GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Desulfovibrio vulgaris Miyazaki F

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 8501896 DvMF_2611 ABC transporter related (RefSeq)

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Miya:8501896
          Length = 234

 Score =  259 bits (663), Expect = 2e-74
 Identities = 133/233 (57%), Positives = 171/233 (73%), Gaps = 1/233 (0%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           ML    V+ +YG IQAL D+++ + +GEIVTLIGANGAGK+T LMT+CG+    +G + +
Sbjct: 1   MLELRNVNAFYGNIQALRDINLTIGQGEIVTLIGANGAGKTTTLMTVCGAVPPRTGEVLF 60

Query: 61  EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF-TDKDDYQVQMDKVLEL 119
           EG+ +  +  + I+R  I+ VPEGR +F  LTV+ENL +G F   DKD     +D +  L
Sbjct: 61  EGKPIHTMKPNEIVRLGISQVPEGRLIFPDLTVQENLDLGAFLRNDKDGIARDLDYIFGL 120

Query: 120 FPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL 179
           FP L +R +Q  GT+SGGEQQMLAI RA+M +P+LLLLDEPSLGLAPIIIQQIF+II ++
Sbjct: 121 FPILAQRRKQAGGTLSGGEQQMLAISRAIMGRPRLLLLDEPSLGLAPIIIQQIFDIIRKI 180

Query: 180 RREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232
             +G TVFLVEQNANQALK+A RAYV+E GRI + DT A LL N  V+ AYLG
Sbjct: 181 NADGTTVFLVEQNANQALKIAHRAYVMETGRITLEDTAANLLVNEDVKKAYLG 233


Lambda     K      H
   0.318    0.136    0.374 

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: 175
Number of extensions: 5
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: 233
Length of database: 234
Length adjustment: 23
Effective length of query: 210
Effective length of database: 211
Effective search space:    44310
Effective search space used:    44310
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 (21.7 bits)
S2: 46 (22.3 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