GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloA in Chryseobacterium arthrosphaerae CC-VM-7

Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate WP_065400523.1 BBI00_RS19475 methylmalonyl-CoA epimerase

Query= BRENDA::Q97H22
         (128 letters)



>NCBI__GCF_001684965.1:WP_065400523.1
          Length = 132

 Score = 57.4 bits (137), Expect = 7e-14
 Identities = 42/131 (32%), Positives = 68/131 (51%), Gaps = 4/131 (3%)

Query: 1   MKVHHIGYAVKNIDSALKKFKRLGYVEESEVVRDEVRKVYIQFVINGGYRVELVAPDGED 60
           MK+ HIG AVK++  +   F RL   +  +    E   V   F   G  ++EL+     +
Sbjct: 1   MKLEHIGIAVKSLGISDNLFARLLGKDSYKQETVEREGVVTSFYETGESKIELLEASNPE 60

Query: 61  SPINKTI-KKGSTPYHICYEVEDIQKSIEEMSQIGYTLFKKAEIAPAIDNRKVAFLF--S 117
           SPI+K I KKG   +H+ + VE+I + ++ + + G+  F   E     DN+ V FL   S
Sbjct: 61  SPISKFIEKKGEGIHHLAFGVENILQEVQRLKKEGFQ-FISEEPKEGADNKLVVFLHPKS 119

Query: 118 TDIGLIELLEK 128
           T+  L+EL ++
Sbjct: 120 TNGVLVELCQE 130


Lambda     K      H
   0.318    0.138    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: 48
Number of extensions: 5
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 128
Length of database: 132
Length adjustment: 14
Effective length of query: 114
Effective length of database: 118
Effective search space:    13452
Effective search space used:    13452
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: 41 (20.4 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