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= 0001.4181.p
         (470 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311574|ref|YP_003775666.1| DNA polymerase, Y family protei...   444   e-126

>gi|300311574|ref|YP_003775666.1| DNA polymerase, Y family protein
           [Herbaspirillum seropedicae SmR1]
          Length = 466

 Score =  444 bits (1143), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 249/466 (53%), Positives = 317/466 (68%), Gaps = 2/466 (0%)

Query: 7   VVLEHARVIAASPGAREAGVRVGMTRGGVLALLPQAPLHDRAPEREAQQRFAVATALLQY 66
           +V E  RV A S  AR  GV  GM RGGV  L P+A L +R P RE       A ALLQY
Sbjct: 1   MVFERERVAALSAAARACGVHEGMRRGGVQLLAPEAQLQERDPAREQAALEQTALALLQY 60

Query: 67  TPQASVSDHATLVLDIGASLRLFGGIRALRRRVCQTVKQLGLTARVSCAPTAAGAALLAR 126
           TPQ S++  A ++L++ ASLRLFGGIRAL R+V  ++ +LGL+A +SCA TA GA +LAR
Sbjct: 61  TPQVSLAPQACVLLEVSASLRLFGGIRALCRKVRVSISRLGLSATLSCAVTATGAWMLAR 120

Query: 127 YGAGNVLQMAHLHRKLDRLPVAASPAAGPYLDWLDGIGCRTLSDLRRLPRAGVQRRADAR 186
           YG    ++   L R+LDRLPV    AA  +L+WL G+GCR L  LR LPRAG+QRR    
Sbjct: 121 YGDVRTVRERSLRRRLDRLPVVLLSAAQAHLEWLHGLGCRQLGQLRALPRAGLQRRCGKA 180

Query: 187 MLELLDRAYGTAPELHTWIEMPPSFRQRIEFNARIESAEAAQHAIQALLVQLCGWLSARQ 246
           +L++L+ AYG APE+H W+  PP F+ R+E   RIE  +      QALL QL GWL+ARQ
Sbjct: 181 LLDMLEHAYGEAPEVHDWVVAPPVFQARVELPDRIEQTDILTAYAQALLTQLAGWLTARQ 240

Query: 247 LAVTQVQVALEHERGRQAVAPTMIQLSLAEPTWVDTHLMRLLKERLAQLELCAPVIAAVL 306
           LAV Q+++ LEHERGRQAVAPT ++++L+ P W + HL  L+KE+LA+  L AP IA  L
Sbjct: 241 LAVKQLRLWLEHERGRQAVAPTDLRIALSAPAWQEDHLYSLVKEKLARSTLPAPAIALGL 300

Query: 307 EATQTEAMAPASEDLFPEPGGSPADYKRLVELLIARLGPEQVRQASPLADYRPEQANRWV 366
            A + E   PAS+ LFPEPGGS  D++RL+ELL+ARLG ++VRQA+P ADYRPE ANRW 
Sbjct: 301 AAEELERRQPASDMLFPEPGGSAEDHQRLLELLVARLGADKVRQAAPRADYRPELANRWC 360

Query: 367 SVMTPAGRLDEH-PFDAHPFAPRPTWLLEQPIALSLRQHRPYYGSRLRPISPPERIEAGW 425
           SVM PA  L      DA    PRP WLL++P+ L + QH+P+Y + L   SPPERIEAGW
Sbjct: 361 SVMQPAASLPAPLSTDAARLPPRPLWLLDEPVPLRVLQHKPFYRTPLEFTSPPERIEAGW 420

Query: 426 WNGQLVTRDYYIAEDVKHCQYWIYRE-RIGDVEGIEPQWYLHGLFG 470
           W G+  TRDY+   D +H  YWI+R+   G+    EPQW+LHGLFG
Sbjct: 421 WEGRPSTRDYFTVRDAQHAYYWIFRQWHGGECPEEEPQWFLHGLFG 466


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.322    0.136    0.417 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 1,604,094
Number of extensions: 70336
Number of successful extensions: 241
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 239
Number of HSP's successfully gapped: 1
Length of query: 470
Length of database: 1,619,870
Length adjustment: 89
Effective length of query: 381
Effective length of database: 1,198,455
Effective search space: 456611355
Effective search space used: 456611355
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 132 (55.5 bits)