GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Paraburkholderia bryophila 376MFSha3.1

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family

Query= uniprot:D8IZC8
         (344 letters)



>FitnessBrowser__Burk376:H281DRAFT_02703
          Length = 333

 Score =  197 bits (500), Expect = 4e-55
 Identities = 121/316 (38%), Positives = 182/316 (57%), Gaps = 16/316 (5%)

Query: 31  RLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTA 90
           R G+ P+   L ++   L++      +  F +     NI+ QV++  + A G TFVI+T+
Sbjct: 23  RSGIGPLFAALVIICIALSI-----ASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITS 77

Query: 91  GIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFS-------GLVMGMVNGAMVALLNI 143
           GIDLSVGS++A++ ++   V  G++PG AI + I         G   G +NG  VA L +
Sbjct: 78  GIDLSVGSLVALTGMVAATVMAGSSPG-AIGLGIAGLCAALAVGAAAGALNGLAVAWLRL 136

Query: 144 NAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPS-FEWIGNGDFLHVPWLIWVAVAVVLLS 202
             F+VTL  M   RG    ++DG T    D P+ F   G      +P  + V + + ++ 
Sbjct: 137 VPFIVTLAMMAMARGLTLAISDGRTKF--DFPNAFTAFGAKTVAGLPMPMIVMLVIFVIG 194

Query: 203 WVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGAN 262
            V+LRKT  G  ++A+GGN +AARL GI V  V+   Y ++G+ + +AG + A RL  A 
Sbjct: 195 HVLLRKTTFGHQVFAVGGNQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSAL 254

Query: 263 GNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAK 322
            +  +G EL  IAAVV+GGTSL GG GSI GT +G ++IGV+N GL++LG++ FW    +
Sbjct: 255 PSAANGLELQVIAAVVIGGTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQ 314

Query: 323 GAVIVLAVILDKWRQK 338
           G VI  AV+LD   Q+
Sbjct: 315 GGVIFAAVLLDALSQR 330


Lambda     K      H
   0.324    0.138    0.417 

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: 327
Number of extensions: 22
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: 344
Length of database: 333
Length adjustment: 28
Effective length of query: 316
Effective length of database: 305
Effective search space:    96380
Effective search space used:    96380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 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