Alignments for a candidate for deh in Verminephrobacter eiseniae EF01-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for deh in Verminephrobacter eiseniae EF01-2

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate WP_011808317.1 VEIS_RS02515 MHS family MFS transporter

Query= TCDB::F8SVK1
         (552 letters)



>NCBI__GCF_000015565.1:WP_011808317.1
          Length = 553

 Score =  788 bits (2036), Expect = 0.0
 Identities = 384/544 (70%), Positives = 461/544 (84%), Gaps = 3/544 (0%)

Query: 12  PMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFA 71
           PMT EEK+VIFASSLGTVFEWYDFYL G+LA+ I+K FFSG++  +AFIF LL FAAGF 
Sbjct: 10  PMTPEEKKVIFASSLGTVFEWYDFYLYGALASIIAKQFFSGLDAGSAFIFALLAFAAGFI 69

Query: 72  VRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQ 131
           VRPFGA+ FGRLGDM+GRKYTFLITI+IMGLST +VG LP YA +G+A+PVI IA+RLLQ
Sbjct: 70  VRPFGAIFFGRLGDMIGRKYTFLITILIMGLSTFLVGILPSYATVGVAAPVILIALRLLQ 129

Query: 132 GLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGA 191
           GLALGGEYGGAATYVAEH+P  +RG YT+WIQTTATLGLFLSL VILGVRT +GE+AF +
Sbjct: 130 GLALGGEYGGAATYVAEHSPHGKRGAYTSWIQTTATLGLFLSLAVILGVRTTLGEEAFAS 189

Query: 192 WGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILA 251
           WGWR+PF+ S+VLLGISVWIR+ + ESPAF+++KAEGKTSKAPL+E+F +WKNLKIVILA
Sbjct: 190 WGWRLPFLLSIVLLGISVWIRLSMSESPAFQKMKAEGKTSKAPLTESFARWKNLKIVILA 249

Query: 252 LIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIG 311
           L+G+TAGQA VWY+GQFYAL FLT+TLKVDGA+ANIL+A+AL+IGTPFF+ FG+LSDRIG
Sbjct: 250 LLGLTAGQAAVWYSGQFYALLFLTETLKVDGATANILVAVALMIGTPFFVVFGTLSDRIG 309

Query: 312 RKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPVGTSK 371
           RKPIIL GCL+AALTYFP+F ALT  ANPAL  A  K+ ++V+A+  ECSFQFNP G  K
Sbjct: 310 RKPIILTGCLLAALTYFPVFGALTKAANPALAEAQAKNQVLVMADASECSFQFNPTGQVK 369

Query: 372 FTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADAKDAGK---AFD 428
           FTSSCDIAK  L++A ++Y+NV A AGT A IK+G+T I +Y  K   A +A K    F 
Sbjct: 370 FTSSCDIAKQVLARASVSYENVPAAAGTPATIKIGETAITSYSSKGLPADEAKKKDAEFK 429

Query: 429 KNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTS 488
           + +G ALKAA YP KADP +++  M + I+T LV+ VTMVYGPIAA+LVEMFPTRIRYTS
Sbjct: 430 QAVGDALKAAGYPAKADPERIDKVMIIAIITYLVLLVTMVYGPIAAILVEMFPTRIRYTS 489

Query: 489 MSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKDSNI 548
           MSLPYHIGNGWFGG LP +AFAIVA  GN+Y+GLW+P++IA AT VIG LF+++TKD +I
Sbjct: 490 MSLPYHIGNGWFGGLLPTSAFAIVAQTGNMYNGLWFPVVIAGATVVIGGLFIKDTKDVDI 549

Query: 549 YAQD 552
           YA D
Sbjct: 550 YAND 553


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: 877
Number of extensions: 37
Number of successful extensions: 7
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: 553
Length adjustment: 36
Effective length of query: 516
Effective length of database: 517
Effective search space:   266772
Effective search space used:   266772
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 24 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