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= 0028.0187.p
         (482 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311159|ref|YP_003775251.1| DNA topoisomerase IV subunit A ...   910   0.0  
gi|300312989|ref|YP_003777081.1| DNA gyrase subunit A protein [H...   361   e-101

>gi|300311159|ref|YP_003775251.1| DNA topoisomerase IV subunit A
           [Herbaspirillum seropedicae SmR1]
          Length = 771

 Score =  910 bits (2352), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 442/461 (95%), Positives = 456/461 (98%)

Query: 1   MTDQPTLFDQAPAAPDGESLTLSTFAERAYLDYAISVVKGRALPDVADGQKPVQRRILYA 60
           MTDQPTLFDQ P+APDGESLTLSTFAERAYLDYAISVVKGRALPDVADGQKPVQRRILYA
Sbjct: 1   MTDQPTLFDQVPSAPDGESLTLSTFAERAYLDYAISVVKGRALPDVADGQKPVQRRILYA 60

Query: 61  MNELSLNSAAKPRKSAAVVGDVLGKLHPHGDQSVYDALVRMAQDFSLRYPLIDGHGNFGS 120
           MNELSLNSAAKPRKSAAVVGDVLGKLHPHGDQSVYDALVRMAQDFSLRYPLIDGHGNFGS
Sbjct: 61  MNELSLNSAAKPRKSAAVVGDVLGKLHPHGDQSVYDALVRMAQDFSLRYPLIDGHGNFGS 120

Query: 121 RDGDGAAAMRYTEARLTPISKLLLDEIDMGTVDFQPNYDGSTEEPRLLPARLPFLLLNGA 180
           RDGDGAAAMRYTEARLTPISKLLLDEIDMGTV+FQPNYDGSTEEPRLLPARLPFLLLNGA
Sbjct: 121 RDGDGAAAMRYTEARLTPISKLLLDEIDMGTVEFQPNYDGSTEEPRLLPARLPFLLLNGA 180

Query: 181 SGIAVGMATEIPSHNLTEVAKAAVAMIRNPKITHAELMELIPGPDFPGGGQIITPKSTIA 240
           SGIAVGMATEIPSHNLTEVAKAAVAMIRNPKI+HAELMELIPGPDFPGGGQIITP++TIA
Sbjct: 181 SGIAVGMATEIPSHNLTEVAKAAVAMIRNPKISHAELMELIPGPDFPGGGQIITPQATIA 240

Query: 241 EMYQSGRGSLKVRARWKIEDLARGQWQAVITELPPGVSSQRVLEEIEELTNPKLKLGKKS 300
           EMYQSGRGSLKVRARWKIEDLARGQWQAVITELPPGVSSQRVLEEIEELTNPK+KLGKKS
Sbjct: 241 EMYQSGRGSLKVRARWKIEDLARGQWQAVITELPPGVSSQRVLEEIEELTNPKVKLGKKS 300

Query: 301 LTPEQQTQKAAILGLLDAVRDESGREAPVRLVFEPKSKNQDQTEFMNTLLAQTSLETSAS 360
           LTPEQQ QKAAILGLLDAVRDESGR+APVRLVFEPKSKNQDQTEFMNTLLAQTSLETSAS
Sbjct: 301 LTPEQQAQKAAILGLLDAVRDESGRDAPVRLVFEPKSKNQDQTEFMNTLLAQTSLETSAS 360

Query: 361 LNLVMIGGDGRPRQKNLTDILTEWISFRFETVTRRTQFRMQKVNDRIHILEGREAVLLNI 420
           LNLVMIGGDGRPRQKNLTDIL+EWISFRFETVTRRTQFRMQKVNDRIHILEGREAVLLNI
Sbjct: 361 LNLVMIGGDGRPRQKNLTDILSEWISFRFETVTRRTQFRMQKVNDRIHILEGREAVLLNI 420

