GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artM in Azospirillum brasilense Sp245

Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate AZOBR_RS18070 AZOBR_RS18070 polar amino acid ABC transporter permease

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



>FitnessBrowser__azobra:AZOBR_RS18070
          Length = 223

 Score =  114 bits (286), Expect = 1e-30
 Identities = 66/210 (31%), Positives = 108/210 (51%), Gaps = 9/210 (4%)

Query: 3   FDYNVIWEAMPLYLGGLLTTLKLLAISLFFGLLAALPLGLMRVSKQPIVNGAAWLYTYVI 62
           FDY+ I E  P+ L GL+TT++L  I   FG+   +     R      +      Y  +I
Sbjct: 5   FDYSWIAEYWPVILKGLVTTVELTLIGTLFGVALGIACAWTRSLGPRWLRPPVVAYVELI 64

Query: 63  RGTPMLVQLFLIYYGLAQFEAVRESFLWPLLSSATFCACLAFAINTSAYTAEIIAGSLKA 122
           R TP L+QLF I++GL         F           A LA  IN  AY+ EII   ++A
Sbjct: 65  RNTPFLIQLFFIFFGLPSLGVQMTEFQ---------AAVLAMVINLGAYSGEIIRAGIEA 115

Query: 123 TPNGEIEAAKAMGMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITG 182
           TP G+ EA  ++ M+R++ +R ++L  +L+R  P  S+++++++  +++ S +   DIT 
Sbjct: 116 TPRGQFEAGASLAMTRFETFRHVVLIPSLQRIWPALSSQIVIVMLGSAVVSQIAAEDITF 175

Query: 183 AARTVNAQFYLPFEAYITAGVFYLCLTFIL 212
           AA  + ++ +  FE+Y      YL L   L
Sbjct: 176 AANFIQSRTFRAFESYFLTTGLYLLLALAL 205


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: 131
Number of extensions: 9
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: 223
Length adjustment: 22
Effective length of query: 210
Effective length of database: 201
Effective search space:    42210
Effective search space used:    42210
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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