GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Frischella perrara PEB0191

Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_039103773.1 FPB0191_RS02510 fumarylacetoacetate hydrolase family protein

Query= uniprot:A0A2E7P912
         (281 letters)



>NCBI__GCF_000807275.1:WP_039103773.1
          Length = 280

 Score =  139 bits (349), Expect = 9e-38
 Identities = 91/283 (32%), Positives = 144/283 (50%), Gaps = 24/283 (8%)

Query: 1   MKLLRYGPVGQEKPGVLDQSG----------KIRDLSAYIKDVNGAVLDDASLDKIRKLD 50
           MKL+ Y   G+   G+L Q G          K  DL + + D  G  +    L+    +D
Sbjct: 1   MKLVSYLVSGRASFGLLTQHGIVDLGKKLGDKYTDLKSLLADEKGLAIAKTYLNDPSDID 60

Query: 51  LESLPAVEGSPRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPND 110
            + +  +   P       N  K +C+G+NYA+  AE N    A P +F ++  +  G   
Sbjct: 61  EKDITYLPVIP-------NPNKILCVGMNYAEKRAEFNETSSA-PTLFVRFPDSQTGHKT 112

Query: 111 DVKIPRGSKKTDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTW- 169
           ++  P  + + D+E EL +VIGK G  I ++DA+S+VAGY    D S R++Q     TW 
Sbjct: 113 NIIKPAITNELDYEGELAIVIGKSGFRIKQEDALSYVAGYSCYMDGSIRDWQY----TWF 168

Query: 170 DKGKGCDTFGPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSR 229
             GK   + G  GP L T DE+ DP+ L +   ++G+  Q  + + ++  V  ++SY+S 
Sbjct: 169 TAGKNWPSTGAFGPCLTTTDEIPDPKALTLVTYLNGQEMQRDSVNNLVHTVPELISYIST 228

Query: 230 FMSLQPGDVISTGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLG 272
           F  L PGDVI TG+P GVG    P  ++++ G  + + I G+G
Sbjct: 229 FTHLSPGDVILTGSPGGVGKKRNP-PIFMKDGDKIEVEITGIG 270


Lambda     K      H
   0.316    0.138    0.419 

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: 239
Number of extensions: 12
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: 281
Length of database: 280
Length adjustment: 26
Effective length of query: 255
Effective length of database: 254
Effective search space:    64770
Effective search space used:    64770
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: 42 (22.0 bits)
S2: 47 (22.7 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