GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Halomonas xinjiangensis TRM 0175

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_043532471.1 JH15_RS16990 acetyl-CoA C-acyltransferase FadA

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_000759345.1:WP_043532471.1
          Length = 392

 Score =  255 bits (652), Expect = 1e-72
 Identities = 162/398 (40%), Positives = 227/398 (57%), Gaps = 18/398 (4%)

Query: 3   REVVVVSGVRTAIGTF-GGSLKDVAPAELGALVVREALAR-AQVSGDDVGHVVFGNVIQT 60
           R++VVV GVRTA+     G+ ++V    L A V++    R A +  ++V  V++G V QT
Sbjct: 6   RDIVVVDGVRTAMAKAKNGAFRNVRAENLSASVMQALFDRNAGLDPNEVDDVIWGCVNQT 65

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
             + M + R AA+  G+  + PA TVNRLCGS + A+  AA  I  G  D  I GG E M
Sbjct: 66  LEQSMNIARNAAIMTGIPRSVPAQTVNRLCGSSMTALHIAAANIKAGMGDFYIIGGVEHM 125

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
              P         A    A    MM            MG+TAE ++K + ++R  QD+  
Sbjct: 126 EHVPMAHGVDVNPAASKYAAKAAMM------------MGLTAELLSKMHGVTREDQDKFG 173

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKG-DVTFDTDEHVRHDATIDDMTKLRPVFVKE 239
           + SH+RA AA + GYF ++IV +     +G       DE VR DA++++M KL+PVF   
Sbjct: 174 VRSHQRAYAANQQGYFDNEIVGIEGHDTQGFKRLIKHDEVVRIDASLEEMAKLKPVFDPR 233

Query: 240 NGTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATK 299
           +GTV+AG +S L+  A+A+ +M    A+  GL+P+AR++S G AG D   MG GPVPA+K
Sbjct: 234 SGTVSAGTSSALSVGASAMAVMSYERAQALGLQPIARVLSTGVAGCDASIMGYGPVPASK 293

Query: 300 IALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPA---KVNPNGSGISLGHPIGATG 356
            AL+ AGL   D+  +E NEAFAAQA  V K LG   A   KVN NG  I+LGHP+G +G
Sbjct: 294 KALKAAGLSSKDIQTVELNEAFAAQAIPVLKDLGFYDAMDEKVNLNGGAIALGHPLGCSG 353

Query: 357 ALITVKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           + I    L+ + +      L TMCIG GQG+A +FER+
Sbjct: 354 SRICTTLLNVMQQQDTTLGLATMCIGMGQGVATVFERL 391


Lambda     K      H
   0.318    0.134    0.381 

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: 388
Number of extensions: 23
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: 394
Length of database: 392
Length adjustment: 31
Effective length of query: 363
Effective length of database: 361
Effective search space:   131043
Effective search space used:   131043
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