GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Collimonas arenae Ter10

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_061532096.1 CAter10_RS02100 acetyl-CoA C-acyltransferase family protein

Query= metacyc::MONOMER-15952
         (401 letters)



>NCBI__GCF_001584165.1:WP_061532096.1
          Length = 396

 Score =  323 bits (828), Expect = 5e-93
 Identities = 197/400 (49%), Positives = 247/400 (61%), Gaps = 10/400 (2%)

Query: 3   EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62
           E +I+ A RT IG Y GAL      +LGAI +K   AR   +D      +I+G       
Sbjct: 6   EVVIVGAARTAIGSYGGALKDFAPGELGAIAVKEAFAR-AGVDPLQAGQIIFGNVIHTEA 64

Query: 63  DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122
            +  V+R+  L AG+       TLNRLCGSGL A+ +AA A++ GE  + + GGVESMSR
Sbjct: 65  RDMYVSRVVGLNAGMGKESTALTLNRLCGSGLQAIITAANAIQLGETDVAVGGGVESMSR 124

Query: 123 APFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQD 182
           + +    + QA    A + D  +    V  L    FG   M  TAENVA ++ ISR +QD
Sbjct: 125 SMY----ATQAARWGARMGDIKMVDMMVGALSDP-FGAGHMGITAENVAEKYGISREEQD 179

Query: 183 AFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTPF 242
           AFAL SQ +A AAIA G    +IV VEI  RKG   + + DE+P+ D T+E LAKL   F
Sbjct: 180 AFALESQRRATAAIAAGHFKSQIVPVEIKTRKG-VTLFDTDEYPKADATMESLAKLKPAF 238

Query: 243 R-QGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVP 301
           + +GG+VTAGNASG+NDGA A +L +++AA + GLK  ARVV    AGV+P IMG GP+P
Sbjct: 239 KKEGGTVTAGNASGINDGAAACVLMAADAAAQAGLKPLARVVSYGVAGVDPTIMGTGPIP 298

Query: 302 ATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGM 361
           A +  L+  GL L+DM+VIE NEAFAAQ L V + LGL  D    N NGGAIALGHPLG 
Sbjct: 299 AVQLALKRAGLHLSDMEVIESNEAFAAQSLGVCKGLGL--DPALTNVNGGAIALGHPLGA 356

Query: 362 SGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           SGA +    L+EL     RY L TMCIG GQGIALIIERI
Sbjct: 357 SGAIIAVKCLYELIRTNKRYGLITMCIGGGQGIALIIERI 396


Lambda     K      H
   0.319    0.134    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: 450
Number of extensions: 21
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: 401
Length of database: 396
Length adjustment: 31
Effective length of query: 370
Effective length of database: 365
Effective search space:   135050
Effective search space used:   135050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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