GapMind for catabolism of small carbon sources

 

Alignments for a candidate for catI in Rhodococcus qingshengii djl-6-2

Align 3-oxoadipate CoA-transferase (EC 2.8.3.6) (characterized)
to candidate WP_050654881.1 C1M55_RS10595 CoA transferase subunit A

Query= reanno::WCS417:GFF1318
         (285 letters)



>NCBI__GCF_002893965.1:WP_050654881.1
          Length = 322

 Score =  285 bits (730), Expect = 7e-82
 Identities = 142/276 (51%), Positives = 192/276 (69%), Gaps = 2/276 (0%)

Query: 5   LALRDAVKQFVNDGDTVALEGFTHLIPTAAGHEIIRQGKKDLTLVRMTPDLIYDQLIGAG 64
           L++++AV ++V DG TVALEGF+HLIP AA HEIIRQG+KDLTL RMTPD++ DQL+ AG
Sbjct: 23  LSMKEAVGRYVEDGMTVALEGFSHLIPFAAAHEIIRQGRKDLTLCRMTPDIVSDQLVAAG 82

Query: 65  CARKLIFSWGGNPGVGSLHRLRDAVEKQWPQPLEIEEHSHADLANAYVAGASGLPFAVLR 124
           C RKL+ S+  +   GSL+ LR  +E Q P PLE+EE+SH  +   Y AGA+ LPF  LR
Sbjct: 83  CVRKLVASFFASGSAGSLYELRRRIENQDPLPLEVEEYSHYGMVCRYQAGAARLPFFPLR 142

Query: 125 AYAGSDLPKVNPLIKTVTCPFTGEVLAAVPSVRPDVTVIHAQKADRKGNVLLWGILGVQK 184
           +YAGSDLP +NP ++ V  P+ G  +  VP + PDVT+I AQ+AD  GN  +WGI GVQ+
Sbjct: 143 SYAGSDLPALNPQLRLVEDPYGGGSVYVVPPLNPDVTIIGAQRADTSGNAQIWGIAGVQQ 202

Query: 185 EAALAAKRCIVTVEEIVDD--LNAPMNSCVLPTWALTAVCHVPGGAHPSYAHGYNERDNR 242
           EA  AAK+ IV VEE+VDD  + +  +  ++P+ A+ AV   P GAHPSYA GY +RD  
Sbjct: 203 EAVYAAKKAIVVVEELVDDEVIRSDPSRTLIPSHAVDAVVVCPRGAHPSYAQGYYDRDCG 262

Query: 243 FYQAWDPIARDRGTFTAWINEYIHGTADFTEFQAKL 278
           FY+ W  I++D      W++E+++   D  E+ AKL
Sbjct: 263 FYRRWTEISKDPSLLRNWLDEWVYTLGDHDEYLAKL 298


Lambda     K      H
   0.320    0.136    0.421 

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: 268
Number of extensions: 9
Number of successful extensions: 2
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: 285
Length of database: 322
Length adjustment: 27
Effective length of query: 258
Effective length of database: 295
Effective search space:    76110
Effective search space used:    76110
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: 48 (23.1 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