GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Pseudomonas simiae WCS417

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>FitnessBrowser__WCS417:GFF2365
          Length = 325

 Score =  236 bits (602), Expect = 6e-67
 Identities = 123/303 (40%), Positives = 203/303 (66%), Gaps = 9/303 (2%)

Query: 44  LLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVM 103
           +L+ +  +F+S  FM   N + IL+ T++NG+LA+  TYVI+T GIDLSVG+++ F  + 
Sbjct: 32  ILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFAGLC 91

Query: 104 AGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVIS 163
           + +V T  G  L   ++A +F GA+ G ++G ++A L +PPF+ATLGM+ + +G++ +++
Sbjct: 92  SAMVATQ-GYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILN 150

Query: 164 GTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFA 223
              PI  +  + + A+     IG + P + +P  ++I  +VA+   ++L  T +GRY +A
Sbjct: 151 DGSPIT-DLPDAYLALG----IGKIGP-IGVP--IIIFAVVALIFWMVLRYTTYGRYVYA 202

Query: 224 LGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAV 283
           +G NE++ R SG+ V     +VY  SG + G+AG+++++R  SA P  G  YELDAIAAV
Sbjct: 203 VGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAV 262

Query: 284 VIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRR 343
           VIGGTSLSGGTG+I+GT+ GA ++ V+ NGL ++ V+  +Q V  G+II+ AV +D+ R+
Sbjct: 263 VIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRK 322

Query: 344 RRR 346
           ++R
Sbjct: 323 KKR 325


Lambda     K      H
   0.326    0.139    0.398 

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: 272
Number of extensions: 13
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: 347
Length of database: 325
Length adjustment: 28
Effective length of query: 319
Effective length of database: 297
Effective search space:    94743
Effective search space used:    94743
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 (21.7 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