GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Cupriavidus basilensis 4G11

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate RR42_RS35915 RR42_RS35915 beta-ketoadipyl CoA thiolase

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



>FitnessBrowser__Cup4G11:RR42_RS35915
          Length = 400

 Score =  585 bits (1507), Expect = e-171
 Identities = 292/401 (72%), Positives = 339/401 (84%), Gaps = 1/401 (0%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M EA I DA+RTPIGRYAG+L+ VR DDLGA+PLKAL+AR+P LDWSA+DDVIYG ANQA
Sbjct: 1   MTEAFICDAIRTPIGRYAGSLSGVRPDDLGAVPLKALMARNPNLDWSAIDDVIYGNANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ LLAGLP SVPG T+NRLCGSG+DA G+AARA++ GEAGLMLAGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPQSVPGATINRLCGSGMDATGTAARAIKSGEAGLMLAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAPFVMGK+  AF R A+IFDTTIGWRF+N  M+  +G+DSMPETAENVA  + ISR D
Sbjct: 121 SRAPFVMGKATSAFSRDAQIFDTTIGWRFINPAMRAAYGVDSMPETAENVATDYKISRED 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QD  ALRSQ KA+ A A+G LA+EI AV IAQ+KG   +VE DEHPR  T++E L KL  
Sbjct: 181 QDLMALRSQEKASRAQADGTLAQEITAVTIAQKKGDPLVVERDEHPRA-TSMEALGKLRG 239

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
             R  G+VTAGNASGVNDGACA+LLAS  AA++HGL  +AR+VGMATAGV PR+MGIGP 
Sbjct: 240 VVRADGTVTAGNASGVNDGACAILLASEAAARQHGLTPKARIVGMATAGVAPRVMGIGPA 299

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PA++K+L+  G+ +  MDVIELNEAFAAQGLAVLRELG+ADDD RVNPNGGAIALGHPLG
Sbjct: 300 PASQKLLKQLGMTIDQMDVIELNEAFAAQGLAVLRELGVADDDARVNPNGGAIALGHPLG 359

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTA+++L    GRYALCTMCIGVGQGIA++IER+
Sbjct: 360 MSGARLVTTAMYQLHRTGGRYALCTMCIGVGQGIAMVIERV 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: 546
Number of extensions: 15
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 RR42_RS35915 RR42_RS35915 (beta-ketoadipyl CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.16353.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16353.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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