GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00900 in Herbaspirillum seropedicae SmR1

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate HSERO_RS05975 HSERO_RS05975 amino acid ABC transporter ATPase

Query= uniprot:D8IUY7
         (241 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05975 HSERO_RS05975 amino acid
           ABC transporter ATPase
          Length = 241

 Score =  464 bits (1195), Expect = e-136
 Identities = 241/241 (100%), Positives = 241/241 (100%)

Query: 1   MTTNILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRV 60
           MTTNILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRV
Sbjct: 1   MTTNILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRV 60

Query: 61  EGHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADI 120
           EGHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADI
Sbjct: 61  EGHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADI 120

Query: 121 DKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIF 180
           DKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIF
Sbjct: 121 DKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIF 180

Query: 181 EVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLGE 240
           EVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLGE
Sbjct: 181 EVIRNVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLGE 240

Query: 241 G 241
           G
Sbjct: 241 G 241


Lambda     K      H
   0.317    0.134    0.365 

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: 323
Number of extensions: 3
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: 241
Length of database: 241
Length adjustment: 23
Effective length of query: 218
Effective length of database: 218
Effective search space:    47524
Effective search space used:    47524
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 (21.6 bits)
S2: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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