GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12060 in Acidovorax sp. GW101-3H11

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC

Query= uniprot:A0A1N7UKA9
         (325 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3036
          Length = 319

 Score =  230 bits (586), Expect = 4e-65
 Identities = 126/301 (41%), Positives = 186/301 (61%), Gaps = 8/301 (2%)

Query: 29  LVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFA 88
           +  IL C   A  SE F++ +N+  IL+Q  +  ++A+G T VILT GIDLS G ++A  
Sbjct: 18  IALILACAFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVMALG 77

Query: 89  GLCSAMVATQGYGLLA--AVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMT 146
           G+    +A   YGL A  A++ GM    + G++NG +V  + +PPF+ TLG L+IA   T
Sbjct: 78  GIVMTKMAAD-YGLSAPVAIACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNIAFAAT 136

Query: 147 FILNDGSPITDLPDAYLALG----IGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYA 202
            + +    ITD+P    ALG    +G+   +   +++ A+  L+ W  LR T  GR+VYA
Sbjct: 137 QLYSGAQTITDIPAGMTALGNTFQLGQTAIVWGAVLMLALY-LVTWFALRETAPGRHVYA 195

Query: 203 VGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAV 262
           VG + ++ R +GI   KV+  VYV++GL  G+A ++  ART +  P AG +  LDAI+AV
Sbjct: 196 VGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENLDAISAV 255

Query: 263 VIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRK 322
           V+GGTSL GG G I+GTL GAL++GV  NGL L+GVSS YQ +  G++++ AV  D   +
Sbjct: 256 VLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVATDQLSR 315

Query: 323 K 323
           K
Sbjct: 316 K 316


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: 246
Number of extensions: 11
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: 319
Length adjustment: 28
Effective length of query: 297
Effective length of database: 291
Effective search space:    86427
Effective search space used:    86427
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: 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