GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Dechlorosoma suillum PS

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 Dsui_1113 Dsui_1113 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__PS:Dsui_1113
          Length = 278

 Score =  186 bits (472), Expect = 4e-52
 Identities = 105/240 (43%), Positives = 148/240 (61%), Gaps = 9/240 (3%)

Query: 2   LSFDKVSTYYGK-IQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQA-----AS 55
           LS + +   Y   I  L  VS+ V KG+IV L+GANGAGKST L  +     A       
Sbjct: 16  LSINNIEVIYDHVILVLKGVSLTVPKGKIVALLGANGAGKSTTLKAISNLLHAERGDVTK 75

Query: 56  GSIRYEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF--TDKDDYQVQM 113
           GS+ ++G  +  L  + ++++ +  V EGR  F+ L++EENL  G +     + + +  +
Sbjct: 76  GSVEFKGTRVDQLTPNELVKRGVIQVMEGRHCFAHLSIEENLLTGAYTRGNSRAELKQNL 135

Query: 114 DKVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIF 173
           + V   FPRLK R   +AG  SGGEQQM AIGRALM+KP+++LLDEPS+GLAP I+++IF
Sbjct: 136 EMVYHYFPRLKTRRTSQAGYTSGGEQQMCAIGRALMAKPEMILLDEPSMGLAPQIVEEIF 195

Query: 174 EIIEQLR-REGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232
           EI++ L  RE V+  L EQN   AL+ AD  Y+LENGR+VM      L +N  V++ YLG
Sbjct: 196 EIVKDLNSRENVSFLLAEQNTMVALRYADLGYILENGRVVMEGDAKELASNEDVKEFYLG 255


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: 159
Number of extensions: 12
Number of successful extensions: 4
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: 278
Length adjustment: 24
Effective length of query: 209
Effective length of database: 254
Effective search space:    53086
Effective search space used:    53086
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: 47 (22.7 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