GapMind for catabolism of small carbon sources

 

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

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 H281DRAFT_02384 H281DRAFT_02384 amino acid/amide ABC transporter ATP-binding protein 2, HAAT family

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Burk376:H281DRAFT_02384
          Length = 254

 Score =  221 bits (564), Expect = 8e-63
 Identities = 111/238 (46%), Positives = 166/238 (69%), Gaps = 6/238 (2%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQA---ASGS 57
           +L  + +S  YGK++ALH  +++V+ G+IV++IG NGAGKSTLL  + G+      A G+
Sbjct: 11  ILDVNGLSVRYGKVEALHGAAIKVRAGQIVSVIGPNGAGKSTLLNAIMGALPTTGHAKGA 70

Query: 58  IRYEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKD---DYQVQMD 114
           + Y+GE++  +P    + + + +VPE R +F+ ++VE+NL +G +   +    ++  QM+
Sbjct: 71  VVYQGEDVSAVPVEKRVARGMCLVPEKRELFASMSVEDNLVLGAYRRKRAGERNFLDQME 130

Query: 115 KVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFE 174
            V +LFPRLKER +Q AGT+SGGE+QMLA+GRALM KP LL+LDEPSLGLAP+I+++IF 
Sbjct: 131 PVFQLFPRLKERRKQAAGTLSGGERQMLAVGRALMGKPDLLMLDEPSLGLAPLIVKEIFH 190

Query: 175 IIEQLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232
           II  LR+ GV   L+EQNA  AL+++D  YVLE G + +    + L  NP+V + YLG
Sbjct: 191 IISALRQTGVATLLIEQNARAALQISDYGYVLETGELALEGAASDLAQNPRVIETYLG 248


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: 178
Number of extensions: 9
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: 254
Length adjustment: 23
Effective length of query: 210
Effective length of database: 231
Effective search space:    48510
Effective search space used:    48510
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