GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM 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)



>FitnessBrowser__Dino:3606890
          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 (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