GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacK in Marinobacter adhaerens HP15

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF960 HP15_939 spermidine/putrescine ABC transporter ATPase subunit

Query= uniprot:D4GP39
         (383 letters)



>lcl|FitnessBrowser__Marino:GFF960 HP15_939 spermidine/putrescine
           ABC transporter ATPase subunit
          Length = 372

 Score =  204 bits (518), Expect = 4e-57
 Identities = 126/341 (36%), Positives = 189/341 (55%), Gaps = 18/341 (5%)

Query: 22  VAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQDRD 81
           +AV+ ++LDI  GE   L+G SG GKST LRM+AG ET   G + L+ + +  +    R 
Sbjct: 28  LAVDNVNLDIHKGEIFALLGGSGSGKSTLLRMLAGFETPNAGSIMLDGQDVTALPPFLRP 87

Query: 82  IAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPGQLS 141
             M+FQSYAL+PH +V  N++ GL++   LP  EIR RV     ++ +     RKP QLS
Sbjct: 88  TNMMFQSYALFPHMTVEQNIAMGLKQDK-LPKSEIRDRVAAMLKLVKMEPYARRKPQQLS 146

Query: 142 GGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTHDQT 201
           GGQQQRVAL R++ + P++ L+DEP+  LD KLR EM+ EL  +   +G T + VTHDQ 
Sbjct: 147 GGQQQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLELVEILENVGATCLMVTHDQE 206

Query: 202 EAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD-----T 256
           EAMTM  R+A++  G + Q+G+P+D Y  PN+   A FIG  S+N+F+  +  D     T
Sbjct: 207 EAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRMTAEFIG--SVNIFEAHIREDEADSVT 264

Query: 257 FRGDGFDYPL---SGATRDQLGGASGLTLGIRPEDV-TVGERRSGQRTFDAEVV-VVEPQ 311
              D  D P+    G T      ++   + +RPE +    ++  G+  +    V  +   
Sbjct: 265 LTSDLLDAPVFIDRGVTTP--AESTATLVALRPEKIYLTPDKPDGENNWSCGTVDNIAYL 322

Query: 312 GNENAVHLRFVDGD--EGTQFTATTTGQSRVEAGDRTTVSF 350
           G+  + +++   G   + T       G+ R   GDR  VS+
Sbjct: 323 GDITSYYVKLASGKRVQATMANVERRGE-RPTWGDRVFVSW 362


Lambda     K      H
   0.316    0.136    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: 368
Number of extensions: 16
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: 383
Length of database: 372
Length adjustment: 30
Effective length of query: 353
Effective length of database: 342
Effective search space:   120726
Effective search space used:   120726
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: 42 (22.0 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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