GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Marinobacter adhaerens HP15

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate GFF2751 HP15_2695 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Marino:GFF2751
          Length = 415

 Score =  592 bits (1525), Expect = e-174
 Identities = 302/406 (74%), Positives = 344/406 (84%), Gaps = 6/406 (1%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           + +A I+DA+RTPIGRY GAL++VRADDLGAIP+KAL  R+P LDWS +DDV+YGCANQA
Sbjct: 7   LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNR+VARM+ LLAGLPV VPG+T+NRLCGSG+DAVGSAARA+R GE  LM+AGGVESM
Sbjct: 67  GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAPFVMGK++ AF R AEIFDTTIGWRFVN ++++ +GIDSMPETAENVAA F ISR D
Sbjct: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFALRSQ + AAA   GRLA EI  V I +RK    +V+ DEHPR +T+LE+LA L T
Sbjct: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPR-ETSLEKLASLPT 245

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
           PFR+ G+VTAGNASGVNDGACALLLA ++A +++ LK RARVV MATAGVEPRIMG GP 
Sbjct: 246 PFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPA 305

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PATRKVL   GL LADMDVIELNEAFAAQ LAV R+LGL DD E VNPNGGAIALGHPLG
Sbjct: 306 PATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLG 365

Query: 361 MSGARLVTTALHELEER-----QGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTAL+ELE R     + RYALCTMCIGVGQGIALIIER+
Sbjct: 366 MSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411


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: 580
Number of extensions: 14
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: 401
Length of database: 415
Length adjustment: 31
Effective length of query: 370
Effective length of database: 384
Effective search space:   142080
Effective search space used:   142080
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 GFF2751 HP15_2695 (acetyl-CoA acetyltransferase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.16092.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16092.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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