GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03055 in Phaeobacter inhibens BS107

Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate GFF3832 PGA1_262p02360 putative histidine-binding periplasmic protein

Query= reanno::pseudo3_N2E3:AO353_03055
         (258 letters)



>FitnessBrowser__Phaeo:GFF3832
          Length = 259

 Score =  177 bits (449), Expect = 2e-49
 Identities = 97/249 (38%), Positives = 147/249 (59%), Gaps = 4/249 (1%)

Query: 11  ALSVLSLPTFADEKPLKIGIEAA-YPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVE 69
           A +V +    A  +P+KIG+ A  YPPFAS    G  VG++ D+ NA+C   ++ CV   
Sbjct: 14  AATVAATCAVAQAEPVKIGVAAEPYPPFASLDSSGQWVGWEIDVINAVCAAAELDCVITP 73

Query: 70  QEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQVSDNLAEL 129
             +DG+IP+L  +++DAI++SMSIT++R K++DF++ YYNTPA +V      +      L
Sbjct: 74  VAWDGIIPSLTGQQVDAIMASMSITEERLKTIDFSDPYYNTPAVIVADKSMDIEATPESL 133

Query: 130 KGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGF 189
            GK +G+Q  +IH  +A+E  K   +E++ Y +Q+E   D+ AGR+D T AD+  + D F
Sbjct: 134 AGKVVGIQASTIHQAYAQEHFK--DSELRVYQTQDEANQDLFAGRIDATQADSIAMAD-F 190

Query: 190 LKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRANGKYKQIQDK 249
           + +D+G      G    DE   G G+G  VRKGD   L  +N  I AI A+G + +I  K
Sbjct: 191 VGSDAGGCCEIKGAVANDEAILGKGVGAGVRKGDSDVLAALNKGIAAILADGTHAEITSK 250

Query: 250 YFNFDIYGK 258
           YF   IY +
Sbjct: 251 YFTTSIYSE 259


Lambda     K      H
   0.318    0.138    0.395 

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: 182
Number of extensions: 11
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: 258
Length of database: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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: 47 (22.7 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:

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