GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Shewanella amazonensis SB2B

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_2941
         (350 letters)



>FitnessBrowser__SB2B:6938538
          Length = 378

 Score =  229 bits (584), Expect = 9e-65
 Identities = 107/233 (45%), Positives = 163/233 (69%)

Query: 4   LQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLD 63
           L++  + K F + RA+  + LTI +GE    +G SG GKSTLLR++AG E    G + LD
Sbjct: 21  LKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLD 80

Query: 64  GRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNL 123
           G+DITD P  +R + M+FQSYAL+PHM+V +N++F LK  K+ K  I ++VQ   +++++
Sbjct: 81  GQDITDLPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLVHM 140

Query: 124 TQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLHRDL 183
            QY +R P +LSGGQRQRVA+ R++ + PK+ L DEP+  LD  LR Q ++E+ ++   +
Sbjct: 141 EQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERV 200

Query: 184 GATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGT 236
           G T + VTHDQ EAMT+A R+ ++ DG I QVG+P+++Y+ P ++ +A+FIGT
Sbjct: 201 GVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIGT 253


Lambda     K      H
   0.320    0.137    0.388 

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: 286
Number of extensions: 16
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: 350
Length of database: 378
Length adjustment: 29
Effective length of query: 321
Effective length of database: 349
Effective search space:   112029
Effective search space used:   112029
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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