GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Rhizorhabdus wittichii RW1

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 WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  113 bits (282), Expect = 4e-30
 Identities = 70/224 (31%), Positives = 122/224 (54%), Gaps = 4/224 (1%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           M+SFD V  +Y     L DVS+ +++G  V L+GA+GAGK+TLL  +    +  +G+I  
Sbjct: 1   MISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAI 60

Query: 61  EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF--TDKDDYQVQMDKVLE 118
           EG ++   P +  +R+ I  V +G  +F  ++V EN+A+        +++   ++ ++L+
Sbjct: 61  EGRDVAAQPVAE-LRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLD 119

Query: 119 LFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQ 178
           L     +  E+R   +SGG+ Q +   RAL ++P ++L+DEP   L P+   ++      
Sbjct: 120 LVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRA 179

Query: 179 LRRE-GVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALL 221
           L    G+T  +V  +  +AL LADR  V+  GRI+      AL+
Sbjct: 180 LHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALI 223


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: 150
Number of extensions: 10
Number of successful extensions: 3
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: 252
Length adjustment: 23
Effective length of query: 210
Effective length of database: 229
Effective search space:    48090
Effective search space used:    48090
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 Apr 09 2024. 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