Aligments for a candidate for deh in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for deh in Acidovorax sp. GW101-3H11

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate Ac3H11_3022 putative sugar transport protein

Query= TCDB::F8SVK1
         (552 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3022 putative sugar
           transport protein
          Length = 543

 Score =  796 bits (2055), Expect = 0.0
 Identities = 392/543 (72%), Positives = 457/543 (84%), Gaps = 3/543 (0%)

Query: 13  MTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAV 72
           M+ EE++VIFASSLGTVFEWYDFYL GSLAA I+K FFSG++  +AFIF LL FAAGF V
Sbjct: 1   MSPEERKVIFASSLGTVFEWYDFYLYGSLAAIIAKQFFSGLDSGSAFIFALLAFAAGFIV 60

Query: 73  RPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQG 132
           RPFGA+ FGRLGDM+GRKYTFL+TI+IMGLST +VG LP YA+IG+A+P+I I +RLLQG
Sbjct: 61  RPFGAIFFGRLGDMIGRKYTFLVTILIMGLSTFIVGILPTYASIGVAAPIILIVLRLLQG 120

Query: 133 LALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAW 192
           LALGGEYGGAATYVAEHAP  RRG YTAWIQTTATLGLFLSL+VILG RT +GE+AF  W
Sbjct: 121 LALGGEYGGAATYVAEHAPHGRRGAYTAWIQTTATLGLFLSLMVILGTRTIVGEEAFADW 180

Query: 193 GWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILAL 252
           GWR+PF+ S+VLL ISVWIR+ ++ESPAF+++KAEGKTSKAPL E+FG+WKNLKIVILAL
Sbjct: 181 GWRVPFIVSIVLLAISVWIRLAMNESPAFQKMKAEGKTSKAPLKESFGEWKNLKIVILAL 240

Query: 253 IGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGR 312
           +G+TAGQAVVWY+GQFYALFFLTQ LKVDGA+ANIL+A++LLIGTPFF+ FGSLSD+IGR
Sbjct: 241 VGLTAGQAVVWYSGQFYALFFLTQALKVDGATANILVAVSLLIGTPFFIVFGSLSDKIGR 300

Query: 313 KPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPVGTSKF 372
           KPIILAGCL+AALTYFP+F ALT  ANPAL  A  K+ +VV+A+ +ECSFQFNP GT KF
Sbjct: 301 KPIILAGCLLAALTYFPVFGALTKAANPALAEAQAKNKVVVVADANECSFQFNPTGTVKF 360

Query: 373 TSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADAKDAGK---AFDK 429
           TSSCDIAK  L+ A ++Y+N    AGT A IK+G+T I  Y  K   A +A K    F K
Sbjct: 361 TSSCDIAKQVLAGASVSYENAPGAAGTPAVIKIGETAITGYSSKGLPADEAKKKDGEFKK 420

Query: 430 NLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSM 489
            +  ALKAA YP KADP++++  M   IL  LV+ VTMVYGPIAAMLVEMFPTRIRYTSM
Sbjct: 421 AVADALKAAGYPTKADPARIDKVMVTAILVYLVLLVTMVYGPIAAMLVEMFPTRIRYTSM 480

Query: 490 SLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKDSNIY 549
           SLPYHIGNGWFGG LP TAFAIVA  GN+Y+GLWYPIIIA AT VIG LF++ETKD +IY
Sbjct: 481 SLPYHIGNGWFGGLLPTTAFAIVAQTGNMYNGLWYPIIIAAATVVIGGLFIKETKDVDIY 540

Query: 550 AQD 552
           A D
Sbjct: 541 AND 543


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: 889
Number of extensions: 33
Number of successful extensions: 6
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: 543
Length adjustment: 36
Effective length of query: 516
Effective length of database: 507
Effective search space:   261612
Effective search space used:   261612
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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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