GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TRIC in Shewanella loihica PV-4

Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate 5208645 Shew_1154 hypothetical protein (RefSeq)

Query= reanno::ANA3:7023996
         (213 letters)



>lcl|FitnessBrowser__PV4:5208645 Shew_1154 hypothetical protein
           (RefSeq)
          Length = 217

 Score =  355 bits (911), Expect = e-103
 Identities = 176/217 (81%), Positives = 195/217 (89%), Gaps = 4/217 (1%)

Query: 1   MQEAQFIGLLWLIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPL 60
           MQEA+FI LLWLIGILAEAMTGAL AGRKQMDLFGVVIIGCATAIGGGTLRD+LLGNYPL
Sbjct: 1   MQEAEFITLLWLIGILAEAMTGALCAGRKQMDLFGVVIIGCATAIGGGTLRDILLGNYPL 60

Query: 61  IWVENVHYLLAIAFASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPT 120
           IWVEN+HYLLAIAFASLLTV I+PVMRYLSKLFLAIDALGLAVFSIVGAQKTL+LGFSPT
Sbjct: 61  IWVENIHYLLAIAFASLLTVIISPVMRYLSKLFLAIDALGLAVFSIVGAQKTLLLGFSPT 120

Query: 121 IAVVMGLVTGVFGGVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLAEWINLVV 180
           +A+VMG+VTGVFGGVIRDILCNQVPLIFKKELYA++SL TA LY+ L ++++ EWINL +
Sbjct: 121 LAIVMGVVTGVFGGVIRDILCNQVPLIFKKELYALVSLTTASLYMLLRSFEVTEWINLAI 180

Query: 181 CLTLGFSLRMLALRYHWSMPTFDYQ----ANGDQHTH 213
            L++GFS RMLA+RYHW MP FDYQ     N D   H
Sbjct: 181 SLSVGFSFRMLAIRYHWGMPKFDYQHGDHGNQDSQAH 217


Lambda     K      H
   0.330    0.143    0.438 

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: 4
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: 213
Length of database: 217
Length adjustment: 22
Effective length of query: 191
Effective length of database: 195
Effective search space:    37245
Effective search space used:    37245
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: 45 (21.9 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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