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= 0001.2638.p
         (345 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311912|ref|YP_003776004.1| DNA polymerase III subunit delt...   641   0.0  
gi|300312975|ref|YP_003777067.1| DNA polymerase III subunit gamm...    76   4e-15

>gi|300311912|ref|YP_003776004.1| DNA polymerase III subunit delta
           [Herbaspirillum seropedicae SmR1]
          Length = 345

 Score =  641 bits (1654), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 326/345 (94%), Positives = 340/345 (98%)

Query: 1   MSVTSSEVLLPWQGESWRQLQQLRERLPHALLFYGAAGTGKTQFVEAFAKSLLCESPTPQ 60
           MS+TSS+VLLPWQGESWRQLQQLRERLPHALLFYGAAGTGKTQFVEAFAKSLLCESPTP+
Sbjct: 1   MSLTSSDVLLPWQGESWRQLQQLRERLPHALLFYGAAGTGKTQFVEAFAKSLLCESPTPE 60

Query: 61  AHACGVCASCNWFSQSNHPDYRRVRPEMLEEEMAEDEAGEEKKSTKASKAPSKDIKIDQI 120
           AHACGVCASCNWFSQSNHPDYRRVRPE+L++E A+DEAGEEKK+ KASKAPSKDIKIDQI
Sbjct: 61  AHACGVCASCNWFSQSNHPDYRRVRPEVLDDETADDEAGEEKKTAKASKAPSKDIKIDQI 120

Query: 121 RALADFMNVSTHRSGLRVVMLYPAEALNTAAANALLKTLEEPPPGTMFLLLSNRLDRLLP 180
           RALADFMNVSTHRSGLRVVMLYPAEALNTAAANALLKTLEEPPPGTMFLLLSNRLDRLLP
Sbjct: 121 RALADFMNVSTHRSGLRVVMLYPAEALNTAAANALLKTLEEPPPGTMFLLLSNRLDRLLP 180

Query: 181 TILSRCRKFALTAPGHDEALAWLKQQGVKDADAWLAEQGGAPLAALQAAQGEGREALDEL 240
           TILSRCRKFAL+APGH EALAWLKQQGVKDADAWLAEQGGAPLAAL+AAQGEGREALDEL
Sbjct: 181 TILSRCRKFALSAPGHGEALAWLKQQGVKDADAWLAEQGGAPLAALEAAQGEGREALDEL 240

Query: 241 LRHLAQPGVDGALRAADKLQKTPAAELVGWVQRWLYDLLSLKSAGVVRYYPRYGKELGRL 300
           LRHLAQPGVDGALRAADKLQKTPAA+LVGWVQRWLYDLLSLKSAGVVRYYPRYGKELGRL
Sbjct: 241 LRHLAQPGVDGALRAADKLQKTPAADLVGWVQRWLYDLLSLKSAGVVRYYPRYGKELGRL 300

Query: 301 AGRVEALALTRALRGMGERRAIADHPLSAKLFIEEMLIDYARLFD 345
           A RV+ALAL+RALRGMG+RRAIADHPLSAKLFIEEMLIDYA LFD
Sbjct: 301 AERVDALALSRALRGMGDRRAIADHPLSAKLFIEEMLIDYAGLFD 345


>gi|300312975|ref|YP_003777067.1| DNA polymerase III subunit
           gamma/tau [Herbaspirillum seropedicae SmR1]
          Length = 712

 Score = 75.9 bits (185), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 76/179 (42%), Gaps = 31/179 (17%)

Query: 24  RERLPHALLFYGAAGTGKTQFVEAFAKSLLCESPTP----QAHACGVCASCNWFSQSNHP 79
           ++RL HA LF G  G GKT      AKSL C  P       A  CGVC +C         
Sbjct: 34  QQRLHHAYLFTGTRGVGKTTLSRILAKSLNCVGPDGAGGITAAPCGVCEACVAIDAGRFV 93

Query: 80  DYRRVRPEMLEEEMAEDEAGEEKKSTKASKAPSKDIKIDQIRALADFMNVSTHRSGLRVV 139
           DY       +E + A +                    +D++  L +    +   +  +V 
Sbjct: 94  DY-------IEMDAASNRG------------------VDEMAQLLEQAIYAPSNARFKVY 128

Query: 140 MLYPAEALNTAAANALLKTLEEPPPGTMFLLLSNRLDRLLPTILSRCRKFAL--TAPGH 196
           M+     L   A NA+LKTLEEPP    F+L +    ++  T+LSRC +F L    PGH
Sbjct: 129 MIDEVHMLTNHAFNAMLKTLEEPPEHIKFILATTDPQKIPVTVLSRCLQFNLKQMPPGH 187


  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
   0.319    0.133    0.396 

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: 893,524
Number of extensions: 29608
Number of successful extensions: 153
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 150
Number of HSP's successfully gapped: 2
Length of query: 345
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 259
Effective length of database: 1,212,660
Effective search space: 314078940
Effective search space used: 314078940
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 (21.8 bits)
S2: 131 (55.1 bits)