GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Cronobacter condimenti 1330

Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate WP_007664885.1 BN137_RS16680 sugar ABC transporter permease

Query= reanno::WCS417:GFF4322
         (281 letters)



>NCBI__GCF_000319285.1:WP_007664885.1
          Length = 283

 Score =  115 bits (287), Expect = 1e-30
 Identities = 71/211 (33%), Positives = 114/211 (54%), Gaps = 4/211 (1%)

Query: 73  YFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQTVLLPASFT 132
           ++WNS+KI+   ++++    +   Y  S +RFKG Q    L L    +P  + L+ A F 
Sbjct: 75  WYWNSMKISFMTMVLTLISVSFTAYAFSRFRFKGRQNGLMLFLLLQMIPQFSALI-AIFV 133

Query: 133 LGKM-GLASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALIKAARLDGAGFFTIFRQII 191
           L ++ GL ++   LV ++V   +   T   + Y  +IP  L ++AR+DGA  F IF +II
Sbjct: 134 LSQLLGLINSHLALVLIYVAGMIPMNTYLMKGYLDAIPKDLDESARMDGASNFRIFIEII 193

Query: 192 LPMSTPIIMVCLIWQFTQIWNDF-LFGVVFSSGDSQPITVALNNLVNTSTGAKEYNVDMA 250
           +P+S PI+ V  ++ FT    DF L   +  + D   + + L NLV    GA  Y    A
Sbjct: 194 MPLSKPIVAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNLVAQKMGA-SYTTYAA 252

Query: 251 AAMIAGLPTLLVYVIAGKYFVRGLTAGAVKG 281
            A++  +P  ++Y+   KYFV GLT+G+ KG
Sbjct: 253 GAVLIAVPVAILYLALQKYFVSGLTSGSTKG 283


Lambda     K      H
   0.328    0.141    0.435 

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: 188
Number of extensions: 8
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: 283
Length adjustment: 26
Effective length of query: 255
Effective length of database: 257
Effective search space:    65535
Effective search space used:    65535
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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