GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Burkholderia phytofirmans PsJN

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BPHYT_RS04430 BPHYT_RS04430 amino acid ABC transporter ATPase

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__BFirm:BPHYT_RS04430
          Length = 244

 Score =  195 bits (495), Expect = 8e-55
 Identities = 110/245 (44%), Positives = 155/245 (63%), Gaps = 11/245 (4%)

Query: 4   LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63
           +L ++++ AGY   V +L GI+  +    +VT+IG NGAGK+T  + I G++ PS GEI 
Sbjct: 1   MLSIRNLHAGY-GKVKVLHGISIDVPKASVVTLIGSNGAGKTTTMRAISGMIRPSAGEIT 59

Query: 64  F----KGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLH------QGPTQ 113
                  + I  L S +I R G+ + P+   VF +++V +NL +GAF        +G  +
Sbjct: 60  MGVGTDAKRIDALDSHRIARLGLAHSPEGRRVFATMSVTDNLILGAFPRLTSARPRGDVK 119

Query: 114 TLKDRIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVK 173
              +R   MFP+L +RR+Q AGTLSGGE+QMLAM RA+M++PDL+LLDEPS  L+PILV+
Sbjct: 120 ADLERAIEMFPRLKERRHQLAGTLSGGEQQMLAMARAIMMNPDLVLLDEPSMGLAPILVE 179

Query: 174 DVFAQIKAINATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELY 233
           +VF  I  + + G  ++LVEQ A  AL +AD GYVLENGR    G    L NDP V   Y
Sbjct: 180 EVFRIIGNLKSQGVTMLLVEQFAAAALNVADYGYVLENGRIAAHGPATELRNDPSVKAAY 239

Query: 234 LGAAY 238
           LGA++
Sbjct: 240 LGASH 244


Lambda     K      H
   0.320    0.139    0.393 

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: 151
Number of extensions: 9
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: 240
Length of database: 244
Length adjustment: 23
Effective length of query: 217
Effective length of database: 221
Effective search space:    47957
Effective search space used:    47957
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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