BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= gi|15645541|ref|NP_207717.1| recombinational DNA repair
protein (recR) [Helicobacter pylori 26695]
(193 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1BF5|A Chain A, Stat-1 Dna Complex 28 0.53
pdb|1KB9|B Chain B, Yeast Cytochrome Bc1 Complex >gi|142777... 27 2.0
pdb|1D5V|A Chain A, Solution Structure Of The Forkhead Doma... 26 2.6
pdb|2HFH| The Nmr Structures Of A Winged Helix Protein: G... 26 3.4
pdb|2HDC|A Chain A, Structure Of Transcription Factor Genes... 26 3.4
pdb|1TF4|A Chain A, EndoEXOCELLULASE FROM THERMOMONOSPORA >... 25 4.5
pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase... 25 5.8
pdb|1JMK|O Chain O, Structural Basis For The Cyclization Of... 25 7.6
>pdb|1BF5|A Chain A, Stat-1 Dna Complex
Length = 545
Score = 28.5 bits (62), Expect = 0.53
Identities = 13/49 (26%), Positives = 27/49 (54%)
Query: 85 QLCMVLHPRDVFILEDLKDFLGRYYVLNSIEEVDFNALEKRLIEENIKE 133
Q CM HP+ +L+ F + +L ++E+++N K L ++++ E
Sbjct: 173 QPCMPTHPQRPLVLKTGVQFTVKLRLLVKLQELNYNLKVKVLFDKDVNE 221
>pdb|1KB9|B Chain B, Yeast Cytochrome Bc1 Complex
pdb|1EZV|B Chain B, Structure Of The Yeast Cytochrome Bc1 Complex Co-
Crystallized With An Antibody Fv-Fragment
pdb|1KYO|B Chain B, Yeast Cytochrome Bc1 Complex With Bound Substrate
Cytochrome C
pdb|1KYO|M Chain M, Yeast Cytochrome Bc1 Complex With Bound Substrate
Cytochrome C
Length = 352
Score = 26.6 bits (57), Expect = 2.0
Identities = 37/166 (22%), Positives = 65/166 (38%), Gaps = 43/166 (25%)
Query: 5 KNSLNHFLNLVDCLEKIPNVGKKSAFKMA---------YHLGLENPYLALKITHALE--- 52
K+ + H LN + N +SA K+ + L+ Y+ LK T +
Sbjct: 28 KDGVAHLLNRFN----FQNTNTRSALKLVRESELLGGTFKSTLDREYITLKATFLKDDLP 83
Query: 53 ---NALENL--KTCSSCNALSES---------EVCEICSDESRQNSQLCMVLHPR----- 93
NAL ++ KT + L+ES V E C +S ++ +
Sbjct: 84 YYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQCPVKSAEDQLYAITFRKGLGNPL 143
Query: 94 -----DVFILEDLKDFLGRYYVLNSIEEVDFNALE---KRLIEENI 131
+ L+D+KDF + Y ++E N +E KR ++E++
Sbjct: 144 LYDGVERVSLQDIKDFADKVYTKENLEVSGENVVEADLKRFVDESL 189
>pdb|1D5V|A Chain A, Solution Structure Of The Forkhead Domain Of The
Adipocyte- Transcription Factor Freac-11 (S12)
Length = 94
Score = 26.2 bits (56), Expect = 2.6
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 4 YKNSLNHFLNLVDCLEKIPNVGKK 27
++NS+ H L+L +C K+P KK
Sbjct: 48 WQNSIRHNLSLNECFVKVPRDDKK 71
>pdb|2HFH| The Nmr Structures Of A Winged Helix Protein: Genesis, 20
Structures
Length = 109
Score = 25.8 bits (55), Expect = 3.4
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 4 YKNSLNHFLNLVDCLEKIP 22
++NS+ H L+L DC KIP
Sbjct: 47 WQNSIRHNLSLNDCFVKIP 65
>pdb|2HDC|A Chain A, Structure Of Transcription Factor GenesisDNA COMPLEX
Length = 97
Score = 25.8 bits (55), Expect = 3.4
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 4 YKNSLNHFLNLVDCLEKIP 22
++NS+ H L+L DC KIP
Sbjct: 46 WQNSIRHNLSLNDCFVKIP 64
>pdb|1TF4|A Chain A, EndoEXOCELLULASE FROM THERMOMONOSPORA
pdb|1TF4|B Chain B, EndoEXOCELLULASE FROM THERMOMONOSPORA
pdb|4TF4|A Chain A, EndoEXOCELLULASE:CELLOPENTAOSE FROM THERMOMONOSPORA
pdb|4TF4|B Chain B, EndoEXOCELLULASE:CELLOPENTAOSE FROM THERMOMONOSPORA
pdb|1JS4|A Chain A, EndoEXOCELLULASE:CELLOBIOSE FROM THERMOMONOSPORA
pdb|1JS4|B Chain B, EndoEXOCELLULASE:CELLOBIOSE FROM THERMOMONOSPORA
pdb|3TF4|A Chain A, EndoEXOCELLULASE:CELLOTRIOSE FROM THERMOMONOSPORA
pdb|3TF4|B Chain B, EndoEXOCELLULASE:CELLOTRIOSE FROM THERMOMONOSPORA
Length = 605
Score = 25.4 bits (54), Expect = 4.5
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 109 YVLNSIE---EVDFNALEKRLIEENIKEIIFAFPPTLANDSLMLYIEDKLQHFHLTFTKI 165
YV N + F++ L+EE + FPPT D +++E ++ TFT+I
Sbjct: 420 YVANEVATDYNAGFSSALAMLVEEYGGTPLADFPPTEEPDGPEIFVEAQINTPGTTFTEI 479
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
Length = 1524
Score = 25.0 bits (53), Expect = 5.8
Identities = 11/30 (36%), Positives = 18/30 (59%)
Query: 100 DLKDFLGRYYVLNSIEEVDFNALEKRLIEE 129
D+ +G + ++E+D ALEK L+EE
Sbjct: 451 DIDARMGAEAIQQLLKELDLEALEKELLEE 480
>pdb|1JMK|O Chain O, Structural Basis For The Cyclization Of The Lipopeptide
Antibiotic Surfactin By The Thioesterase Domain Srfte
pdb|1JMK|C Chain C, Structural Basis For The Cyclization Of The Lipopeptide
Antibiotic Surfactin By The Thioesterase Domain Srfte
Length = 230
Score = 24.6 bits (52), Expect = 7.6
Identities = 10/35 (28%), Positives = 20/35 (56%)
Query: 126 LIEENIKEIIFAFPPTLANDSLMLYIEDKLQHFHL 160
++ ++ ++IIFAFPP L + + +L + L
Sbjct: 11 IMNQDQEQIIFAFPPVLGYGLMYQNLSSRLPSYKL 45
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.320 0.136 0.390
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,034,321
Number of Sequences: 13198
Number of extensions: 37467
Number of successful extensions: 102
Number of sequences better than 10.0: 8
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 95
Number of HSP's gapped (non-prelim): 8
length of query: 193
length of database: 2,899,336
effective HSP length: 83
effective length of query: 110
effective length of database: 1,803,902
effective search space: 198429220
effective search space used: 198429220
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: 51 (24.3 bits)