GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Marinobacter adhaerens HP15

Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate GFF4003 HP15_3943 acetyl-CoA C-acyltransferase

Query= SwissProt::P09110
         (424 letters)



>FitnessBrowser__Marino:GFF4003
          Length = 365

 Score =  256 bits (655), Expect = 6e-73
 Identities = 152/361 (42%), Positives = 224/361 (62%), Gaps = 10/361 (2%)

Query: 68  VMTAVLKDVNLRPEQLGDICVGNVLQPGA-GAIMARIAQFLSDIPETVPLSTVNRQCSSG 126
           V+   ++   + P  + D+ +G   Q GA G  +AR+A   + +P T    ++NR CSSG
Sbjct: 5   VIKHAVERAGIDPSIVEDVIMGAAYQEGAQGRNIARLAAIRAGLPVTTAGFSINRFCSSG 64

Query: 127 LQAVASIAGGIRNGSYDIGMACGVESMSLA--DRGNPGNITSRLMEKEKARDCLIPMGIT 184
           LQ++A  A  + +      +A GVES+SL   ++ N  + T+  + K K  +  + M  T
Sbjct: 65  LQSIALAAQRVVSEKVPAMVAGGVESISLVQNEKINSFHATNEWLMKNKP-ELYLSMIET 123

Query: 185 SENVAERFGISREKQDTFALASQQKAARAQSKGCFQAEIVPVTTTVH-DDKGT----KRS 239
           ++ VA+R+ +SRE QD ++L SQQ+ A AQ  G F  EIVP   T+   DK T    ++ 
Sbjct: 124 ADIVAKRYNVSREAQDEYSLISQQRTAAAQQAGKFDDEIVPFDATMLVKDKETGEVSEKQ 183

Query: 240 ITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAGNSSQVSDGAAAILLARRSKAEELGLP 299
           +T+  DE  RP+TT+EGLA L+P    +   TAGN+SQ+SDGA+   +   + AE+  + 
Sbjct: 184 VTLKGDECNRPNTTLEGLAGLEPVRGPEQFITAGNASQLSDGASVCTVMNSTYAEKHNIE 243

Query: 300 ILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKL 359
            +G+ R +AV G  PD MGIGP YAIP  L++ GLT+ D+D++E+NEAFASQ  YC ++L
Sbjct: 244 PMGIFRGFAVAGCEPDEMGIGPVYAIPRLLERNGLTMDDIDLWELNEAFASQVIYCRDRL 303

Query: 360 RLPPEKVNPLGGAVALGHPLGCTGARQVITLLNELKRRGKRAYGVVSMCIGTGMGAAAVF 419
            +P EK+N  GG++++GHP G TGARQ    L E KRRG + Y V++MCIG G GAA +F
Sbjct: 304 GIPMEKLNVNGGSISIGHPFGVTGARQTGHALIEGKRRGAK-YVVITMCIGGGQGAAGLF 362

Query: 420 E 420
           E
Sbjct: 363 E 363


Lambda     K      H
   0.317    0.134    0.385 

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: 378
Number of extensions: 16
Number of successful extensions: 4
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: 424
Length of database: 365
Length adjustment: 31
Effective length of query: 393
Effective length of database: 334
Effective search space:   131262
Effective search space used:   131262
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)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory