GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Paraburkholderia bryophila 376MFSha3.1

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate H281DRAFT_04268 H281DRAFT_04268 L-glutamate ABC transporter membrane protein /L-aspartate ABC transporter membrane protein

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__Burk376:H281DRAFT_04268
          Length = 225

 Score =  105 bits (261), Expect = 2e-27
 Identities = 70/227 (30%), Positives = 124/227 (54%), Gaps = 13/227 (5%)

Query: 210 SALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEF 269
           S +P ALP +    + G ++   I + AIV+ +  G +LA+ R S     +  + G +  
Sbjct: 7   SGIPGALPTL----WTGAVVTFKITLIAIVIGIVWGTVLAMLRLSSFKPFEWFAKGYVTI 62

Query: 270 VRGVPLITLLFTASLLLQYFLPP--GTNFDLILRV---VILVTLFAAAYIAEVIRGGLAA 324
            R +PL+ +L    L++   L    G + D+ +R+   ++  +LF AAY +E+IR G+ +
Sbjct: 63  FRSIPLVMVLLWFFLIVPQVLQNVLGLSPDIDIRLASAMVAFSLFEAAYYSEIIRAGIQS 122

Query: 325 LPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLK 384
           +PRGQ  A+ ALG++Y Q+ RL+++PQA +  +P +++  I LF+DT+LV  + L D  +
Sbjct: 123 VPRGQVNASFALGMNYAQSMRLVVLPQAFRAMVPLLLTQGIVLFQDTSLVYVISLADFFR 182

Query: 385 GISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKLKR 431
             +N+   D    GT  E  +F    +F+     S     L++K+ R
Sbjct: 183 TATNIGDRD----GTNVEMVLFAGACYFVICVIASSLVKGLQKKVAR 225


Lambda     K      H
   0.329    0.143    0.457 

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: 245
Number of extensions: 10
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: 434
Length of database: 225
Length adjustment: 27
Effective length of query: 407
Effective length of database: 198
Effective search space:    80586
Effective search space used:    80586
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