GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Arenitalea lutea P7-3-5

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_019388681.1 P735_RS0114015 ATP-binding cassette domain-containing protein

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>NCBI__GCF_000283015.1:WP_019388681.1
          Length = 227

 Score = 83.6 bits (205), Expect = 5e-21
 Identities = 66/217 (30%), Positives = 104/217 (47%), Gaps = 9/217 (4%)

Query: 3   LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62
           L L   S   G    L ++++ +  G    L+G T  GK+S M+ + G    T G   + 
Sbjct: 6   LQLKDASIFQGDSLVLSNVNVEINKGEFVYLIGKTGTGKSSFMKTLYGDLPLTEGEGHIV 65

Query: 63  GKDVTGMPVRD-----RNVAMVYQQFINYPSMKVAANIASPLKLRGEKNID---ARVREI 114
             D+  +  +D     R + +V+Q F       +  N+   LK  G K+ D    RV E+
Sbjct: 66  DFDLKNLKEKDIPYLRRKLGVVFQDFKLLTDRTINDNLLFVLKATGWKDKDKMKTRVEEV 125

Query: 115 ASRLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELT 174
            +++ +     ++P ELSGG+QQRVA+ARAL     L+L DEP  NLD +   E+ E L 
Sbjct: 126 LTKVDMKTKGFKFPHELSGGEQQRVAIARALLNNPELILADEPTGNLDPQTSVEVMEVLQ 185

Query: 175 QLFAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQ 211
            +   G +T++ AT +    L     T   DE Q+ +
Sbjct: 186 DINKNG-NTILMATHDYALLLKYPSKTLKCDENQVYE 221


Lambda     K      H
   0.318    0.133    0.375 

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: 119
Number of extensions: 3
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: 363
Length of database: 227
Length adjustment: 26
Effective length of query: 337
Effective length of database: 201
Effective search space:    67737
Effective search space used:    67737
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 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