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= 048533
(591 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 = 33.1 bits (74), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 29/117 (24%), Positives = 46/117 (39%), Gaps = 11/117 (9%)
Query: 247 KKGMHYEALAVQDRMEREGISPDIVTYNSLIHGFCREGRMREARR---------LFRD-- 295
KKG EAL + D R G+ YN L++ E+ +F+
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97
Query: 296 IKGATPNHVTYTTLIDGYCRANDLEEALRLREVMAAKGVYPGVVTYNSILRKLCKEG 352
+ PN T+T +D E A + + M A G+ P + +Y L C++G
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154
Score = 32.3 bits (72), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 26/108 (24%), Positives = 48/108 (44%), Gaps = 9/108 (8%)
Query: 186 KVYKKMVQLGVVANIHLYNVLIHAC------CKSSDVDKVEK---LLCEMEFKDVRADLF 236
++Y + + GV + + YNVL++ C +SS + + + +M V +
Sbjct: 47 RLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEA 106
Query: 237 TYNTLIALYCKKGMHYEALAVQDRMEREGISPDIVTYNSLIHGFCREG 284
T+ L K A + +M+ GI P + +Y + GFCR+G
Sbjct: 107 TFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154
Score = 32.0 bits (71), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 149 GLQVFDQMRVHNLMPHLHACTVLLN-SLAKDRLTDMVWKVYKKMVQLGVVANIHLYNVLI 207
G +F QM V ++P+ T ++AKD +M + + K+M G+ + Y +
Sbjct: 89 GFDIFKQMIVDKVVPNEATFTNGARLAVAKDD-PEMAFDMVKQMKAFGIQPRLRSYGPAL 147
Query: 208 HACCKSSDVDKV 219
C+ D DK
Sbjct: 148 FGFCRKGDADKA 159
>pdb|2R6A|A Chain A, Crystal Form Bh1
pdb|2R6A|B Chain B, Crystal Form Bh1
pdb|2R6E|A Chain A, Crystal Form B2
pdb|2R6E|B Chain B, Crystal Form B2
pdb|2R6C|A Chain A, Crystal Form Bh2
pdb|2R6C|B Chain B, Crystal Form Bh2
pdb|2R6C|C Chain C, Crystal Form Bh2
pdb|2R6C|D Chain D, Crystal Form Bh2
pdb|2R6C|E Chain E, Crystal Form Bh2
pdb|2R6C|F Chain F, Crystal Form Bh2
pdb|2R6D|A Chain A, Crystal Form B1
pdb|2R6D|B Chain B, Crystal Form B1
pdb|2R6D|C Chain C, Crystal Form B1
pdb|2R6D|D Chain D, Crystal Form B1
pdb|2R6D|E Chain E, Crystal Form B1
pdb|2R6D|F Chain F, Crystal Form B1
pdb|4ESV|A Chain A, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|B Chain B, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|C Chain C, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|D Chain D, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|E Chain E, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|F Chain F, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|G Chain G, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|H Chain H, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|I Chain I, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|J Chain J, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|K Chain K, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
pdb|4ESV|L Chain L, A New Twist On The Translocation Mechanism Of Helicases
From The Structure Of Dnab With Its Substrates
Length = 454
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 42/91 (46%), Gaps = 16/91 (17%)
Query: 344 ILRKLCKEGRIRDANRLLNEMNEKKIAPDN-----VTCNTLINAYCKIGDTASA----MK 394
++R LC EG I N + K+ P++ + +L NA I DT S ++
Sbjct: 248 VMRMLCAEGNINAQN-----LRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIR 302
Query: 395 VKNRML--EAGLMLDQFTYKALIHGFCKAKE 423
K R L E+GL + Y LI G ++KE
Sbjct: 303 AKCRRLKQESGLGMIVIDYLQLIQGSGRSKE 333
