GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03045 in Marivita geojedonensis DPG-138

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_085638697.1 MGEO_RS13240 ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_03045
         (232 letters)



>NCBI__GCF_002115805.1:WP_085638697.1
          Length = 240

 Score =  223 bits (567), Expect = 3e-63
 Identities = 111/229 (48%), Positives = 155/229 (67%), Gaps = 1/229 (0%)

Query: 4   DYNVIWEALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIR 63
           D+ +I++ L  +  G   TL+L  L+LL G L A+PL + R  ++P++N   W YTY  R
Sbjct: 2   DFMLIFDNLDRFVEGAWVTLQLTFLALLLGGLIAIPLAIARAYRKPVLNPIIWGYTYAFR 61

Query: 64  GTPMLVQLFLIYYGLAQFEAVRESFLW-PWLSSATFCACLAFAINTSAYTAEIIAGSLRA 122
           GTP+LVQ +L Y+GL QFEAVR SFLW P LS   +C  +AF +NT+AYT E + G++  
Sbjct: 62  GTPLLVQTYLFYFGLGQFEAVRNSFLWSPILSDPWWCVLIAFTLNTAAYTTEFLRGAIET 121

Query: 123 TPNGEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITG 182
           TP GEIEAAKA GMS +   + ++LPSA RRALP YSNEVI  L  + +AS VTL D+ G
Sbjct: 122 TPRGEIEAAKAAGMSPWTRMRLVVLPSAFRRALPAYSNEVIFTLHGSVIASTVTLQDLLG 181

Query: 183 AARTVNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGYLAPRK 231
             R +N +YYL +E ++TA +FY+ + F++   F+ AE R+L +L PR+
Sbjct: 182 VGRWLNGRYYLAYEGFVTAMLFYMAIVFMISLAFRYAEKRYLKHLRPRE 230


Lambda     K      H
   0.329    0.139    0.427 

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: 165
Number of extensions: 5
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: 232
Length of database: 240
Length adjustment: 23
Effective length of query: 209
Effective length of database: 217
Effective search space:    45353
Effective search space used:    45353
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