GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artM in Amantichitinum ursilacus IGB-41

Align AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate WP_053937456.1 WG78_RS08860 amino acid ABC transporter permease

Query= TCDB::O50183
         (232 letters)



>NCBI__GCF_001294205.1:WP_053937456.1
          Length = 221

 Score =  126 bits (317), Expect = 3e-34
 Identities = 73/221 (33%), Positives = 120/221 (54%), Gaps = 17/221 (7%)

Query: 6   SVIWDSLPLYFDGLLVTLKLLSISLLIGLLLAVPLALMRVSKQPLVNFPAWLYTYVIRGT 65
           +++  + P    G   TL     +++ GLL+   LA++R+S    + +PA LY   +RGT
Sbjct: 5   ALLQSAWPYLLKGTGYTLLFAVGAMVGGLLVGALLAVLRLSGIKALQWPAALYVSAMRGT 64

Query: 66  PMLVQLFLIYYGLA----QFDAVRESALWPWLSNASFCACLAFAINTSAYTAEILAGSLK 121
           P+LVQ+F+IYYGL     QF+ +                 LA ++NT AY +E + G++ 
Sbjct: 65  PLLVQIFIIYYGLPAIGIQFEPIT-------------AGILALSLNTGAYVSETMRGAIN 111

Query: 122 ATPHGEIEAAKAMGMSRLKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLVDIT 181
               G+ EAA + GM R +    I+ P ALR A+P  SN +I +++ TSL S++ + ++ 
Sbjct: 112 GVDRGQWEAAFSQGMGRWQTLHYIVWPQALRLAVPSLSNSLISLIKDTSLVSVIAVTELM 171

Query: 182 GAARTVYSQYYLPFEAFITAGLFYLCLTFILVRLFKLAERR 222
            A + V S  + PF  ++ A   Y CL+ I  ++ +L ERR
Sbjct: 172 LATKEVISTTFQPFPLYVAAAAIYWCLSLIFEQVQRLLERR 212


Lambda     K      H
   0.330    0.140    0.425 

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: 126
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: 221
Length adjustment: 22
Effective length of query: 210
Effective length of database: 199
Effective search space:    41790
Effective search space used:    41790
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 (21.9 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