GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Kocuria flava HO-9041

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_058860019.1 AS188_RS15780 acetyl-CoA C-acyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>NCBI__GCF_001482365.1:WP_058860019.1
          Length = 399

 Score =  410 bits (1054), Expect = e-119
 Identities = 218/400 (54%), Positives = 290/400 (72%), Gaps = 5/400 (1%)

Query: 4   EVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGE 63
           E ++    RTP+GR+GG+L++VR DDLAA+ VK  V  +  +D   +DEV LG AN AGE
Sbjct: 3   EAFLVGGARTPVGRYGGALSSVRPDDLAALVVKHAVT-DAGIDPHDVDEVILGNANGAGE 61

Query: 64  DNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSR 123
           +NRNVARMA LLAG PD+VPG+T+NRLCAS + A+  A   I +G A++V+AGGVESMSR
Sbjct: 62  ENRNVARMAWLLAGFPDTVPGITVNRLCASSLSAIIMASHMIKAGAADVVVAGGVESMSR 121

Query: 124 APYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVD-AMPETADNVADDYKVSRADQ 182
           AP+VM K  +AF +  ++ DT+IGWRF NP  K    +  +MPETA+ VA    ++R D 
Sbjct: 122 APWVMEKPATAFAKPGEVFDTSIGWRFTNPEFKKHDKMTYSMPETAEEVAAVDGITREDA 181

Query: 183 DAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKG-ETVVDADEHLRPDTTLEALAKLKPV 241
           DAFA+ S + A  A  AG FA+EIVPV +KG+KG ETVVD DE  RP TT++ LAKL+PV
Sbjct: 182 DAFAVASHEKAIAAIDAGRFADEIVPVTVKGRKGAETVVDTDEGPRPGTTMDVLAKLRPV 241

Query: 242 NGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVP 301
                 VTAGN+S +NDG+ A+++ S  A +K+GL ARA+++  ASAGVAP +MG+GPVP
Sbjct: 242 VTHGSVVTAGNSSSLNDGASAILVVSERAAEKYGLTARARIVDGASAGVAPEIMGLGPVP 301

Query: 302 AVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGA 361
           A +K+LER    + D   +ELNEAFA+Q LA  R LG+  D+  VN +GGAIALGH LG+
Sbjct: 302 ATQKVLERTGWGIGDLGAVELNEAFASQSLACIRRLGL--DEGIVNNDGGAIALGHALGS 359

Query: 362 SGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401
           SG+RLV+T + ++E+ G +RGL TMCVGVGQG A+ VE++
Sbjct: 360 SGSRLVVTLLGRMEREGAERGLATMCVGVGQGTAMLVEKI 399


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: 467
Number of extensions: 18
Number of successful extensions: 5
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: 399
Length adjustment: 31
Effective length of query: 370
Effective length of database: 368
Effective search space:   136160
Effective search space used:   136160
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 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