GapMind for catabolism of small carbon sources

 

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

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_058860019.1 AS188_RS15780 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>NCBI__GCF_001482365.1:WP_058860019.1
          Length = 399

 Score =  249 bits (636), Expect = 1e-70
 Identities = 159/407 (39%), Positives = 221/407 (54%), Gaps = 25/407 (6%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           MTEA +V  ARTP+G+ Y GAL++     L    ++HAV  AGIDP +V++V++G A   
Sbjct: 1   MTEAFLVGGARTPVGR-YGGALSSVRPDDLAALVVKHAVTDAGIDPHDVDEVILGNANGA 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G    N+AR A L AG P T  G T++R CAS L AI +A+  +     ++ V GG ES+
Sbjct: 60  GEENRNVARMAWLLAGFPDTVPGITVNRLCASSLSAIIMASHMIKAGAADVVVAGGVESM 119

Query: 121 S---LVQNDKMNTFHAVDPALEAIKG------------DVYMAMLDTAETVAKRYGISRE 165
           S    V       F       +   G             +  +M +TAE VA   GI+RE
Sbjct: 120 SRAPWVMEKPATAFAKPGEVFDTSIGWRFTNPEFKKHDKMTYSMPETAEEVAAVDGITRE 179

Query: 166 RQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPET 225
             D +++ S  +  AA   G+F DEI P++ K        GA    +  +  DEGPRP T
Sbjct: 180 DADAFAVASHEKAIAAIDAGRFADEIVPVTVK-----GRKGA----ETVVDTDEGPRPGT 230

Query: 226 TAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGC 285
           T + LA L+ V   G  +TAGN+S L+DGASA +++S++ A   GL          S G 
Sbjct: 231 TMDVLAKLRPVVTHGSVVTAGNSSSLNDGASAILVVSERAAEKYGLTARARIVDGASAGV 290

Query: 286 EPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGA 345
            P+ MG+GPV A  ++L+R G  + D+G  ELNEAFA Q L C  +LG+D   +N +GGA
Sbjct: 291 APEIMGLGPVPATQKVLERTGWGIGDLGAVELNEAFASQSLACIRRLGLDEGIVNNDGGA 350

Query: 346 ISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
           I++GH  G SG+RL    L    R  A+  + TMCVG G G+A L E
Sbjct: 351 IALGHALGSSGSRLVVTLLGRMEREGAERGLATMCVGVGQGTAMLVE 397


Lambda     K      H
   0.316    0.134    0.378 

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: 430
Number of extensions: 27
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 395
Length of database: 399
Length adjustment: 31
Effective length of query: 364
Effective length of database: 368
Effective search space:   133952
Effective search space used:   133952
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