GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Methanobacterium veterum MK4

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_048082254.1 EJ01_RS09405 ABC transporter ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>NCBI__GCF_000745485.1:WP_048082254.1
          Length = 222

 Score = 85.9 bits (211), Expect = 6e-22
 Identities = 67/218 (30%), Positives = 113/218 (51%), Gaps = 17/218 (7%)

Query: 11  LLEVENVHAGYI---KDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTG 67
           +LE +NV   Y    + V+ L G+N  +E G    V+GP+G+GKST       L  P  G
Sbjct: 5   VLEFKNVWKTYTMGDETVNALAGLNLALEKGSFTAVMGPSGSGKSTFLHVAGILDMPTRG 64

Query: 68  KITFKGKNIAGLKSNQIVRLG---MCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKD 124
                GK    L   +  RL    + ++ Q  N+   L+V EN+ M   I+ D+ + + D
Sbjct: 65  TFQINGKETHKLSVKEQARLRRDEIGFIFQRFNLMSQLTVLENV-MLPMIKEDTKKAV-D 122

Query: 125 KIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFE 184
            +  M   L+ +  +R G LSGGE+Q +A+ +AL+ +PS+++ DEP+  L       + +
Sbjct: 123 LLNKM--GLAGKYNKRPGQLSGGEQQRVAIARALINDPSIILADEPTGELDTKNADSIMQ 180

Query: 185 QVKQINQ-EGTAIILVEQN------ARKALEMADRGYV 215
            ++ +N+ EG +I++V  N      A + L M+D  +V
Sbjct: 181 ILQDLNRDEGVSIVMVTHNPSSAEFAGEILHMSDGNFV 218


Lambda     K      H
   0.317    0.136    0.377 

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: 153
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: 247
Length of database: 222
Length adjustment: 23
Effective length of query: 224
Effective length of database: 199
Effective search space:    44576
Effective search space used:    44576
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 (21.6 bits)
S2: 46 (22.3 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