GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Ruegeria conchae TW15

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_010440841.1 G7G_RS0109505 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_000192475.1:WP_010440841.1
          Length = 390

 Score =  283 bits (725), Expect = 5e-81
 Identities = 171/401 (42%), Positives = 238/401 (59%), Gaps = 12/401 (2%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M +V I  A RTP+G F G   GV A DL    ++A ++   A   D VDEV  GC   A
Sbjct: 1   MNEVVIAGAARTPMGGFQGMFDGVTAADLGGAAIRAALKGAGA---DTVDEVLMGCVLPA 57

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           G+  +  AR A   AGL E +P  TLN++C SGM A   AF  IA G  +  +AGG+ESM
Sbjct: 58  GQ-GQAPARQAGFAAGLGEEVPATTLNKMCGSGMKAAMIAFDQIALGHTQTMVAGGMESM 116

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           + AP+++ K   G           +   F++ L  +      M   A++ A+ YQ +R  
Sbjct: 117 TNAPYLLPKMRGGARIG---HGQVVDHMFLDGLEDAYDKGRLMGTFAEDCAESYQFTREA 173

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTL-EALTKLKP 239
           QD +ALRS   A +AQ    F +EI  V I  +KGE +++ DE  +P++   E +  LKP
Sbjct: 174 QDEYALRSLSNALSAQENNAFDQEITSVSIQTRKGEVVLDADE--QPQSARPEKIPTLKP 231

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
               D TVTA N+S ++DGAAAL+LASAE  +K  LT RAR+LG AS   AP +    PV
Sbjct: 232 AFREDGTVTAANSSSISDGAAALVLASAEEAEKQNLTVRARILGHASHAQAPGLFTTAPV 291

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
           PA +KL +R+G    D D+ E+NEAFA   +A + E+G++ +   VN NGGA ALGHP+G
Sbjct: 292 PAAQKLLDRIGWKKEDVDLWEVNEAFAVVPMAFMHEMGLSREI--VNVNGGACALGHPIG 349

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
            SGAR+++T L+ LEK   ++G+A +C+G G+G A+AIERV
Sbjct: 350 ASGARIMVTLLNALEKRDLKRGVAAICIGGGEGTAIAIERV 390


Lambda     K      H
   0.318    0.134    0.383 

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: 368
Number of extensions: 12
Number of successful extensions: 6
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: 400
Length of database: 390
Length adjustment: 31
Effective length of query: 369
Effective length of database: 359
Effective search space:   132471
Effective search space used:   132471
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 24 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