GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deh in Burkholderia phytofirmans PsJN

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate BPHYT_RS16375 BPHYT_RS16375 major facilitator transporter

Query= TCDB::F8SVK1
         (552 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS16375 BPHYT_RS16375 major
           facilitator transporter
          Length = 552

 Score = 1008 bits (2605), Expect = 0.0
 Identities = 497/552 (90%), Positives = 527/552 (95%)

Query: 1   MATVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI 60
           MATV GQISH PMT+EEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI
Sbjct: 1   MATVGGQISHVPMTREEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI 60

Query: 61  FTLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMAS 120
           FTLL FAAGFAVRPFGA+VFGRLGDMVGRKYTFL+TIVIMGLST +VGFLPGYA+IG AS
Sbjct: 61  FTLLSFAAGFAVRPFGAIVFGRLGDMVGRKYTFLVTIVIMGLSTFLVGFLPGYASIGFAS 120

Query: 121 PVIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGV 180
           PVIFIAMR+LQGLALGGEYGGAATYVAEHAPA RRGFYTAWIQTTATLGLFLSLLVILGV
Sbjct: 121 PVIFIAMRMLQGLALGGEYGGAATYVAEHAPAGRRGFYTAWIQTTATLGLFLSLLVILGV 180

Query: 181 RTAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFG 240
           RTAMGEDAFG WGWRIPF+ S++LL +SVWIR+QLHESP FERIK+EGKTSKAPL+EAFG
Sbjct: 181 RTAMGEDAFGDWGWRIPFIVSILLLAVSVWIRLQLHESPVFERIKSEGKTSKAPLTEAFG 240

Query: 241 QWKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFF 300
           QWKNLKIVILALIG+TAGQAVVWYTGQFY LFFLTQTLKVDG+SANI+IAIALLIGTPFF
Sbjct: 241 QWKNLKIVILALIGLTAGQAVVWYTGQFYTLFFLTQTLKVDGSSANIMIAIALLIGTPFF 300

Query: 301 LFFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDEC 360
           LFFGSLSDRIGRKPII+AG LIAA TYFPLFKAL HY NPALEAAT K+PIVVIANPDEC
Sbjct: 301 LFFGSLSDRIGRKPIIMAGLLIAACTYFPLFKALAHYTNPALEAATAKAPIVVIANPDEC 360

Query: 361 SFQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADA 420
           SFQFNPVGT+KFTSSCDIAKSALSKAGLNY+NVAAPAGTLAQIKVGDT I+TYDGKAADA
Sbjct: 361 SFQFNPVGTAKFTSSCDIAKSALSKAGLNYENVAAPAGTLAQIKVGDTVINTYDGKAADA 420

Query: 421 KDAGKAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMF 480
           KD GKAFDK L T LK A Y PKADP+Q+NWPMTVVILTI++IYVTMVYGPIAAMLVEMF
Sbjct: 421 KDQGKAFDKTLATTLKTAGYAPKADPTQINWPMTVVILTIMMIYVTMVYGPIAAMLVEMF 480

Query: 481 PTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFV 540
           PTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNI+SGLWYPI+IAL TFVIG+LFV
Sbjct: 481 PTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIFSGLWYPIVIALVTFVIGMLFV 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: 36
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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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