GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Herbaspirillum seropedicae SmR1

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate HSERO_RS20660 HSERO_RS20660 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__HerbieS:HSERO_RS20660
          Length = 401

 Score =  558 bits (1439), Expect = e-164
 Identities = 276/399 (69%), Positives = 332/399 (83%), Gaps = 1/399 (0%)

Query: 3   DVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGE 62
           +  ICDAIRTP GR+GGAL  VRADDLAA P+++L+E NP V W +V+++ +GCANQAGE
Sbjct: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61

Query: 63  DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSR 122
           DNRNVARMA LLAGLP ++PG T+NRLC S +DA+G A RAI SGE++L IAGGVESM+R
Sbjct: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121

Query: 123 APFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQD 182
           APFVMGKAES ++R+  + DTTIGWRF+NPLMK+QYG+DSMPETA+NVA D+Q++RADQD
Sbjct: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181

Query: 183 AFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKLKPVN 241
           AFALRSQQ+ AAAQAAGFFA EI P+ I  KKG+  +V  DEH RP+TTL  L KLK V 
Sbjct: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241

Query: 242 GPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPA 301
            PD TVTAGNASGVNDGA AL+LAS +A   + L PRARVLGMA+ GVAPR+MG GP PA
Sbjct: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301

Query: 302 VRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMS 361
           VRK+  ++G+ ++  DVIELNEAFA+QGLAV+R+LG+ DDA  VNPNGGAIA+GHPLG S
Sbjct: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361

Query: 362 GARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GARLV TA++QLE+SGGR  L TMC+GVGQG+AL IERV
Sbjct: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400


Lambda     K      H
   0.318    0.134    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 549
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 400
Length of database: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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: 50 (23.9 bits)

Align candidate HSERO_RS20660 HSERO_RS20660 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.20076.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20076.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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