GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artM in Dinoroseobacter shibae DFL-12

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q9HU29
         (230 letters)



>lcl|FitnessBrowser__Dino:3606890 Dshi_0320 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 432

 Score = 95.1 bits (235), Expect = 2e-24
 Identities = 70/205 (34%), Positives = 115/205 (56%), Gaps = 18/205 (8%)

Query: 31  AGLALALPLGIA----RASRHWYVRAVPYAYIFFFRGTPLLLQLFIVYYGLAQFEEVRKS 86
           +G+AL+LPLGIA    R S    ++ V   +I F RG PL+  LF+    LA F     S
Sbjct: 234 SGIALSLPLGIALALGRQSNLPIIKGVCVVFIEFIRGVPLITLLFVASVMLAYFLPPGTS 293

Query: 87  AFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVGEVEAARALGMSRRQALWHIIL 146
            F   LR      ++ +TL  +AYIAE +RG + ++P G+ EA  +LG+   Q++  IIL
Sbjct: 294 -FDLVLR-----VIIMITLFASAYIAEAIRGGLAALPRGQYEAGDSLGLDYWQSMRLIIL 347

Query: 147 PRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMAR-TIIART-----YESMLFFCLA 200
           P+A++I +P+  N  I + K + +V  +++FD++GM +  I++ T     Y  +L F  A
Sbjct: 348 PQALKISIPSIVNIAIGLFKDTTLVSIISMFDMLGMIQGPILSSTEWFGVYWELLGF--A 405

Query: 201 GALYLVITIVLTRIFRLIERWLRVD 225
           G L+ V    +++  + +ER L  +
Sbjct: 406 GVLFFVFCYGISQYSQWLERQLATE 430


Lambda     K      H
   0.332    0.142    0.443 

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: 304
Number of extensions: 17
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 230
Length of database: 432
Length adjustment: 27
Effective length of query: 203
Effective length of database: 405
Effective search space:    82215
Effective search space used:    82215
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 48 (23.1 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 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, 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