>pdb|1N9E|A Chain A, Crystal Structure Of Pichia Pastoris Lysyl Oxidase Pplo
pdb|1N9E|B Chain B, Crystal Structure Of Pichia Pastoris Lysyl Oxidase Pplo
pdb|1N9E|C Chain C, Crystal Structure Of Pichia Pastoris Lysyl Oxidase Pplo
pdb|1N9E|D Chain D, Crystal Structure Of Pichia Pastoris Lysyl Oxidase Pplo
Length = 787
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 80 SHWTMIHILTKNKHFKSAQNMLEKIALRDFLSTPSV 115
S W M+ + NK + SA+ + E + DF++ P +
Sbjct: 261 SQWKMLEYIYNNKVYTSAEELYEAMQKDDFVTLPKI 296
>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 = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 28/117 (23%), Positives = 44/117 (37%), Gaps = 11/117 (9%)
Query: 247 KKGMHYEALAVQDRMEREGISPDIVTYNSLIHGFCREGRMREARR---------LFRD-- 295
KKG EAL + D R G+ YN L++ E+ +F+
Sbjct: 38 KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXI 97
Query: 296 IKGATPNHVTYTTLIDGYCRANDLEEALRLREVMAAKGVYPGVVTYNSILRKLCKEG 352
+ PN T+T +D E A + A G+ P + +Y L C++G
Sbjct: 98 VDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKG 154
>pdb|1RKY|A Chain A, Pplo + Xe
pdb|1W7C|A Chain A, Pplo At 1.23 Angstroms
Length = 747
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 80 SHWTMIHILTKNKHFKSAQNMLEKIALRDFLSTPSV 115
S W M+ + NK + SA+ + E + DF++ P +
Sbjct: 221 SQWKMLEYIYNNKVYTSAEELYEAMQKDDFVTLPKI 256
>pdb|2VYE|A Chain A, Crystal Structure Of The Dnac-Ssdna Complex
pdb|2VYE|B Chain B, Crystal Structure Of The Dnac-Ssdna Complex
pdb|2VYF|A Chain A, Crystal Structure Of The Dnac
pdb|2VYF|B Chain B, Crystal Structure Of The Dnac
Length = 454
Score = 28.9 bits (63), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 41/91 (45%), Gaps = 16/91 (17%)
Query: 344 ILRKLCKEGRIRDANRLLNEMNEKKIAPDN-----VTCNTLINAYCKIGDTASA----MK 394
++R LC EG I N + K+ P++ + +L NA I DT S ++
Sbjct: 248 VMRMLCAEGNINAQN-----LRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIR 302
Query: 395 VKNRML--EAGLMLDQFTYKALIHGFCKAKE 423
K R L E+GL + Y LI G + +E
Sbjct: 303 AKCRRLKQESGLGMVVIDYLQLIQGSGRNRE 333
>pdb|1B89|A Chain A, Clathrin Heavy Chain Proximal Leg Segment (Bovine)
Length = 449
Score = 28.5 bits (62), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 34/141 (24%), Positives = 55/141 (39%), Gaps = 15/141 (10%)
Query: 310 IDGYCRANDLEEALRLREVMAAKGVYPGVVTYNSILRKLCKEGRIR--------DANRLL 361
ID Y +A+D + + + G + +V Y + RK +E + NRL
Sbjct: 52 IDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLA 111
Query: 362 NEMNEKKIAPDNVTCNTLINAYC---KIGDTASAM--KVKNRMLEAGLMLDQFTYKALIH 416
E+ E P+N + C K+ D A + V N A ++ Y+A +
Sbjct: 112 -ELEEFINGPNNAHIQQ-VGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVD 169
Query: 417 GFCKAKEMDIAKELLFGMLDA 437
G KA KE+ F +D
Sbjct: 170 GARKANSTRTWKEVCFACVDG 190
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
0.325 0.136 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,666,603
Number of Sequences: 62578
Number of extensions: 658336
Number of successful extensions: 1809
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1793
Number of HSP's gapped (non-prelim): 23
length of query: 591
length of database: 14,973,337
effective HSP length: 104
effective length of query: 487
effective length of database: 8,465,225
effective search space: 4122564575
effective search space used: 4122564575
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: 54 (25.4 bits)