GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Lactobacillus silagei IWT126

Align glucosamine-6-phosphate deaminase subunit (EC 3.5.99.6) (characterized)
to candidate WP_054654195.1 CES79_RS05010 glucosamine-6-phosphate deaminase

Query= metacyc::MONOMER-13104
         (235 letters)



>NCBI__GCF_002217945.1:WP_054654195.1
          Length = 237

 Score =  257 bits (657), Expect = 1e-73
 Identities = 127/233 (54%), Positives = 165/233 (70%)

Query: 1   MKIIQVENQVEGGKVALELLKEKLAQGAKTLGLATGSSPEEFYKQIVESDLDFSEMTSVN 60
           M +I V+N+ EGGK   E+ +     GA+  GLATGS+P   Y+++ +SDLDFS+MTSVN
Sbjct: 1   MNVIIVKNRAEGGKKGFEVFENAYRNGAQVFGLATGSTPVTTYEELTQSDLDFSQMTSVN 60

Query: 61  LDEYVGLQEEDPQSYRYFMNQHLFNQKPFKASFLPNGAAKDLEAEVARYNQLLTEHPADL 120
           LDEYVGL  + PQSY YFM QHLF+QKPF  S++P+G   D  AE+ RY+Q++ ++P DL
Sbjct: 61  LDEYVGLAPDHPQSYHYFMQQHLFDQKPFAHSYVPDGLNSDAAAEMKRYDQIIADNPIDL 120

Query: 121 QILGIGTNGHIGFNEPGTSFDSQTHLVDLTPSTIQSNARFFDKMEDVPTQAISMGIGNIL 180
           QILG+G NGHIGFNEPGT     TH V LT STI++N+RFFD  ++VP  A SMGI +IL
Sbjct: 121 QILGLGQNGHIGFNEPGTDPALGTHKVALTESTIKANSRFFDNEDEVPRYAYSMGIASIL 180

Query: 181 NAKSIILFAYGSAKAKAIAGTVEGEVTEELPGSALQKHPDVVIIADKEALSLL 233
            +K I+L AYG  KA A+   +EG VT ++P S LQ+H  V II D+ A S L
Sbjct: 181 KSKHILLEAYGPEKAAAVKAMIEGPVTTDVPASFLQRHDQVTIIIDEAAASQL 233


Lambda     K      H
   0.313    0.132    0.362 

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: 184
Number of extensions: 7
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: 235
Length of database: 237
Length adjustment: 23
Effective length of query: 212
Effective length of database: 214
Effective search space:    45368
Effective search space used:    45368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 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