GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Kocuria flava HO-9041

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_083529437.1 AS188_RS12245 ATP-binding cassette domain-containing protein

Query= TCDB::Q8DQH8
         (254 letters)



>NCBI__GCF_001482365.1:WP_083529437.1
          Length = 313

 Score =  104 bits (260), Expect = 2e-27
 Identities = 73/238 (30%), Positives = 112/238 (47%), Gaps = 21/238 (8%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           +LE + L++ FGG T V DV+  +  G + G +G NGAGKTT   +LTGV   + G V  
Sbjct: 22  VLEARGLSRAFGGRTVVEDVSFRVEPGRMTGFVGANGAGKTTTMRMLTGVLRTTAGEVLW 81

Query: 63  DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122
           DG  +           G G   +   L+    VLD  L   G  H               
Sbjct: 82  DGRPVTAAD-----RAGFGYMPEERGLYPRQPVLDQ-LCYLGRLHGM------------- 122

Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182
              +   A+A  LL+  DL G        LS G Q+R++I  AL   P  L LDEP +G+
Sbjct: 123 -DRRAALAEARRLLERLDLAGRERDPLGTLSLGNQQRVQIAAALLHGPTALVLDEPFSGL 181

Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240
           +P     +T L+R  + E  + ++   H ++LV  + + + VL  GR++A G  ++++
Sbjct: 182 DPVAVDAMTGLLRE-RLEQGVPVLFSSHQLDLVDRLCDSLVVLSAGRVLAAGAVEDLR 238


Lambda     K      H
   0.319    0.139    0.385 

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: 161
Number of extensions: 8
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: 254
Length of database: 313
Length adjustment: 26
Effective length of query: 228
Effective length of database: 287
Effective search space:    65436
Effective search space used:    65436
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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