Aligments for a candidate for deh in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for deh in Pseudomonas putida KT2440

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate PP_2569 PP_2569 Metabolite MFS transporter, MHS family

Query= TCDB::F8SVK1
         (552 letters)



>lcl|FitnessBrowser__Putida:PP_2569 PP_2569 Metabolite MFS
           transporter, MHS family
          Length = 558

 Score =  787 bits (2033), Expect = 0.0
 Identities = 383/550 (69%), Positives = 464/550 (84%), Gaps = 3/550 (0%)

Query: 2   ATVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIF 61
           +T +G      +TKEE++VIFASSLGTVFEWYDFYL GSLAA I++ FF+GVN T +FIF
Sbjct: 6   STSTGSAPQRGITKEERKVIFASSLGTVFEWYDFYLYGSLAAIIARHFFAGVNETTSFIF 65

Query: 62  TLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASP 121
            LL FAAGFAVRPFGA+VFGRLGDM+GRKYTFLITIVIMGLST VVG LPGYA IG+A+P
Sbjct: 66  ALLAFAAGFAVRPFGAIVFGRLGDMIGRKYTFLITIVIMGLSTAVVGLLPGYATIGVAAP 125

Query: 122 VIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVR 181
           +I I +RLLQGLALGGEYGGAATYVAEHAP  RRGF+TAWIQTTATLGLFLSLLVI+  R
Sbjct: 126 IILITLRLLQGLALGGEYGGAATYVAEHAPKGRRGFFTAWIQTTATLGLFLSLLVIMACR 185

Query: 182 TAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQ 241
           TAMG +AF AWGWRIPF+ S++LL ISV+IR+QL+ESP F ++KAEGK SKAPL+E+F +
Sbjct: 186 TAMGTEAFEAWGWRIPFLLSILLLAISVYIRLQLNESPVFMKMKAEGKASKAPLTESFAR 245

Query: 242 WKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFL 301
           W NLK+VI++L+G TAGQAVVWYTGQFYALFFL QTLK++  +AN+LIA +LLIGTPFF+
Sbjct: 246 WDNLKVVIMSLLGGTAGQAVVWYTGQFYALFFLLQTLKIEAQTANLLIAGSLLIGTPFFI 305

Query: 302 FFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECS 361
           FFGSLSDRIGRK II+AGC+IAALTYFP+FKALT Y NP +  A +++P+VV+A+P +C+
Sbjct: 306 FFGSLSDRIGRKKIIMAGCIIAALTYFPIFKALTEYGNPDVFVAQEQNPVVVVADPGQCA 365

Query: 362 FQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGK---AA 418
           FQF+PVG +KFTSSCDIAKS L+K  + Y N AA  G++AQI++G+  + ++DG    AA
Sbjct: 366 FQFDPVGKAKFTSSCDIAKSLLAKRAIPYTNEAAEPGSVAQIRIGERVLPSFDGSSLAAA 425

Query: 419 DAKDAGKAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVE 478
           D K   +AF   L  ALK A YP KAD +++++PM +++LTILVIYVTMVYGPIAA LVE
Sbjct: 426 DFKVQSEAFTATLSGALKEAGYPEKADQAKIHYPMVLLLLTILVIYVTMVYGPIAAWLVE 485

Query: 479 MFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLL 538
           +FP RIRYTSMSLPYHIGNGWFGGFLP  AFA+VAA G+IY GLWYPI+IA+ T V+G+ 
Sbjct: 486 LFPARIRYTSMSLPYHIGNGWFGGFLPTVAFAMVAATGDIYYGLWYPIVIAVMTAVLGIF 545

Query: 539 FVRETKDSNI 548
           F+ ETKD +I
Sbjct: 546 FLPETKDRDI 555


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: 901
Number of extensions: 38
Number of successful extensions: 5
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: 558
Length adjustment: 36
Effective length of query: 516
Effective length of database: 522
Effective search space:   269352
Effective search space used:   269352
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)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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, 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

GapMind for catabolism of small carbon sources