GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12060 in Dyella japonica UNC79MFTsu3.2

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein

Query= uniprot:A0A1N7UKA9
         (325 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2414
          Length = 358

 Score =  152 bits (385), Expect = 9e-42
 Identities = 102/311 (32%), Positives = 168/311 (54%), Gaps = 24/311 (7%)

Query: 28  PLVFILLCVVMAFSSEYF-------MTWR------NWMDILRQTSINGILAVGMTYVILT 74
           PL++ LL +++  +           + WR      N +DI  + +   ++++GMT VI  
Sbjct: 29  PLLWPLLTLILLLAGNGLFNPGFLALQWRDGHLYGNLIDIAHRAAPLALVSLGMTLVIAL 88

Query: 75  KGIDLSVGSILAFAGLCSAMVA--TQGYGLLA---AVSAGMFAGAMLGVVNGFMVANLSI 129
           +G+D+SVG++LA A   +A         GLL    A++A + AGA+ G+ NG++V    +
Sbjct: 89  RGLDISVGAVLAIAATVAAWTIGHVSNDGLLPLWLAIAAALAAGALCGLWNGWLVVGAGM 148

Query: 130 PPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVAL--IF 187
            P VATL ++   RG+   ++ G  +T     Y  LG G +  +G+P  +F V A+  + 
Sbjct: 149 QPIVATLILMVAGRGIAQSISGGQILTLYYAPYSFLGNGFV--LGLPFSLFVVAAVFALL 206

Query: 188 WMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSA- 246
            + LR T  G +V A+G N ++A  +G+  R +    YV  G+ A LAG+++S+   SA 
Sbjct: 207 QLALRKTALGLFVRAIGHNPQAAHVAGVRARAITLGAYVFCGIAAALAGLLVSSNVNSAD 266

Query: 247 LPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVA 306
              AG+  ELDAI AV +GG+ L GG  S+ G+L GAL+I  +   +  +GV        
Sbjct: 267 ANNAGLLLELDAILAVALGGSLLGGGRFSLAGSLLGALIIQALTTTIYAIGVPPQVNLAV 326

Query: 307 KGLIIVFAVLI 317
           K  ++VFAV++
Sbjct: 327 KA-VLVFAVML 336


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: 257
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 325
Length of database: 358
Length adjustment: 29
Effective length of query: 296
Effective length of database: 329
Effective search space:    97384
Effective search space used:    97384
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 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