GapMind for catabolism of small carbon sources

 

Alignments for a candidate for celEIIB in Tatumella morbirosei LMG 23360

Align PTS system cellobiose-specific EIIB component; Cellobiose-specific phosphotransferase enzyme IIB component; EC 2.7.1.205 (characterized)
to candidate WP_038018225.1 HA49_RS13185 PTS sugar transporter subunit IIB

Query= SwissProt::Q9CIF0
         (108 letters)



>NCBI__GCF_000757425.2:WP_038018225.1
          Length = 99

 Score = 91.3 bits (225), Expect = 3e-24
 Identities = 53/100 (53%), Positives = 65/100 (65%), Gaps = 5/100 (5%)

Query: 4   KVIALACAAGMSTSLLVSKMQKAAADNGKDYEIFAKSTADIDNMLAGTGSPKPDVLLLGP 63
           K I L CAAGMSTS+LVS+MQK AAD   D EI A S  ++D+ LA       D  LLGP
Sbjct: 2   KNILLCCAAGMSTSMLVSRMQKYAADQAIDVEINAISINELDSHLANI-----DCCLLGP 56

Query: 64  QVAFMKGEVAKKAEIAGVPMDVIKMQDYGMMRGDKVLAAA 103
           QV +   EV +K     +P+ VI ++DYGMMRGDKVL +A
Sbjct: 57  QVKYKLAEVQQKLAPLNIPVAVIDIRDYGMMRGDKVLESA 96


Lambda     K      H
   0.316    0.130    0.353 

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: 50
Number of extensions: 2
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: 108
Length of database: 99
Length adjustment: 11
Effective length of query: 97
Effective length of database: 88
Effective search space:     8536
Effective search space used:     8536
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: 40 (21.2 bits)
S2: 40 (20.0 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