GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Fibrella aestuarina BUZ 2

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_015334118.1 FAES_RS25660 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_000331105.1:WP_015334118.1
          Length = 221

 Score =  102 bits (255), Expect = 5e-27
 Identities = 69/229 (30%), Positives = 115/229 (50%), Gaps = 20/229 (8%)

Query: 9   VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68
           +L    + + +G L  L+DV ++I  G+V  ++G +GAGK+T  +++  L  PD G+  L
Sbjct: 3   ILHATNLRRAYGPLPVLNDVSLSIDAGEVVSIVGASGAGKSTLLHILGTLDRPDGGSVTL 62

Query: 69  AGKPYEPTAVHEVAK---AGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTK 125
           AG+        ++A+     I   FQ   L  E TALENV +        G  G      
Sbjct: 63  AGQDVFSLTDKQLARFRNEQIGFVFQFHNLLPEFTALENVAI-------PGFIGG----- 110

Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185
               +E A+ +RA ELL  +G+     +    LS G+Q+R+ +ARAL   P ++  DEP+
Sbjct: 111 ---RDEKAVRQRAAELLSRLGLADRQQHFPAQLSGGEQQRVAVARALINQPAVVFADEPS 167

Query: 186 AGMNATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYG 233
             +++    +L +L   +R+   +T +++ H+  L M L DR   L  G
Sbjct: 168 GNLDSRNAEELHQLFFDLRDTFGQTFIIVTHNETLAM-LADRSITLRDG 215


Lambda     K      H
   0.319    0.137    0.384 

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: 140
Number of extensions: 6
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: 260
Length of database: 221
Length adjustment: 23
Effective length of query: 237
Effective length of database: 198
Effective search space:    46926
Effective search space used:    46926
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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