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

GapMind for catabolism of small carbon sources

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

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate H281DRAFT_04211 H281DRAFT_04211 Predicted arabinose efflux permease, MFS family

Query= TCDB::F8SVK1
         (552 letters)



>FitnessBrowser__Burk376:H281DRAFT_04211
          Length = 552

 Score = 1008 bits (2607), Expect = 0.0
 Identities = 498/552 (90%), Positives = 527/552 (95%)

Query: 1   MATVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI 60
           MATV G IS  PMT++EKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTA FI
Sbjct: 1   MATVGGHISPVPMTRDEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAGFI 60

Query: 61  FTLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMAS 120
           FTLL FAAGFAVRPFGA+VFGRLGDMVGRKYTFL+TIVIMGLST +VGFLPGYAAIG+AS
Sbjct: 61  FTLLSFAAGFAVRPFGAVVFGRLGDMVGRKYTFLVTIVIMGLSTFLVGFLPGYAAIGIAS 120

Query: 121 PVIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGV 180
           PVIFIAMR+LQGLALGGEYGGAATYVAEHAP  RRGFYTAWIQTTATLGLFLSLLVILGV
Sbjct: 121 PVIFIAMRMLQGLALGGEYGGAATYVAEHAPPGRRGFYTAWIQTTATLGLFLSLLVILGV 180

Query: 181 RTAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFG 240
           RTAMGEDAFGAWGWRIPF+AS++LLG+SVWIR+QLHESP FERIKAEGKTSKAPLSEAFG
Sbjct: 181 RTAMGEDAFGAWGWRIPFIASILLLGVSVWIRLQLHESPVFERIKAEGKTSKAPLSEAFG 240

Query: 241 QWKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFF 300
           QWKNLK+VILALIG+TAGQAVVWYTGQFY LFFLTQTLKVDGA+ANI+IAIALLIGTPFF
Sbjct: 241 QWKNLKVVILALIGLTAGQAVVWYTGQFYTLFFLTQTLKVDGATANIMIAIALLIGTPFF 300

Query: 301 LFFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDEC 360
           LFFGSLSDRIGRKPII+AG LIAALTYFPLFKALTHY NPALE AT K+PIVVIANPDEC
Sbjct: 301 LFFGSLSDRIGRKPIIMAGLLIAALTYFPLFKALTHYVNPALETATAKAPIVVIANPDEC 360

Query: 361 SFQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADA 420
           SFQFNPVGTSKFTSSCDIAKSALSK+GLNY+NVAAP GTLAQIKVGDT + TYDGKAADA
Sbjct: 361 SFQFNPVGTSKFTSSCDIAKSALSKSGLNYENVAAPVGTLAQIKVGDTVVSTYDGKAADA 420

Query: 421 KDAGKAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMF 480
           KD GK FDK+L T LK+A YPPKAD SQ+NWPM+VVILTILVIYVTMVYGPIAAMLVEMF
Sbjct: 421 KDQGKVFDKSLSTTLKSAGYPPKADSSQINWPMSVVILTILVIYVTMVYGPIAAMLVEMF 480

Query: 481 PTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFV 540
           PTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPI+IAL TFVIG+LFV
Sbjct: 481 PTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIVIALITFVIGMLFV 540

Query: 541 RETKDSNIYAQD 552
           RETKDS+IYA+D
Sbjct: 541 RETKDSDIYAKD 552


Lambda     K      H
   0.325    0.139    0.422 

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: 1069
Number of extensions: 39
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: 552
Length of database: 552
Length adjustment: 36
Effective length of query: 516
Effective length of database: 516
Effective search space:   266256
Effective search space used:   266256
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: 53 (25.0 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources