BLASTP 2.2.18 [Mar-02-2008]


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= 0566.0004.p
         (390 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           2,715,099 sequences; 757,237,578 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|ZP_00060122.1| hypothetical protein [Clostridium thermocellu...    65   3e-09
ref|ZP_00059775.1| COG0860: N-acetylmuramoyl-L-alanine amidase [...    62   2e-08
ref|ZP_00059658.1| hypothetical protein [Clostridium thermocellu...    62   2e-08
ref|ZP_00062184.1| hypothetical protein [Clostridium thermocellu...    59   2e-07
ref|ZP_00062237.1| hypothetical protein [Clostridium thermocellu...    59   3e-07

>ref|ZP_00060122.1| hypothetical protein [Clostridium thermocellum ATCC 27405]
          Length = 265

 Score = 65.1 bits (157), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 37/123 (30%), Positives = 59/123 (47%), Gaps = 5/123 (4%)

Query: 256 GDYEFMHDTPVPVQKPIAVSLNGENVPLTAGVITRNGQNFVPLRSLFDKLGAEIGFDGTS 315
           G + F           I V LNG  +        +NG+  VP R++F+ LG +I ++G +
Sbjct: 30  GSFSFAVQNSYASADEIKVFLNGVEIKFDVAPYIKNGRTMVPFRAIFEALGVDISWNGVN 89

Query: 316 KLATVTRTNPSLPALKISVNAKNGQTTLNGQAVTLENKPFTVNGTLYLPLRFISEKLGAT 375
           +  T+  TN +    +I +        +NG  V L+ +   V G  ++PLRF+SE  GA 
Sbjct: 90  R--TILATNDT---TEIYIEIGKAFAYVNGYKVNLDAEAEIVGGRTFVPLRFVSENAGAD 144

Query: 376 VEW 378
           V W
Sbjct: 145 VSW 147


>ref|ZP_00059775.1| COG0860: N-acetylmuramoyl-L-alanine amidase [Clostridium
           thermocellum ATCC 27405]
          Length = 980

 Score = 62.0 bits (149), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 62/101 (61%), Gaps = 7/101 (6%)

Query: 288 ITRNGQNFVPLRSLFDKLGAEIGFDGTSKLATVTRTNPSLPALKIS-VNAKNGQTTLNGQ 346
           I  NG++ VP+R++F+KLGA++G+D  SK  T++  + ++  LKI+ VNA      +NG 
Sbjct: 90  IIINGRSLVPVRAIFEKLGAKVGWDAASKKVTISYDSNTIE-LKINDVNA-----LVNGT 143

Query: 347 AVTLENKPFTVNGTLYLPLRFISEKLGATVEWLPKEERISI 387
            V +E     +N    +P+RF+ E+LG  V W  ++  I++
Sbjct: 144 KVAMEVPAKIINDRTVVPVRFVGEQLGMEVGWNAEKGEITL 184


>ref|ZP_00059658.1| hypothetical protein [Clostridium thermocellum ATCC 27405]
          Length = 276

 Score = 62.0 bits (149), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 65/133 (48%), Gaps = 6/133 (4%)

Query: 256 GDYEFMHDTPVPVQKPIAVSLNGENVPLTAGVITRNGQNFVPLRSLFDKLGAEIGFDGTS 315
            DY    +T   + K + V LNG+ +      I +NG+  VPLR++F+ + A + +D  +
Sbjct: 147 ADYSLTVNTVGGIPK-VKVFLNGKRIRFDQPPIIQNGRTLVPLRAIFEAMNATVSWDDKT 205

Query: 316 KLATVTRTNPSLPALKISVNAKNGQTTLNGQAVTLENKPFTVNGTLYLPLRFISEKLGAT 375
           K  T  + + +     I +   N     NG A+ L+  P  VNG   +P R ++E  GA 
Sbjct: 206 KTVTAKKGDTT-----IVMTIGNKTMKKNGVAIELDVPPQIVNGRTLVPARAVAESFGAK 260

Query: 376 VEWLPKEERISIT 388
           V+W      ++IT
Sbjct: 261 VDWDGSTRTVTIT 273


>ref|ZP_00062184.1| hypothetical protein [Clostridium thermocellum ATCC 27405]
          Length = 243

 Score = 58.5 bits (140), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 67/126 (53%), Gaps = 7/126 (5%)

Query: 254 GYGDYEFMHDTPVPVQKPIAVSLNGENVPL-TAGVITRNGQNFVPLRSLFDKLGAEIGFD 312
           G G+ ++ +D P  +   I V +NG+ V          NG+  VP+R++ +++GAE+ ++
Sbjct: 113 GIGEEDYTYDIP-ALSDGINVVMNGKVVYFPDVKPENVNGRVLVPIRTISEEMGAEVTYN 171

Query: 313 GTSKLATVTRTNPSLPALKISVNAKNGQTTLNGQAVTLENKPFTVNGTLYLPLRFISEKL 372
             +K   + + +      +I +   + +  +NG+ + L+     + G   +PLRFISE +
Sbjct: 172 DATKQVLIAKDDT-----EILLTIGSQEAYVNGEKIMLDVPAMIIEGRTMVPLRFISESM 226

Query: 373 GATVEW 378
            ATVEW
Sbjct: 227 NATVEW 232


>ref|ZP_00062237.1| hypothetical protein [Clostridium thermocellum ATCC 27405]
          Length = 269

 Score = 58.5 bits (140), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 58/110 (52%), Gaps = 7/110 (6%)

Query: 271 PIAVSLNGENV--PLTAGVITRNGQNFVPLRSLFDKLGAEIGFDGTSKLATVTRTNPSLP 328
           P+ V +NGE +  P     I  NG+   P R + + LGA + +DG +K A    +  +L 
Sbjct: 28  PLRVVVNGEELYFPDEKPFIDANGRTQTPARFIGEALGATVTWDGNAKKAVFKMSGTTL- 86

Query: 329 ALKISVNAKNGQTTLNGQAVTLENKPFTVNGTLYLPLRFISEKLGATVEW 378
             ++ +  +  Q  LNGQ   ++ +   +NG  ++P R+++E  GATV W
Sbjct: 87  --ELFIGEREYQ--LNGQKKQMDTEALLINGRTFVPARYVAEAFGATVRW 132


  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Mar 24, 2004  1:53 AM
  Number of letters in database: 757,237,578
  Number of sequences in database:  2,715,099
  
Lambda     K      H
   0.315    0.133    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 2715099
Number of Hits to DB: 590,170,806
Number of extensions: 24701658
Number of successful extensions: 60987
Number of sequences better than 1.0e-05: 18
Number of HSP's gapped: 60968
Number of HSP's successfully gapped: 18
Length of query: 390
Length of database: 757,237,578
Length adjustment: 128
Effective length of query: 262
Effective length of database: 409,704,906
Effective search space: 107342685372
Effective search space used: 107342685372
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 127 (53.5 bits)