GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Brucella inopinata BO1

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease

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



>NCBI__GCF_000182725.1:WP_008511689.1
          Length = 323

 Score =  147 bits (372), Expect = 2e-40
 Identities = 76/212 (35%), Positives = 135/212 (63%), Gaps = 2/212 (0%)

Query: 2   ELDFSPVWAGVPQLLA-GALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYV 60
           +L FS +   +  L+  G + T+ I+A S+ +  ++ L+  I +L+ +  V+Y L T Y 
Sbjct: 104 DLSFSFIARKISFLITQGTVTTLYISAISIAIATIIALIGAIAKLS-QNGVIYGLSTFYT 162

Query: 61  AAIRGTPLLVQLFILFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQM 120
           +  RG PLL+Q++I++ GLPQ G ++ A   G++ L +  GAY++E+ R  I+SI  GQ 
Sbjct: 163 SLFRGLPLLMQIYIIYLGLPQIGYVIGAIPAGILALSLCYGAYMTEIFRAGIESIPHGQK 222

Query: 121 EAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKII 180
           EAA ++G+ S   M  V+LPQA+  +IPP GN+FIA++K+S+LVS++ + +LM+  +   
Sbjct: 223 EAATALGLGSAQTMWLVILPQAMRIIIPPTGNQFIAMLKDSSLVSVIGVWELMYVARTQG 282

Query: 181 SVSYRSLEVYLAIAVVYFILTGATTLVLRRIE 212
              +R +E+ +  +++Y+IL+ +   +  RIE
Sbjct: 283 QTEFRHIEMLITASMIYWILSISFEFIQSRIE 314


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: 181
Number of extensions: 10
Number of successful extensions: 1
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: 323
Length adjustment: 25
Effective length of query: 197
Effective length of database: 298
Effective search space:    58706
Effective search space used:    58706
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