GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Collimonas arenae Ter10

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_061532096.1 CAter10_RS02100 acetyl-CoA C-acyltransferase family protein

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_001584165.1:WP_061532096.1
          Length = 396

 Score =  498 bits (1282), Expect = e-145
 Identities = 252/393 (64%), Positives = 303/393 (77%)

Query: 2   TREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTE 61
           TREVV+V   RTAIG++GG+LKD AP ELGA+ V+EA ARA V     G ++FGNVI TE
Sbjct: 4   TREVVIVGAARTAIGSYGGALKDFAPGELGAIAVKEAFARAGVDPLQAGQIIFGNVIHTE 63

Query: 62  PRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMS 121
            RDMY+ RV  +N G+   + ALT+NRLCGSGLQAI++AA  I LG+TDVA+GGG ESMS
Sbjct: 64  ARDMYVSRVVGLNAGMGKESTALTLNRLCGSGLQAIITAANAIQLGETDVAVGGGVESMS 123

Query: 122 RAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAAL 181
           R+ Y   AARWGARMGD  +VDMM+GAL DPF   HMG+TAENVA++Y ISR +QD  AL
Sbjct: 124 RSMYATQAARWGARMGDIKMVDMMVGALSDPFGAGHMGITAENVAEKYGISREEQDAFAL 183

Query: 182 ESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENG 241
           ES RRA+AAI AG+FK QIVPV  K RKG   FDTDE+ + DAT++ + KL+P F KE G
Sbjct: 184 ESQRRATAAIAAGHFKSQIVPVEIKTRKGVTLFDTDEYPKADATMESLAKLKPAFKKEGG 243

Query: 242 TVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIA 301
           TVTAGNASG+ND AAA V+M    A + GLKPLAR+VSYG AGVDP  MG GP+PA ++A
Sbjct: 244 TVTAGNASGINDGAAACVLMAADAAAQAGLKPLARVVSYGVAGVDPTIMGTGPIPAVQLA 303

Query: 302 LERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITV 361
           L+RAGL +SD++VIE+NEAFAAQ+  V K LGLDPA  N NG  I+LGHP+GA+GA+I V
Sbjct: 304 LKRAGLHLSDMEVIESNEAFAAQSLGVCKGLGLDPALTNVNGGAIALGHPLGASGAIIAV 363

Query: 362 KALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           K L+EL R   RY L+TMCIGGGQGIA I ERI
Sbjct: 364 KCLYELIRTNKRYGLITMCIGGGQGIALIIERI 396


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: 509
Number of extensions: 14
Number of successful extensions: 1
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: 396
Length adjustment: 31
Effective length of query: 363
Effective length of database: 365
Effective search space:   132495
Effective search space used:   132495
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