GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Burkholderia phytofirmans PsJN

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS04430 BPHYT_RS04430 amino acid ABC transporter ATPase

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__BFirm:BPHYT_RS04430
          Length = 244

 Score =  223 bits (569), Expect = 2e-63
 Identities = 116/241 (48%), Positives = 169/241 (70%), Gaps = 8/241 (3%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +L ++ L   YG ++ + G+  +V +  +V+LIGSNGAGKTTTM+AI+G +  + G I  
Sbjct: 1   MLSIRNLHAGYGKVKVLHGISIDVPKASVVTLIGSNGAGKTTTMRAISGMIRPSAGEITM 60

Query: 69  -LGKSIKGKGAWD---LVKEGLVMVPEGRGVFARMTITENLQMGAYIR----KDKAGILA 120
            +G   K   A D   + + GL   PEGR VFA M++T+NL +GA+ R    + +  + A
Sbjct: 61  GVGTDAKRIDALDSHRIARLGLAHSPEGRRVFATMSVTDNLILGAFPRLTSARPRGDVKA 120

Query: 121 DIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDK 180
           D+E+   +FPRL+ER+ QLAGT+SGGEQQMLAM RA+M  P ++LLDEPSMGL+PI+V++
Sbjct: 121 DLERAIEMFPRLKERRHQLAGTLSGGEQQMLAMARAIMMNPDLVLLDEPSMGLAPILVEE 180

Query: 181 IFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYL 240
           +F ++ ++ + GVT++LVEQ A+ AL +AD GYV+E+G I   GP  +L NDP V+AAYL
Sbjct: 181 VFRIIGNLKSQGVTMLLVEQFAAAALNVADYGYVLENGRIAAHGPATELRNDPSVKAAYL 240

Query: 241 G 241
           G
Sbjct: 241 G 241


Lambda     K      H
   0.317    0.136    0.373 

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: 178
Number of extensions: 8
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: 242
Length of database: 244
Length adjustment: 23
Effective length of query: 219
Effective length of database: 221
Effective search space:    48399
Effective search space used:    48399
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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