GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Marinobacter adhaerens HP15

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate GFF2975 HP15_2919 amino acid ABC transporter, permease protein

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>FitnessBrowser__Marino:GFF2975
          Length = 223

 Score =  157 bits (396), Expect = 2e-43
 Identities = 86/219 (39%), Positives = 134/219 (61%), Gaps = 6/219 (2%)

Query: 1   MELDFSPVWAG----VPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALC 56
           ME  F   W      +P L+ G   T+ I+   LL+G  +G+  G+  +N K  + +   
Sbjct: 1   MEFQFQFDWQAAIDSIPFLIKGIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLRWP-A 59

Query: 57  TAYVAAIRGTPLLVQLFILFFGLPQF-GILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSI 115
           TAY+   RGTP+LVQ+  +F+GLP   G  +     G+  + + SGAY+SEVVRG +QSI
Sbjct: 60  TAYIEIFRGTPILVQVLFIFYGLPDLIGGPIDPLTAGIAAIALNSGAYISEVVRGGVQSI 119

Query: 116 DKGQMEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHE 175
           DKGQ EA  S+G+S      +VV PQA  RMIPPLGN+ I  IK+++L S++ + +L+ +
Sbjct: 120 DKGQTEAGLSLGLSRTQTFWSVVWPQAFRRMIPPLGNQAIVSIKDTSLFSVIGVGELVRQ 179

Query: 176 GQKIISVSYRSLEVYLAIAVVYFILTGATTLVLRRIELR 214
           GQ  I+ ++ + EVY  +A++Y  +T + +++LR +E R
Sbjct: 180 GQIYIANTFTAFEVYFVVAILYLAITLSLSIILRFVERR 218


Lambda     K      H
   0.328    0.143    0.412 

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: 153
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: 222
Length of database: 223
Length adjustment: 22
Effective length of query: 200
Effective length of database: 201
Effective search space:    40200
Effective search space used:    40200
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:

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