GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artM in Lutibaculum baratangense AMV1

Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate WP_081718345.1 N177_RS02595 ABC transporter permease

Query= reanno::WCS417:GFF4243
         (232 letters)



>NCBI__GCF_000496075.1:WP_081718345.1
          Length = 248

 Score =  174 bits (442), Expect = 1e-48
 Identities = 89/213 (41%), Positives = 133/213 (62%), Gaps = 2/213 (0%)

Query: 16  LGGLLTTLKLLAISLFFGLLAALPLGLMRVSKQPIVNGAAWLYTYVIRGTPMLVQLFLIY 75
           L G  TT++L+ +SL  G   +LP+   R+S  P++   A+ Y Y  RGTP+L Q FL+Y
Sbjct: 32  LSGFWTTIELVTLSLLIGAAISLPVAAGRLSPNPVIGALAYGYVYFFRGTPLLAQTFLVY 91

Query: 76  YGLAQFEAVRESF-LWPLLSSATFCACLAFAINTSAYTAEIIAGSLKATPNGEIEAAKAM 134
           YG   F A  ++  LW     A FCA   F++NTSAY AEI+AG+++  P  +IEA +A+
Sbjct: 92  YGAGSFRAELDAVGLWTFFRDAWFCAVFTFSLNTSAYQAEILAGAIRTVPRSQIEAGQAL 151

Query: 135 GMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQFYLP 194
           G+SRY +  RI+LP AL  AL  Y NEV++M++ +++ASI+T+ D+ G  R   ++ +  
Sbjct: 152 GLSRYVIATRIVLPQALVVALRPYGNEVVLMIKGSAIASIITIYDLMGETRRAFSRSF-D 210

Query: 195 FEAYITAGVFYLCLTFILVRLFKLAERRWLSYL 227
           F+ YI A + YL L   L RL+ + ERR   +L
Sbjct: 211 FQTYIWAAILYLVLVETLRRLWDVMERRLTRHL 243


Lambda     K      H
   0.329    0.140    0.422 

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: 148
Number of extensions: 7
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: 232
Length of database: 248
Length adjustment: 23
Effective length of query: 209
Effective length of database: 225
Effective search space:    47025
Effective search space used:    47025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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