP +S +GKN G+ + L G+SR +T MND +DI+
Sbjct: 69 FPEAIS---FIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMNDAYDIVKMKKS 125
Query: 111 SIMAKF 116
+I F
Sbjct: 126 NISPNF 131
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 0.135 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,047,074
Number of Sequences: 62578
Number of extensions: 151187
Number of successful extensions: 287
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: 281
Number of HSP's gapped (non-prelim): 10
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
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: 47 (22.7 bits)