GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Marivita geojedonensis DPG-138

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_085640649.1 MGEO_RS17175 ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>NCBI__GCF_002115805.1:WP_085640649.1
          Length = 251

 Score =  187 bits (476), Expect = 1e-52
 Identities = 94/251 (37%), Positives = 155/251 (61%), Gaps = 3/251 (1%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           +LEV  +  RFGGL A+  VNL V E    ++IGPNGAGK+T+ NCL G   P  G +  
Sbjct: 3   LLEVKDVNKRFGGLQALGNVNLSVAENTCHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124
           DG+ + G    +I + G+ R FQ   +F ++T +EN+L+      + +F     ++    
Sbjct: 63  DGQSVLGRTPFEINQMGISRVFQTPEIFGDLTVMENMLIPCFAKRDGSFALHGIRSVL-- 120

Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
            SE E  + A   L++VN+ +  N  + +++ G +RRLE+A C++  P++L+LDEP AG+
Sbjct: 121 -SEGELRDQAEQMLDDVNMLDKRNMHSASMSRGDKRRLEMAMCLVQNPKLLLLDEPTAGM 179

Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244
              +T++   L+ +++ + ++T+ +IEHDM +V S+++ I V+ QG PL + TPE I+ +
Sbjct: 180 ARADTNNTIDLLKEIKEKRDITIAIIEHDMHVVFSLAERITVLAQGTPLVEDTPENIKGH 239

Query: 245 PDVIKAYLGEA 255
           P V +AYLGEA
Sbjct: 240 PKVKEAYLGEA 250


Lambda     K      H
   0.320    0.137    0.391 

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: 168
Number of extensions: 4
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: 255
Length of database: 251
Length adjustment: 24
Effective length of query: 231
Effective length of database: 227
Effective search space:    52437
Effective search space used:    52437
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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