GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12640 in Methanococcus aeolicus Nankai-3

Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_011972867.1 MAEO_RS00720 ATP-binding cassette domain-containing protein

Query= reanno::Phaeo:GFF1248
         (251 letters)



>NCBI__GCF_000017185.1:WP_011972867.1
          Length = 281

 Score = 90.5 bits (223), Expect = 3e-23
 Identities = 66/225 (29%), Positives = 116/225 (51%), Gaps = 12/225 (5%)

Query: 1   MGILEVKNVGKRF-GGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGS 59
           M I+E K++  ++  G  AL   N+SV +  + A++GPNGAGKSTL     G L P +G 
Sbjct: 1   MAIIEAKDIVYKYPDGTLALDRANISVEKGDMVALLGPNGAGKSTLFLHFNGILKPKSGK 60

Query: 60  VMFDGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAV 119
           ++  G      AP + +   +  V +T  I    S  ++ +     K+D AF    ++  
Sbjct: 61  ILLKG------APIKYDAKSLMEVRKTVGIVFQNS--DDQLFAPTVKQDVAF--GPLNLG 110

Query: 120 SGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGM 179
             + ++ ++ +  L+E+ M    +     +S G K+R+ I   L+  P +++LDEPTAG+
Sbjct: 111 LKEEEVEKRVKEALKEVGMEGFENKPPHHLSGGQKKRVAIAGILAMHPEIMVLDEPTAGL 170

Query: 180 ARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQ 224
                +  + LL ++  E  ITI I  HD+ +V   A++I V+ +
Sbjct: 171 DPMGASKIMKLLYKLNKE-GITIIISTHDVDLVPIYANKIFVMGK 214


Lambda     K      H
   0.318    0.135    0.379 

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: 166
Number of extensions: 8
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: 251
Length of database: 281
Length adjustment: 25
Effective length of query: 226
Effective length of database: 256
Effective search space:    57856
Effective search space used:    57856
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 Apr 09 2024. 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