GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Caulobacter crescentus NA1000

Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate CCNA_01507 CCNA_01507 cystine transport system permease protein

Query= TCDB::Q52814
         (384 letters)



>FitnessBrowser__Caulo:CCNA_01507
          Length = 219

 Score =  105 bits (261), Expect = 2e-27
 Identities = 69/212 (32%), Positives = 108/212 (50%), Gaps = 12/212 (5%)

Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233
           G   T+VLS +G+++ + +G LLAL R SR  ++R     ++   RG PL+  LF+    
Sbjct: 18  GAGYTIVLSVIGMSIGVVLGFLLALMRLSRSALLRWPAGVYVSAFRGTPLLVQLFLIYYG 77

Query: 234 LPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLGYWQKTR 293
           LP F   G  +  L+ A IG S+  +AY  E++R  + A+ KGQ+E A  LG+   Q  R
Sbjct: 78  LPQF---GLEMPPLVAAGIGFSLNVAAYSCEILRSAIAAVDKGQWEAASVLGMSRGQTLR 134

Query: 294 LIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAVT--PIT 351
            +I+PQA +  +  + N+FI   KDTSL   I + +L       F  A   +A T    T
Sbjct: 135 RVILPQAARTAVAPLSNSFISLVKDTSLAATIQVPEL-------FRQAQLITARTYEIFT 187

Query: 352 GLIFAGFIFWLFCFGMSRYSGFMERHLDTGHK 383
             + A  I+W+    ++     +ER    G +
Sbjct: 188 LYLAAAAIYWILSTILAAAQTRLERRAAEGRR 219


Lambda     K      H
   0.330    0.145    0.469 

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: 204
Number of extensions: 9
Number of successful extensions: 2
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: 384
Length of database: 219
Length adjustment: 26
Effective length of query: 358
Effective length of database: 193
Effective search space:    69094
Effective search space used:    69094
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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