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_RS19990 HSERO_RS19990 acetyl-CoA acetyltransferase

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



>FitnessBrowser__HerbieS:HSERO_RS19990
          Length = 400

 Score =  570 bits (1469), Expect = e-167
 Identities = 289/401 (72%), Positives = 339/401 (84%), Gaps = 2/401 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M+DVFICDAIRTPIGR+GGAL  VRADDL AVPL+AL+E NP V W  VD+V +GCANQA
Sbjct: 1   MKDVFICDAIRTPIGRYGGALKDVRADDLGAVPLRALMERNPQVDWKAVDDVIYGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARM+LLLAGLP+ +PG T+NRLC SGMDA+GTA RAI SGE +L IAGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPQEVPGSTINRLCGSGMDALGTAARAIKSGETQLMIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           +RAPFVMGKA+S +SR   ++DTTIGWRF+N LMK +YGVD+MPETA+NVA D++VSRAD
Sbjct: 121 TRAPFVMGKADSAFSRQAAIQDTTIGWRFVNALMKQKYGVDAMPETAENVAVDFKVSRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKLKP 239
           QD FA+RSQ KAAAAQA G  A+EIVPV I  KKG+ I V +DEH R  T++EAL +LK 
Sbjct: 181 QDQFAVRSQAKAAAAQANGTLAQEIVPVVIPQKKGDPITVTQDEHPR-ATSMEALARLKG 239

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
           V  PD +VTAGNASGVNDGA AL+LASAEAV+K+ L PRAR+LGMA+ GVAPR+MG+GP 
Sbjct: 240 VVKPDGSVTAGNASGVNDGACALLLASAEAVEKYQLKPRARILGMATAGVAPRIMGMGPA 299

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
           PA +K+  +LG+ +   DVIELNEAFASQGLAVLRELGVADD  +VNPNGGAIALGHPLG
Sbjct: 300 PASKKVLAQLGMTIDQMDVIELNEAFASQGLAVLRELGVADDDARVNPNGGAIALGHPLG 359

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           MSGARLV TA +QLE++GGR  L TMC+GVGQG+A+ IERV
Sbjct: 360 MSGARLVTTATYQLERTGGRYALCTMCIGVGQGIAMVIERV 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: 546
Number of extensions: 18
Number of successful extensions: 1
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: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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_RS19990 HSERO_RS19990 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.3895.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3895.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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