GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Methanospirillum lacunae Ki8-1

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_109968115.1 DK846_RS06450 ATP-binding cassette domain-containing protein

Query= TCDB::Q8DQH8
         (254 letters)



>NCBI__GCF_003173355.1:WP_109968115.1
          Length = 329

 Score =  133 bits (334), Expect = 5e-36
 Identities = 75/238 (31%), Positives = 131/238 (55%), Gaps = 17/238 (7%)

Query: 3   LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62
           +++   LTK FG  TAV  ++LE+++GE+ GL+GPNGAGKTT  ++L  + +P+ GT  +
Sbjct: 4   IIKTFNLTKIFGSNTAVNSISLEVHKGEVFGLLGPNGAGKTTFLSMLCTILKPTSGTAVI 63

Query: 63  DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122
           +G+ +   S     S+G+   FQ+  +  D+T  +N+           +      +P   
Sbjct: 64  NGYDIVQDSAMVRRSIGI--VFQDPSVDTDMTSRENL----------QMHADLYDVPV-- 109

Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182
               E  ++  E+L +  L+  A+      S G +RRLEI R L   P++LFLDEP  G+
Sbjct: 110 ---SEQASRIQEVLTLVQLEDRADDFLNTYSGGMRRRLEIARGLLHYPRVLFLDEPTIGL 166

Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240
           +PQ    +   IR++++   +T++L  H M    E+ +RI ++++G ++A  TP  +K
Sbjct: 167 DPQSREHIWSYIRQLREREDMTLILTTHYMEEADELCDRIAIIDHGSIVALDTPSALK 224


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: 156
Number of extensions: 7
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: 329
Length adjustment: 26
Effective length of query: 228
Effective length of database: 303
Effective search space:    69084
Effective search space used:    69084
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: 48 (23.1 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