GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12060 in Collimonas pratensis Ter91

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate WP_061940318.1 CPter91_RS11535 ABC transporter permease

Query= uniprot:A0A1N7UKA9
         (325 letters)



>NCBI__GCF_001584185.1:WP_061940318.1
          Length = 334

 Score =  182 bits (461), Expect = 1e-50
 Identities = 117/306 (38%), Positives = 168/306 (54%), Gaps = 12/306 (3%)

Query: 22  LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSV 81
           L   G  L  I LC+     +  F T  N M++L +T+  GI+AVGMT+VI++ GIDLSV
Sbjct: 21  LKGLGPVLGLIGLCIAGTLLNGDFATVDNLMNVLTRTAFIGIIAVGMTFVIISGGIDLSV 80

Query: 82  GSILAFAG---------LCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPF 132
           GS+ A            L SA        LL  ++  +  G   G ++G ++    I  F
Sbjct: 81  GSMAALIAGSMIYFMNMLMSAGTLGPLTILLIGIAMALLLGLAFGCLHGLLITKGKIEAF 140

Query: 133 VATLGMLSIARGMTFILNDGSPIT---DLPDAYLALGIGKIGPIGVPIIIFAVVALIFWM 189
           + TLG L I R +   L DG  +T    L D Y  +    +  I +PI +F  VAL   +
Sbjct: 141 IVTLGTLGIFRSVLTYLADGGALTLDNQLSDLYSPVYYTSLLGIPIPIWVFLAVALGGAL 200

Query: 190 VLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQ 249
           +L  T +GR+V A+G NE+ AR + I V  V    Y++ G+  G+A V+   R  SA P 
Sbjct: 201 ILNRTAFGRHVQAIGSNEQVARYAAIRVDFVKTCTYMLLGVCVGIATVLYVPRLGSASPT 260

Query: 250 AGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGL 309
            G+ +EL+AIAAVV+GGT+L GG+G IVGT+ GA+L+ VI+N LNL  + S Y   A   
Sbjct: 261 TGLLWELEAIAAVVVGGTALKGGSGRIVGTVVGAILLSVISNILNLTSIISVYLNAAVQG 320

Query: 310 IIVFAV 315
           +++ AV
Sbjct: 321 VVIIAV 326


Lambda     K      H
   0.326    0.141    0.412 

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: 236
Number of extensions: 10
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: 325
Length of database: 334
Length adjustment: 28
Effective length of query: 297
Effective length of database: 306
Effective search space:    90882
Effective search space used:    90882
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 (21.6 bits)
S2: 49 (23.5 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