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|15646053|ref|NP_208235.1| small protein (smpB)
[Helicobacter pylori 26695]
         (152 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|1K8H|A  Chain A, Nmr Structure Of Small Protein B (Smpb)...    99  3e-22
pdb|1FWU|A  Chain A, Crystal Structure Of The Cysteine-Rich ...    28  0.35
pdb|1DQG|A  Chain A, Crystal Structure Of The Cysteine Rich ...    28  0.35
pdb|1CG2|A  Chain A, Carboxypeptidase G2 >gi|2780969|pdb|1CG...    25  5.1
pdb|1CZ3|B  Chain B, Dihydrofolate Reductase From Thermotoga...    24  6.6
>pdb|1K8H|A Chain A, Nmr Structure Of Small Protein B (Smpb) From Aquifex
           Aeolicus
          Length = 133

 Score = 98.6 bits (244), Expect = 3e-22
 Identities = 57/128 (44%), Positives = 91/128 (70%), Gaps = 5/128 (3%)

Query: 4   IASNKKAYFDYEILETLEAGLALLGSEVKALRQT-RVNLKDNFVKIIKGEAFLFGVHISY 62
           IA NK+A   Y+ILET EAG+ L GSEVK+LR+   V+ KD+FV+I  GEA+L+ ++I+ 
Sbjct: 9   IAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAP 68

Query: 63  LDTIHAYYKPNE-RRERKLLLHKKQLLKWQIEASKERLSIVGLKLYFNQRNRAKIQIALV 121
               HA  + ++  R+RKLLLHK+++++   +  ++  +I+ LKLY+ + N+ K+ IAL 
Sbjct: 69  YK--HATIENHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYW-KNNKVKVLIALA 125

Query: 122 KGKRLHDK 129
           KGK+L+D+
Sbjct: 126 KGKKLYDR 133
>pdb|1FWU|A Chain A, Crystal Structure Of The Cysteine-Rich Domain Of Mannose
           Receptor Complexed With 3-So4-Lewis(X)
 pdb|1FWV|A Chain A, Crystal Structure Of The Cysteine-Rich Domain Of Mannose
           Receptor Complexed With 3-So4-Lewis(A)
          Length = 134

 Score = 28.5 bits (62), Expect = 0.35
 Identities = 16/43 (37%), Positives = 22/43 (50%), Gaps = 1/43 (2%)

Query: 84  KKQLLKWQIEASKERLSIVGLKLYFNQRNRAKIQIALVKGKRL 126
           K +  KW+ + +     I G +LYFN  NR +  I L KG  L
Sbjct: 74  KSEYQKWECK-NDTLFGIKGTELYFNYGNRQEKNIKLYKGSGL 115
>pdb|1DQG|A Chain A, Crystal Structure Of The Cysteine Rich Domain Of Mannose
           Receptor
 pdb|1DQO|A Chain A, Crystal Structure Of The Cysteine Rich Domain Of Mannose
           Receptor Complexed With Acetylgalactosamine-4-Sulfate
          Length = 135

 Score = 28.5 bits (62), Expect = 0.35
 Identities = 16/43 (37%), Positives = 22/43 (50%), Gaps = 1/43 (2%)

Query: 84  KKQLLKWQIEASKERLSIVGLKLYFNQRNRAKIQIALVKGKRL 126
           K +  KW+ + +     I G +LYFN  NR +  I L KG  L
Sbjct: 75  KSEYQKWECK-NDTLFGIKGTELYFNYGNRQEKNIKLYKGSGL 116
>pdb|1CG2|A Chain A, Carboxypeptidase G2
 pdb|1CG2|C Chain C, Carboxypeptidase G2
 pdb|1CG2|B Chain B, Carboxypeptidase G2
 pdb|1CG2|D Chain D, Carboxypeptidase G2
          Length = 393

 Score = 24.6 bits (52), Expect = 5.1
 Identities = 16/48 (33%), Positives = 25/48 (51%)

Query: 20 LEAGLALLGSEVKALRQTRVNLKDNFVKIIKGEAFLFGVHISYLDTIH 67
          LEA L  LG  V   +   + + DN V  IKG      + +S++DT++
Sbjct: 48 LEAELKNLGFTVTRSKSAGLVVGDNIVGKIKGRGGKNLLLMSHMDTVY 95
>pdb|1CZ3|B Chain B, Dihydrofolate Reductase From Thermotoga Maritima
 pdb|1D1G|A Chain A, Dihydrofolate Reductase From Thermotoga Maritima
 pdb|1D1G|B Chain B, Dihydrofolate Reductase From Thermotoga Maritima
 pdb|1CZ3|A Chain A, Dihydrofolate Reductase From Thermotoga Maritima
          Length = 168

 Score = 24.3 bits (51), Expect = 6.6
 Identities = 17/72 (23%), Positives = 29/72 (39%), Gaps = 2/72 (2%)

Query: 24  LALLGSEVKALRQTRVNLKDNFVKIIKGEAFLFGVHISYLDTIHAYYKPNERRERKLLLH 83
           +A++G +       R  L D     +  E ++FG  I + D    Y+       R+L   
Sbjct: 97  VAVIGGKTVFTEFLREKLVDELFVTV--EPYVFGKGIPFFDEFEGYFPLKLLEMRRLNER 154

Query: 84  KKQLLKWQIEAS 95
               LK+ +E S
Sbjct: 155 GTLFLKYSVEKS 166
  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
   0.321    0.138    0.380 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 767,863
Number of Sequences: 13198
Number of extensions: 25985
Number of successful extensions: 54
Number of sequences better than 10.0: 5
Number of HSP's better than 10.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 47
Number of HSP's gapped (non-prelim): 5
length of query: 152
length of database: 2,899,336
effective HSP length: 80
effective length of query: 72
effective length of database: 1,843,496
effective search space: 132731712
effective search space used: 132731712
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)