GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Tistlia consotensis USBA 355

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_085121636.1 B9O00_RS06430 acetyl-CoA C-acyltransferase

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_900177295.1:WP_085121636.1
          Length = 393

 Score =  463 bits (1192), Expect = e-135
 Identities = 242/392 (61%), Positives = 294/392 (75%), Gaps = 2/392 (0%)

Query: 4   EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63
           EVV VS VR+AIGTFGG+L   +P  LGA VVREALARA V G+ VGHVVFGNVIQTEPR
Sbjct: 3   EVVFVSAVRSAIGTFGGALAGESPCSLGAAVVREALARAGVEGEQVGHVVFGNVIQTEPR 62

Query: 64  DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123
           D YL RVAA++GGV   APA+T+NRLCGSG QAIVSAAQ+ILLGD +VA+ GGAE+MSRA
Sbjct: 63  DAYLARVAALDGGVAKAAPAMTLNRLCGSGAQAIVSAAQSILLGDAEVAVAGGAEAMSRA 122

Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183
           P+L    R+G RMGD   VD ++G L DPF    MG+TAE VA ++ I R +QD  ALES
Sbjct: 123 PHLLTTGRFGQRMGDTAAVDALVGILTDPFGNGIMGLTAERVADKWGIGRERQDAFALES 182

Query: 184 HRRASAAIKAGYFKDQIVPV-VSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGT 242
            RRA+ AI  G F+ QI+P+ V +G +   +F  DEH +   T +D+  L+P F ++ G+
Sbjct: 183 QRRAARAIGEGRFESQILPLEVGRGSRAR-SFAVDEHPKPQTTAEDLANLKPAFRRDGGS 241

Query: 243 VTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIAL 302
           VTAGNASG+ND AAA+V+M    AER G +PL RLV Y HAGV+P  MGIGPVPA +  L
Sbjct: 242 VTAGNASGINDGAAALVLMSAEAAERGGHRPLGRLVGYAHAGVEPGEMGIGPVPAVRGLL 301

Query: 303 ERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVK 362
            R GL V D D++E+NEAFAAQA AV+  LGLDP +VNPNG  I+LGHP+GATGA++TVK
Sbjct: 302 ARTGLAVEDFDLVESNEAFAAQALAVSDELGLDPERVNPNGGAIALGHPVGATGAILTVK 361

Query: 363 ALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           AL+EL R  GR ALVT+CIGGGQGIA   ER+
Sbjct: 362 ALYELARSGGRRALVTLCIGGGQGIALALERL 393


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: 511
Number of extensions: 17
Number of successful extensions: 3
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: 393
Length adjustment: 31
Effective length of query: 363
Effective length of database: 362
Effective search space:   131406
Effective search space used:   131406
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