GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16925 in Paraburkholderia bryophila 376MFSha3.1

Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family

Query= uniprot:B2SYR4
         (338 letters)



>FitnessBrowser__Burk376:H281DRAFT_02703
          Length = 333

 Score =  202 bits (515), Expect = 7e-57
 Identities = 107/302 (35%), Positives = 171/302 (56%), Gaps = 5/302 (1%)

Query: 38  LIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSVGSTVA 97
           L    V++   +S+    F +   +  + + +S +G+ +    F + +   DLSVGS VA
Sbjct: 29  LFAALVIICIALSIASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITSGIDLSVGSLVA 88

Query: 98  FAGVLCAMVL-----NATGNTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITTLATMEI 152
             G++ A V+      A G     + AA+A G   G +NG  +A+LR+   I TLA M +
Sbjct: 89  LTGMVAATVMAGSSPGAIGLGIAGLCAALAVGAAAGALNGLAVAWLRLVPFIVTLAMMAM 148

Query: 153 VRGLGFIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTL 212
            RGL   +S G+      + F A G  +  G+ +P+ V L+ F++  V+L +T +G    
Sbjct: 149 ARGLTLAISDGRTKFDFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFGHQVF 208

Query: 213 AIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVISA 272
           A+GGN EA+RLAGI V R     +++ G   A+AG++LA R+ S  P+AA G EL VI+A
Sbjct: 209 AVGGNQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQVIAA 268

Query: 273 CVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQLK 332
            V+GG SL GGR +I G  IGV+++G +   ++L+ ++ F+   ++G ++ AAVLLD L 
Sbjct: 269 VVIGGTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLLDALS 328

Query: 333 NR 334
            R
Sbjct: 329 QR 330


Lambda     K      H
   0.326    0.139    0.396 

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: 337
Number of extensions: 20
Number of successful extensions: 2
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: 338
Length of database: 333
Length adjustment: 28
Effective length of query: 310
Effective length of database: 305
Effective search space:    94550
Effective search space used:    94550
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