GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Pseudarthrobacter sulfonivorans Ar51

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_058929093.1 AU252_RS00785 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_001484605.1:WP_058929093.1
          Length = 405

 Score =  244 bits (622), Expect = 4e-69
 Identities = 154/416 (37%), Positives = 219/416 (52%), Gaps = 38/416 (9%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQ 59
           MTEAVIVS AR+PIG+A +G+L       L    +  A+ +   +DP ++ D+++G  + 
Sbjct: 1   MTEAVIVSIARSPIGRAMKGSLVDMRPDDLAAQMVRAALDKVPALDPTDINDLLLGCGLP 60

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
            G  G N+ R   ++ G      GTTI R C+S LQ   +A  ++     ++ +  G E+
Sbjct: 61  GGEQGYNMGRNVAVQLGYDFMP-GTTITRYCSSSLQTTRMALHAIKAGEGDVFISAGVET 119

Query: 120 ISLVQN-------DKMNTFHA----------------VDPALEAIKGDVYMAMLDTAETV 156
           +S           D  N  +A                 DP    +  D Y+AM  TAE V
Sbjct: 120 VSRFVKGNSDSLPDTHNPLYADAQTRTEKLAQGGQTWEDPRKVGLVADTYIAMGQTAENV 179

Query: 157 AKRYGISRERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLS 216
           A+  GISRE QD +++ SQ R   A   G +  EI P++   G V             +S
Sbjct: 180 AQMTGISREEQDRWAVRSQNRAEKAIINGFYEREITPVTLPDGTV-------------VS 226

Query: 217 QDEGPRPETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGI 276
            D+GPR  TT E ++ LK +     T+TAGNA  L+DGA+A VIMSD  A   GL P+  
Sbjct: 227 TDDGPRAGTTYEAVSQLKPIFRPDGTVTAGNACPLNDGAAALVIMSDTKAKELGLTPIAR 286

Query: 277 FRGMVSYGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDP 336
                  G  P+ MG+GP+ A  R L   G+ + DI L+E+NEAFAVQVL    +LGID 
Sbjct: 287 IVSTGVSGLSPEIMGLGPIEASKRALAIAGMGIGDIDLFEINEAFAVQVLGSARELGIDE 346

Query: 337 EKLNVNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
           +KLNV+GG I++GHP+GM+GAR+    L   +    ++ + TMCVGGG G A + E
Sbjct: 347 DKLNVSGGGIALGHPFGMTGARITATLLNNLQTYDKQFGLETMCVGGGQGMAMVLE 402


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: 439
Number of extensions: 22
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: 395
Length of database: 405
Length adjustment: 31
Effective length of query: 364
Effective length of database: 374
Effective search space:   136136
Effective search space used:   136136
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 Apr 09 2024. 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