Query: 421 DKVIKIIRESDEPKPALMDAFKLSDRQAEDILEIRPSRSSR 461
           DKVI+IIRESDEPKPAL++AF+LSDRQAEDILEIR  + +R
Sbjct: 421 DKVIRIIRESDEPKPALIEAFRLSDRQAEDILEIRLRQLAR 461


>gi|300312989|ref|YP_003777081.1| DNA gyrase subunit A protein
           [Herbaspirillum seropedicae SmR1]
          Length = 881

 Score =  361 bits (927), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 206/427 (48%), Positives = 270/427 (63%), Gaps = 27/427 (6%)

Query: 20  LTLSTFAERAYLDYAISVVKGRALPDVADGQKPVQRRILYAMNELSLNSAAKPR-KSAAV 78
           ++L     ++YLDYA+SV+ GRALPDV DG KPV RR+LYAM+E++ N   +P  K A V
Sbjct: 11  ISLEEEMRKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMHEMN-NVWNRPFVKCARV 69

Query: 79  VGDVLGKLHPHGDQSVYDALVRMAQDFSLRYPLIDGHGNFGSRDGDGAAAMRYTEARLTP 138
           VG+V+GK HPHGD S+YD LVRMAQDFSLRY L+DG GNFGS DGDGAAAMRYTE RL  
Sbjct: 70  VGEVMGKYHPHGDASIYDTLVRMAQDFSLRYTLVDGQGNFGSIDGDGAAAMRYTECRLDK 129

Query: 139 ISKLLLDEIDMGTVDFQPNYDGSTEEPRLLPARLPFLLLNGASGIAVGMATEIPSHNLTE 198
           IS  LL +I+  TVDF PNYDG  +EP +LP R+P LL+NG+SGIAVGMAT IP HN+TE
Sbjct: 130 ISNELLADIEKETVDFVPNYDGKEKEPSVLPTRIPNLLVNGSSGIAVGMATNIPPHNITE 189

Query: 199 VAKAAVAMIRNPKITHAELMELIPGPDFPGGGQIITPKSTIAEMYQSGRGSLKVRARWKI 258
           V   A+ ++ N + T  EL+EL+P PDFP GG II   S + + Y++GRG + +RA+   
Sbjct: 190 VINGALHLLANEQCTIDELIELVPAPDFPTGG-IIYGVSGVRDGYRTGRGRVVMRAKTHF 248

Query: 259 EDLAR-GQWQAVITELPPGVSSQRVLEEIEELTNPKLKLGKKSLTPEQQTQKAAILGLLD 317
           E+  R G+   ++ ELP  V+ + +LE I EL   K   G   L                
Sbjct: 249 EEYGREGRIAIIVDELPYQVNKKALLERIAELVRDKKLEGISDL---------------- 292

Query: 318 AVRDESGREAPVRLVFEPKSKNQDQTEFMNTLLAQTSLETSASLNLVMIGGDGRPRQKNL 377
             RDES +   +R+V E K     +   +N L  QT L+ +  +N+V +  DG+PR  NL
Sbjct: 293 --RDESDKSG-MRVVIELKRGEVPEV-VLNNLYKQTQLQDTFGMNMVAL-VDGQPRLLNL 347

Query: 378 TDILTEWISFRFETVTRRTQFRMQKVNDRIHILEGREAVLLNIDKVIKIIRESDEPKPAL 437
             +L  ++S R E VTRRT F ++K  +R H+LEG    L NID  I IIR +  P P +
Sbjct: 348 KQLLECFLSHRREVVTRRTVFELRKARERGHVLEGLAVALANIDDFIAIIRAA--PTPPI 405

Query: 438 MDAFKLS 444
             A  +S
Sbjct: 406 AKAELMS 412


  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
   0.317    0.134    0.386 

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: 1,482,008
Number of extensions: 61054
Number of successful extensions: 208
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 205
Number of HSP's successfully gapped: 2
Length of query: 482
Length of database: 1,619,870
Length adjustment: 89
Effective length of query: 393
Effective length of database: 1,198,455
Effective search space: 470992815
Effective search space used: 470992815
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 (21.7 bits)
S2: 132 (55.5 bits)