GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Burkholderia phytofirmans PsJN

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate BPHYT_RS17345 BPHYT_RS17345 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__BFirm:BPHYT_RS17345
          Length = 400

 Score =  588 bits (1516), Expect = e-173
 Identities = 295/401 (73%), Positives = 343/401 (85%), Gaps = 1/401 (0%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           MN+A I DA+RTPIGRY GAL  VRADDLGA+P+KALI R+P +DW  VDDVIYGCANQA
Sbjct: 1   MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ALLAGLPV  PG+T+NRLCGSG+DAVG+AARA++ GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           +RAPFVMGK+  AF R A+I+DTTIGWRF+N LM++ +G+DSMPETAENVAA+F++SRAD
Sbjct: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFAL SQ KAA A  +G LA+EIV VEIAQ+KG       DEHPR +T+LE L KL  
Sbjct: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPR-ETSLESLGKLKG 239

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
             R  GSVTAGNASGVNDGACALLLA+ +AA ++GL+ RARVVGMATAGVEPRIMGIGP 
Sbjct: 240 VVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPA 299

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PAT+K+L+  G+ L  +DVIELNEAFA+QGLAVLR LGL DDD RVNPNGGAIALGHPLG
Sbjct: 300 PATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLG 359

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
            SGARL+TTAL++LE   GR+ALCTMCIGVGQGIAL+IER+
Sbjct: 360 ASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400


Lambda     K      H
   0.319    0.134    0.384 

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: 572
Number of extensions: 16
Number of successful extensions: 2
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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: 50 (23.9 bits)

Align candidate BPHYT_RS17345 BPHYT_RS17345 (acetyl-CoA acetyltransferase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.23334.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23334.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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