GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3022
          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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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