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= 042101
(380 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Q57|A Chain A, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|B Chain B, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|C Chain C, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|D Chain D, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|E Chain E, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|F Chain F, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
pdb|1Q57|G Chain G, The Crystal Structure Of The Bifunctional Primase-helicase
Of Bacteriophage T7
Length = 503
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 50/166 (30%), Positives = 71/166 (42%), Gaps = 33/166 (19%)
Query: 203 HNGVLVGCKYRSMERKFRQEKGTEK--WLYGLDDINETAEVIIVEGEIDKLSVEEAGFQN 260
NG +V K R ++ F+ G+ K L+G N ++++ EGEID L+V E Q+
Sbjct: 51 QNGNIVSQKVRDKDKNFKT-TGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVME--LQD 107
Query: 261 C----VSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALA 316
C VS+ GA +K Y E+ D+ +IIL D D G
Sbjct: 108 CKYPVVSLGHGASAA---------KKTCAANY-----EYFDQFEQIILMFDMDEAGRKAV 153
Query: 317 EELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIE 362
EE A+ L + P KDANE C G RE++E
Sbjct: 154 EEAAQVLPAGKVRVAVLP-------CKDANE---CHLNGHDREIME 189
>pdb|1NUI|A Chain A, Crystal Structure Of The Primase Fragment Of Bacteriophage
T7 Primase- Helicase Protein
pdb|1NUI|B Chain B, Crystal Structure Of The Primase Fragment Of Bacteriophage
T7 Primase- Helicase Protein
Length = 255
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 50/166 (30%), Positives = 71/166 (42%), Gaps = 33/166 (19%)
Query: 203 HNGVLVGCKYRSMERKFRQEKGTEK--WLYGLDDINETAEVIIVEGEIDKLSVEEAGFQN 260
NG +V K R ++ F+ G+ K L+G N ++++ EGEID L+V E Q+
Sbjct: 114 QNGNIVSQKVRDKDKNFKT-TGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVME--LQD 170
Query: 261 C----VSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALA 316
C VS+ GA +K Y E+ D+ +IIL D D G
Sbjct: 171 CKYPVVSLGHGASAA---------KKTCAANY-----EYFDQFEQIILMFDMDEAGRKAV 216
Query: 317 EELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIE 362
EE A+ L + P KDANE C G RE++E
Sbjct: 217 EEAAQVLPAGKVRVAVLP-------CKDANE---CHLNGHDREIME 252
>pdb|1Q1J|L Chain L, Crystal Structure Analysis Of Anti-Hiv-1 Fab 447-52d In
Complex With V3 Peptide
pdb|1Q1J|M Chain M, Crystal Structure Analysis Of Anti-Hiv-1 Fab 447-52d In
Complex With V3 Peptide
Length = 215
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 33/141 (23%), Positives = 56/141 (39%), Gaps = 16/141 (11%)
Query: 36 LLSYPTHVTGNP----SLQCNSDAESFGEHKDDTIDISKLTEVKQKLKLVGINCDDSCIP 91
+L+ P V+ P ++ C+ + + G + + + KL + G N S IP
Sbjct: 3 VLTQPPSVSAAPGQKVTISCSGSSSNIGNNY--VLWYQQFPGTAPKLLIYGNNKRPSGIP 60
Query: 92 GRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGR-AFAGSNKIRKVM 150
R++ G +L + +Q GD A + C D G + F G K+ V+
Sbjct: 61 DRFS--------GSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLT-VL 111
Query: 151 SSRQVAEKSLGLEPLGEKLIA 171
S + A P E+L A
Sbjct: 112 SQPKAAPSVTLFPPSSEELQA 132
>pdb|3C2A|L Chain L, Antibody Fab Fragment 447-52d In Complex With Ug1033
Peptide
pdb|3C2A|M Chain M, Antibody Fab Fragment 447-52d In Complex With Ug1033
Peptide
pdb|3GHB|L Chain L, Crystal Structure Of Anti-Hiv-1 Fab 447-52d In Complex
With V3 Peptide W2rw020
pdb|3GHB|M Chain M, Crystal Structure Of Anti-Hiv-1 Fab 447-52d In Complex
With V3 Peptide W2rw020
Length = 216
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 33/141 (23%), Positives = 56/141 (39%), Gaps = 16/141 (11%)
Query: 36 LLSYPTHVTGNP----SLQCNSDAESFGEHKDDTIDISKLTEVKQKLKLVGINCDDSCIP 91
+L+ P V+ P ++ C+ + + G + + + KL + G N S IP
Sbjct: 3 VLTQPPSVSAAPGQKVTISCSGSSSNIGNNY--VLWYQQFPGTAPKLLIYGNNKRPSGIP 60
Query: 92 GRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGR-AFAGSNKIRKVM 150
R++ G +L + +Q GD A + C D G + F G K+ V+
Sbjct: 61 DRFS--------GSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLT-VL 111
Query: 151 SSRQVAEKSLGLEPLGEKLIA 171
S + A P E+L A
Sbjct: 112 SQPKAAPSVTLFPPSSEELQA 132
>pdb|4E2K|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
pdb|4EDG|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Atp And Manganese
pdb|4EDK|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Gtp And Manganese
pdb|4EDR|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Utp And Manganese
pdb|4EDT|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Ppgpp And Manganese
pdb|4EDV|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Pppgpp And Manganese
pdb|4EE1|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain
Bound To Ctp And Manganese
Length = 329
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 29/100 (29%), Positives = 44/100 (44%), Gaps = 16/100 (16%)
Query: 181 GTLQRNSVMQRLHDQA---IAFPYWH-NGVLVGCK---YRSMERKFRQEKGT-----EKW 228
G L RN +D+ I FP + G +VG Y E K+ T K
Sbjct: 79 GLLSRNEENFSYYDRFRNRIMFPLKNAQGRIVGYSGRTYTGQEPKYLNSPETPIFQKRKL 138
Query: 229 LYGLD----DINETAEVIIVEGEIDKLSVEEAGFQNCVSV 264
LY LD I + E++++EG +D + + AG +N V+
Sbjct: 139 LYNLDKARKSIRKLDEIVLLEGFMDVIKSDTAGLKNVVAT 178
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
0.319 0.136 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,826,725
Number of Sequences: 62578
Number of extensions: 502662
Number of successful extensions: 1329
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1327
Number of HSP's gapped (non-prelim): 6
length of query: 380
length of database: 14,973,337
effective HSP length: 101
effective length of query: 279
effective length of database: 8,652,959
effective search space: 2414175561
effective search space used: 2414175561
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)