GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate H281DRAFT_05513 H281DRAFT_05513 branched-chain amino acid transport system permease protein

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Burk376:H281DRAFT_05513
          Length = 597

 Score =  193 bits (491), Expect = 6e-54
 Identities = 101/249 (40%), Positives = 154/249 (61%), Gaps = 4/249 (1%)

Query: 10  LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69
           L V  +SK++GG+ A+SDV  ++  GQ++GLIGPNGAGK+T  N+I G Y  D+G   L 
Sbjct: 346 LTVESVSKQYGGVLAVSDVSFSVAAGQIHGLIGPNGAGKSTLVNLIAGNYLCDSGRVRLD 405

Query: 70  GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGS-GLFGAVFRTKGFK 128
           G         + AK G+ARTFQN++L   +  LENV++G     G    F   +  + F 
Sbjct: 406 GADVSNLVTADRAKRGLARTFQNLQLVEALPVLENVLLGMSSADGHVANFAKWWMGRAFD 465

Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188
             E    + A E+L + GI          LSYG ++ +E+ARA+A  P+L+ LDEP AG+
Sbjct: 466 LPER---REALEILAFFGIEHLCQAYPTELSYGHRKLVELARAIAQRPRLMLLDEPIAGL 522

Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248
           N  E +++ +++ R+R+   TILLIEH+++ VM LCD ++VL+ G+ I  G P E++ +E
Sbjct: 523 NGAEAMEVAKVVGRLRDAGVTILLIEHNMEFVMSLCDSISVLEQGRLIGTGTPEEIRSDE 582

Query: 249 KVIEAYLGT 257
           +++ AYLGT
Sbjct: 583 RILRAYLGT 591


Lambda     K      H
   0.319    0.137    0.384 

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: 389
Number of extensions: 16
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: 260
Length of database: 597
Length adjustment: 31
Effective length of query: 229
Effective length of database: 566
Effective search space:   129614
Effective search space used:   129614
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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