Alignments for a candidate for deh in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for deh in Phyllobacterium brassicacearum STM 196

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate WP_106712722.1 CU102_RS19315 MFS transporter

Query= TCDB::F8SVK1
         (552 letters)



>NCBI__GCF_003010955.1:WP_106712722.1
          Length = 628

 Score =  589 bits (1519), Expect = e-173
 Identities = 303/450 (67%), Positives = 352/450 (78%), Gaps = 4/450 (0%)

Query: 1   MATVS-GQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAF 59
           MAT S    S   MT+EEK+VIFASSLGTVFEWYDFYL GSLAAFI  +FFS        
Sbjct: 1   MATTSVADTSSRGMTREEKKVIFASSLGTVFEWYDFYLYGSLAAFIGAAFFSEYPEATRN 60

Query: 60  IFTLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMA 119
           IF LL FAAGF VRPFGALVFGR+GD+VGRKYTFL+TI+IMGLST +VG LPG A+ G+A
Sbjct: 61  IFALLAFAAGFLVRPFGALVFGRIGDLVGRKYTFLVTIMIMGLSTFLVGVLPGSASWGIA 120

Query: 120 SPVIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILG 179
           +P+I I +R+LQGLALGGEYGGAATYVAEHAP N+RG+YT+WIQTTATLGLFLSL+VIL 
Sbjct: 121 APIILIGLRMLQGLALGGEYGGAATYVAEHAPDNKRGYYTSWIQTTATLGLFLSLIVILV 180

Query: 180 VRTAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAF 239
           ++  +G+DAF AWGWRIPF+ S VLLGISVWIR+ L ESP F+R+K EGK SKAPLSEAF
Sbjct: 181 IQNWLGKDAFAAWGWRIPFILSFVLLGISVWIRLSLSESPTFQRMKEEGKGSKAPLSEAF 240

Query: 240 GQWKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPF 299
           GQWKN KI +LAL G+TAGQAVVWY+GQFYALFFL   LKVDG + NI+IAIALL+GT F
Sbjct: 241 GQWKNAKIALLALFGLTAGQAVVWYSGQFYALFFLQNVLKVDGQAVNIMIAIALLLGTGF 300

Query: 300 FLFFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDE 359
           F+FFG LSD+IGRKPII+AG  +A LTYFPLFKALT  ANPAL AA Q     V A P +
Sbjct: 301 FVFFGWLSDKIGRKPIIMAGLALAILTYFPLFKALTWAANPALAAAQQDVRATVTAAPGD 360

Query: 360 CSFQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPA-GTLAQIKVGDTTIDTYDGKA- 417
           C FQFNP GT+KFT+SCDIA S L++  + YD VA  A GT A +K+G  T+++YD  A 
Sbjct: 361 CKFQFNPTGTAKFTTSCDIATSFLTRNSVPYDVVATAAPGTAATVKIGQETVESYDAAAA 420

Query: 418 -ADAKDAGKAFDKNLGTALKAASYPPKADP 446
            ADAK    AF K +  AL+   YP   DP
Sbjct: 421 GADAKTKEAAFAKAVNIALQDGGYPLVRDP 450



 Score =  174 bits (440), Expect = 1e-47
 Identities = 86/153 (56%), Positives = 111/153 (72%), Gaps = 4/153 (2%)

Query: 401 AQIKVGDTTIDTYDGKAAD----AKDAGKAFDKNLGTALKAASYPPKADPSQLNWPMTVV 456
           A I+ G+ T+   D    D    A++A  A +  + T   A ++   ADP+ ++W   + 
Sbjct: 473 AAIRAGEKTMVPVDQAIKDKLITAEEAAGATEVAVYTVPGAGAFKMVADPAAVSWTKVIA 532

Query: 457 ILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKG 516
           IL +LVIYVTMVYGPIAA+LVEMFPTRIRYT MSLPYHIGNGWFGG LPAT FA+ A KG
Sbjct: 533 ILFVLVIYVTMVYGPIAAILVEMFPTRIRYTGMSLPYHIGNGWFGGLLPATVFAMSAFKG 592

Query: 517 NIYSGLWYPIIIALATFVIGLLFVRETKDSNIY 549
           +IY GLWYPI+IA  T +IGL+FVR+TKD++++
Sbjct: 593 DIYYGLWYPIVIAAMTLIIGLIFVRDTKDTDLH 625


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: 947
Number of extensions: 30
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 552
Length of database: 628
Length adjustment: 37
Effective length of query: 515
Effective length of database: 591
Effective search space:   304365
Effective search space used:   304365
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)
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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 2024 update 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