GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlK in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit

Query= reanno::Phaeo:GFF1302
         (334 letters)



>lcl|FitnessBrowser__psRCH2:GFF4209 Psest_4282 spermidine/putrescine
           ABC transporter ATP-binding subunit
          Length = 383

 Score =  223 bits (568), Expect = 6e-63
 Identities = 111/241 (46%), Positives = 158/241 (65%), Gaps = 2/241 (0%)

Query: 4   IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63
           +K++ VTK F     +  + L+I  GE    +G SG GKSTLLR++AG E  T G I +D
Sbjct: 23  LKIDRVTKKFDETVAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIFLD 82

Query: 64  GEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNL 123
           G+D T++PP +R + M+FQSYAL+PHM+V +NIAF +K  G+P  E + R+      + +
Sbjct: 83  GQDITDMPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDGLPKAEIEERVKEMLGLVQM 142

Query: 124 TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRL 183
           T Y  R+P QLSGGQRQRVA+ R++ + P   L DEP+  LD  LR  M+LE+ ++ +R+
Sbjct: 143 TQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVQIIERV 202

Query: 184 ATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLLT 243
             T + VTHDQ EAMTMA++I ++  G I QVGSPM++Y  P +  V  FIG+  +NL  
Sbjct: 203 GVTCVMVTHDQEEAMTMAERIAIMHLGWIAQVGSPMDIYETPASRLVCEFIGN--VNLFD 260

Query: 244 G 244
           G
Sbjct: 261 G 261


Lambda     K      H
   0.320    0.138    0.400 

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: 290
Number of extensions: 7
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: 334
Length of database: 383
Length adjustment: 29
Effective length of query: 305
Effective length of database: 354
Effective search space:   107970
Effective search space used:   107970
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.

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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