GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21219 in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate BPHYT_RS35660 BPHYT_RS35660 membrane protein

Query= reanno::Smeli:SM_b21219
         (281 letters)



>FitnessBrowser__BFirm:BPHYT_RS35660
          Length = 283

 Score =  135 bits (339), Expect = 1e-36
 Identities = 85/270 (31%), Positives = 139/270 (51%), Gaps = 14/270 (5%)

Query: 19  LAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFIASLL 78
           L VV+L P A +L  ++ PA+++   P  W P     S +  +  A      A F  +L 
Sbjct: 20  LVVVVLFPFAVMLFTALKPASEIFVYPARWLPVHWQWSNFSDMWVA------ANFGVALR 73

Query: 79  NSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWSLYA--VIATYMLPPVALAVPLYMGLAY 136
           NS  ++ ++T  A+ V++PAA+A++R P     LY   ++ T ML P+ L V L+   A 
Sbjct: 74  NSTVISLLSTALALAVSLPAAYALARFPFRGRGLYRQFLLVTQMLSPILLVVGLFRLAAM 133

Query: 137 F-----GLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQILRIL 191
                  L++S  G+ + Y      F  W+L S F ++PR++E +A ++G    + +  +
Sbjct: 134 IPYGDGNLVDSKIGVIVSYAAFNIAFAVWMLSSYFQTVPRDLEESAWLEGCGRTKAVFKV 193

Query: 192 TLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGR-VSDYGLIAT 250
            LPLA P +  +A+F F+ AW+EF            KTLTV + D+  G+ V  + L+  
Sbjct: 194 FLPLAVPAIVVTAIFTFINAWNEFAVVYTLIRSPENKTLTVQVTDMVAGKYVVQWHLVMA 253

Query: 251 AGVLAALPPVLIGLIMQRALISGLTSGGVK 280
           A + A LP  ++   +QR L+ GL  G VK
Sbjct: 254 ATLCATLPVSVVFAWLQRYLVKGLALGAVK 283


Lambda     K      H
   0.325    0.136    0.402 

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: 205
Number of extensions: 13
Number of successful extensions: 4
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: 281
Length of database: 283
Length adjustment: 26
Effective length of query: 255
Effective length of database: 257
Effective search space:    65535
Effective search space used:    65535
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 (21.7 bits)
S2: 47 (22.7 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