GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Herbaspirillum seropedicae SmR1

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate HSERO_RS01180 HSERO_RS01180 acetyl-CoA acetyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__HerbieS:HSERO_RS01180
          Length = 391

 Score =  315 bits (806), Expect = 2e-90
 Identities = 177/398 (44%), Positives = 258/398 (64%), Gaps = 10/398 (2%)

Query: 4   EVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGE 63
           +V I  A RT IG+FGG+L+ + A DL A  +KAL+ +   +    + EV LG    AG 
Sbjct: 3   DVVIVAAQRTAIGKFGGALSKIAAADLGAQVIKALLAKTG-IKPEAISEVILGQVLTAGL 61

Query: 64  DNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSR 123
             +N AR +++ +GLPD VP   + ++C SG+ AV  A +AI  G+A++VIAGG E+MS 
Sbjct: 62  -GQNPARQSVIKSGLPDMVPAFVVGKVCGSGLKAVQLAAQAIRCGDAQIVIAGGQENMSA 120

Query: 124 APYVMGKADSAFGRGQ-KIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQ 182
           +P+V+  +   F  G  K+ DT I    ++ L    Y    M  TA+NVA  +++SR +Q
Sbjct: 121 SPHVLNNSRDGFRMGDAKLTDTMI----VDGLWDV-YNQYHMGITAENVAKKFEISREEQ 175

Query: 183 DAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVN 242
           DAFA  SQ  A  AQ AG F +EIVP+ IKGKK   V D DE ++   T E+LA L+P  
Sbjct: 176 DAFAAASQNKAEAAQKAGKFKDEIVPIEIKGKKETVVFDTDEFVKHGVTAESLATLRPAF 235

Query: 243 GPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPA 302
               TVTAGNASG+NDG+ A+++ SA+   + GL   AK+   +SAG+ P +MG+GPVPA
Sbjct: 236 DKAGTVTAGNASGINDGAAAVVVTSAKLAAELGLPVLAKIKAYSSAGLDPSIMGMGPVPA 295

Query: 303 VRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGAS 362
            +  L++   +  D D++E+NEAFAAQ +AV +++G   D +++N NGGAIALGHP+GAS
Sbjct: 296 SQLTLKKAGWTPQDLDLMEINEAFAAQAIAVNKQMGW--DTSKINVNGGAIALGHPIGAS 353

Query: 363 GARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400
           G R+++T +H++ +   ++GL ++C+G G GVALAVER
Sbjct: 354 GCRVLVTLLHEMVRRDAKKGLASLCIGGGMGVALAVER 391


Lambda     K      H
   0.317    0.134    0.379 

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: 401
Number of extensions: 14
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: 401
Length of database: 391
Length adjustment: 31
Effective length of query: 370
Effective length of database: 360
Effective search space:   133200
Effective search space used:   133200
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 (21.6 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