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= 023133
(287 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 119 IEKALLIFDHIKGLKCKPDLITYNIVLDILGRVGRVNDMLNEFASMKEAGVVPDFISYNT 178
++ A L+ + GL + +L+T + V+D+LG+ G AS+ AG F+ T
Sbjct: 336 VDTAGLVLNDGSGL-SRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVG-GT 393
Query: 179 LLNNLRK 185
L N +R
Sbjct: 394 LANRMRG 400
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 31.6 bits (70), Expect = 0.52, Method: Composition-based stats.
Identities = 29/102 (28%), Positives = 51/102 (50%), Gaps = 13/102 (12%)
Query: 123 LLIFDHIKGLKCKPDLIT---YNIVLDILGRVGRVNDMLNEFASMKEAGVVPDFISYNTL 179
LL+ H G + K L+T YN V+ R G +++ +K+AG+ PD +SY
Sbjct: 149 LLVVHH--GQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA 206
Query: 180 LNNLRKIRR----LDLCLIYFREMGESGIKPDLLTYTALIDS 217
L + + + ++ CL +M + G+K L +TA++ S
Sbjct: 207 LQCMGRQDQDAGTIERCL---EQMSQEGLKLQAL-FTAVLLS 244
>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 = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 119 IEKALLIFDHIKGLKCKPDLITYNIVLDILGRVGRVNDMLNEFASMKEAGVVPDFISYNT 178
++ A L+ + GL + +L+T + V+D+LG+ G AS+ AG F+ T
Sbjct: 336 VDTAGLVLNDGSGL-SRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVG-GT 393
Query: 179 LLNNLRK 185
L N +R
Sbjct: 394 LANRMRG 400
>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 = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 29/129 (22%), Positives = 50/129 (38%), Gaps = 10/129 (7%)
Query: 11 KAGNVSAAVRLLQSLRDKNIFLPN-AYNCVL----VASAETND-----IDLSFQILKDLL 60
K G+V A+RL R + L YN +L +A A T + F I K ++
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97
Query: 61 VSSRTLSSDCYTNFARAFIMTDDCTQLLIFIEEVVQIASPESIIVVNRIIFAFAKSRQIE 120
V + +TN AR + DD ++++ + +F F + +
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 121 KALLIFDHI 129
KA + H+
Sbjct: 158 KAYEVDAHM 166
>pdb|3KEZ|A Chain A, Crystal Structure Of Putative Sugar Binding Protein
(Yp_001299726.1) From Bacteroides Vulgatus Atcc 8482 At
1.90 A Resolution
pdb|3KEZ|B Chain B, Crystal Structure Of Putative Sugar Binding Protein
(Yp_001299726.1) From Bacteroides Vulgatus Atcc 8482 At
1.90 A Resolution
Length = 461
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 68 SDCYTNFARAFIMTDDCTQLLIFIEEVVQIASPESII 104
S+ Y N A A + T D + + ++ +VQ A+PE+ +
Sbjct: 338 SEAYLNAAEAAVQTGDNAKAVKYLNSIVQRANPENSV 374
>pdb|3L6A|A Chain A, Crystal Structure Of The C-Terminal Region Of Human P97
Length = 364
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 12 AGNVSAAVRLLQSLRDKNIFLPNAYNCVLVASAETNDIDLS-FQILKDLLVSSRTLSSDC 70
+GN + AV ++ +R FLP + V++ S + +D D L LL +SD
Sbjct: 25 SGNANEAVNGVREMRAPKHFLPEMLSKVIILSLDRSDEDKEKASSLISLLKQEGIATSD- 83
Query: 71 YTNFARAFI-MTDDCTQL 87
NF +AF+ + D C +L
Sbjct: 84 --NFMQAFLNVLDQCPKL 99
>pdb|1F8H|A Chain A, Structure Of The Second Eps15 Homology Domain Of Human
Eps15 In Complex With Ptgssstnpfr
Length = 95
Score = 27.7 bits (60), Expect = 7.2, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 129 IKGLKCKPDLITYNIVLDILGRVGRVNDMLNEFASMKEAGVVPDFISYNTL 179
+ G K KP L+ + +DILGRV ++D+ ++ ++ V F+ Y L
Sbjct: 26 LSGDKVKPVLLNSKLPVDILGRVWELSDIDHDGMLDRDEFAVAMFLVYCAL 76
>pdb|1FF1|A Chain A, Structure Of The Second Eps15 Homology Domain Of Human
Eps15 In Complex With Ptgssstnpfl
Length = 95
Score = 27.7 bits (60), Expect = 7.2, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 129 IKGLKCKPDLITYNIVLDILGRVGRVNDMLNEFASMKEAGVVPDFISYNTL 179
+ G K KP L+ + +DILGRV ++D+ ++ ++ V F+ Y L
Sbjct: 26 LSGDKVKPVLLNSKLPVDILGRVWELSDIDHDGMLDRDEFAVAMFLVYCAL 76
>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 = 27.7 bits (60), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 27/128 (21%), Positives = 45/128 (35%), Gaps = 10/128 (7%)
Query: 11 KAGNVSAAVRLLQSLRDKNIFLPN-AYNCVL---------VASAETNDIDLSFQILKDLL 60
K G+V A+RL R + L YN +L S+ + F I K +
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXI 97
Query: 61 VSSRTLSSDCYTNFARAFIMTDDCTQLLIFIEEVVQIASPESIIVVNRIIFAFAKSRQIE 120
V + +TN AR + DD +++ + +F F + +
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDAD 157
Query: 121 KALLIFDH 128
KA + H
Sbjct: 158 KAYEVDAH 165
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
0.324 0.140 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,499,404
Number of Sequences: 62578
Number of extensions: 279218
Number of successful extensions: 853
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 845
Number of HSP's gapped (non-prelim): 16
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)