GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Acidovorax sp. GW101-3H11

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized)
to candidate Ac3H11_4900 Putative amino acid ABC transporter, permease protein

Query= reanno::pseudo3_N2E3:AO353_16280
         (223 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4900
          Length = 217

 Score = 99.4 bits (246), Expect = 5e-26
 Identities = 64/203 (31%), Positives = 108/203 (53%), Gaps = 15/203 (7%)

Query: 22  TLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFRSIPLLLVITWFYLAVPFV 81
           T+ L+++  +GG ++G LL ++RLS  + +    GAYV  F+  PLL+ +   Y  +   
Sbjct: 20  TVSLSLIAFIGGGLVGLLLLVLRLSKVRGVDRAVGAYVQVFQGTPLLMQLFLAYFGIA-- 77

Query: 82  LRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAKALGMGYGQMMR 141
              + G  T    +T+  VA  ++ +AY  EI R  V SIPKGQ  AA++L   +G+ +R
Sbjct: 78  ---LFGIKT--SPWTAAAVALTLYTSAYLTEIWRGCVASIPKGQWEAAQSLAFNFGEQLR 132

Query: 142 LIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNATRASGDIIGRA--NEFLIIA 199
            ++LPQA R   P  +   + + + T+L   +G V+   A    G +I  A    FL+ A
Sbjct: 133 HVVLPQALRIAVPPTVGFLVQVIKGTALASVIGFVELTKA----GSMISNATYKPFLVYA 188

Query: 200 --GLVYFTISFAASRLVKRLQKR 220
              L+YF + F  S + + L+++
Sbjct: 189 CVALLYFVLCFPVSLVAQSLERK 211


Lambda     K      H
   0.331    0.143    0.425 

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: 127
Number of extensions: 7
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: 223
Length of database: 217
Length adjustment: 22
Effective length of query: 201
Effective length of database: 195
Effective search space:    39195
Effective search space used:    39195
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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:

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