GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Dechlorosoma suillum PS

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate Dsui_1833 Dsui_1833 nitrate transport ATP-binding subunits C and D

Query= TCDB::P31134
         (377 letters)



>FitnessBrowser__PS:Dsui_1833
          Length = 266

 Score =  152 bits (384), Expect = 1e-41
 Identities = 81/203 (39%), Positives = 129/203 (63%), Gaps = 6/203 (2%)

Query: 34  AVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLDGVDLSQVPPYLRPI 93
           A+ DV L+I +GE  AL+G SGCGKSTLL ++AG  +P+ G ++ DG +++   P     
Sbjct: 23  ALRDVDLSIRQGEFIALIGHSGCGKSTLLNLIAGLTRPTDGALICDGREIAGPGPER--- 79

Query: 94  NMMFQSYALFPHMTVEQNIAFGLKQ---DKLPKAEIASRVNEMLGLVHMQEFAKRKPHQL 150
            ++FQ+++L P +T   N+   +++    K  KA++  R ++ L LV +     + PH++
Sbjct: 80  GVVFQNHSLLPWLTCFDNVYLAVERVFAAKEGKAKLKQRTHDALALVGLTHAETKFPHEI 139

Query: 151 SGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGVTCVMVTHDQ 210
           SGG +QRV +AR+L+ +PK+LL+DEP GALD   R ++Q E++ I +    T VMVTHD 
Sbjct: 140 SGGMKQRVGIARALSMQPKVLLMDEPFGALDALTRAKLQDELMKICDATQATVVMVTHDV 199

Query: 211 EEAMTMAGRIAIMNRGKFVQIGE 233
           +EA+ ++ RI +M  G    IGE
Sbjct: 200 DEAVLLSDRIVMMTNGPAATIGE 222


Lambda     K      H
   0.321    0.137    0.400 

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: 231
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: 377
Length of database: 266
Length adjustment: 27
Effective length of query: 350
Effective length of database: 239
Effective search space:    83650
Effective search space used:    83650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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