GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Neptunomonas antarctica S3-22

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_054341133.1 Nant_RS08065 acetyl-CoA C-acyltransferase FadA

Query= BRENDA::Q0KAI3
         (392 letters)



>NCBI__GCF_001305295.1:WP_054341133.1
          Length = 392

 Score =  280 bits (716), Expect = 5e-80
 Identities = 175/397 (44%), Positives = 230/397 (57%), Gaps = 23/397 (5%)

Query: 5   VIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERN-KLDPGLVDDVITGCVTQAGE 63
           VIVD IR+PMG+SK GS F  + A  L A ++KGL+ RN  ++P  ++DV+ GCV Q  E
Sbjct: 9   VIVDGIRTPMGKSKGGS-FRNVRAESLSASIMKGLLARNPNVNPADIEDVVWGCVNQTKE 67

Query: 64  QSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIESMSR 123
           Q     R A + AG P  V   TI+R CGSS  A+H AAQ IM G  D  I  G+E M  
Sbjct: 68  QGFNIARNALVLAGLPHTVGGQTINRLCGSSMSALHNAAQSIMTGNGDTFIVGGVEHMGH 127

Query: 124 VPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELAATA 183
           + +    +        M    A   +  G+ AE++     +SR   D + ARSH LA  A
Sbjct: 128 LNI----LHGIDLNSEMSKYVAKAAMMMGITAEMLGKMNGISREMQDEFGARSHRLAHEA 183

Query: 184 RESGAFRREILGIS--TPNG---LVEQDETIRPGTSVEKLGTLQASFRNDELSARFPQIG 238
           RE+G F  EI+ I     NG   L+EQDE IRP T+ E L +L+ +F         P++G
Sbjct: 184 RETGRFDNEIIAIEGHDANGFKSLLEQDEVIRPETTFEVLQSLKPAF--------VPKVG 235

Query: 239 WNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPASQR 298
             VTAG +S  SDGAS ML+MS + AQ LGLKPRA   +  V G DP +M   P+PA+Q+
Sbjct: 236 -TVTAGTSSAFSDGASGMLVMSAAKAQSLGLKPRAVIRSMAVAGCDPSIMGYGPVPATQK 294

Query: 299 AIKKSGLKLDQIDHYEINEAFACVPLA---WQRALGADPARLNPRGGAIALGHPLGASGV 355
           A+K++GLK+D ID+ E+NEAFA   LA     + L      +N  GGAIALGHPLG SG 
Sbjct: 295 ALKRAGLKMDDIDYIELNEAFAAQGLAVLKGLKLLDRMEENVNLNGGAIALGHPLGCSGT 354

Query: 356 RLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392
           R+ TT+L+ LE     +GL +MC   G   AT+ ERL
Sbjct: 355 RISTTLLNVLEQKNGTFGLATMCIGMGQGVATVFERL 391


Lambda     K      H
   0.318    0.132    0.384 

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: 389
Number of extensions: 19
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: 392
Length of database: 392
Length adjustment: 31
Effective length of query: 361
Effective length of database: 361
Effective search space:   130321
Effective search space used:   130321
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.

Links

Downloads

Related tools

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