GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fcbT3 in Desulfovibrio vulgaris Miyazaki F

Align FcbT3, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= TCDB::Q9RBQ9
         (439 letters)



>FitnessBrowser__Miya:8501407
          Length = 427

 Score =  206 bits (525), Expect = 9e-58
 Identities = 139/431 (32%), Positives = 226/431 (52%), Gaps = 17/431 (3%)

Query: 9   LLLGGTTVLLFLGLPVAYS-----FFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLT 63
           +L GG  +L  L  PVA +     F A+   G  + +G +  L   V+       SF L 
Sbjct: 5   ILFGGMVLLFALNAPVAVALGGAAFAAVLAKGLTMPVGLEPMLA--VQRLYAGADSFPLL 62

Query: 64  PIPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAM 123
            +PLF+L GEL+   G+++R +   D ++  LPG LA ++VV+  FF+ +SGS  A TA 
Sbjct: 63  AVPLFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAADTAA 122

Query: 124 LGSLMLPMMLARGYEPKLGMGPIIAIGG-VDMLIPPSALAVLLGSLAGISISKLLIGGVL 182
           +GS+++P M+ RGY   L  G + A GG + ++IPPS   ++ G+L G SI +L  GGVL
Sbjct: 123 VGSILIPAMIRRGYPAPLA-GAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAGGVL 181

Query: 183 PGLLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVIS 242
           PGLL+  S VA  V  A+ R    P         W   R    + L    I   I+  I 
Sbjct: 182 PGLLMGASLVALCVVEAR-RTGRVPERRFDARALWPAIRS-GAWALGAPAI---ILGTII 236

Query: 243 GGVATPTEAAAIGCAATLAITL-MYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQV 301
           GGVAT TE+AA+  A  L + L  +R LRW+ L +        S +++ II AA+ F  V
Sbjct: 237 GGVATATESAAMAVAYALPVGLYAHRELRWRDLPRLALCAGVTSAVVMLIIAAASLFGWV 296

Query: 302 LSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLG 361
           ++       I   + S       ++ ++  +L+ +G F++  + +LL +P  +P++ +LG
Sbjct: 297 MALERLPQAIAAWMLSLSGDRIVLLLLVNLLLLVVGAFLETTAAILLFVPVLVPLLPALG 356

Query: 362 IDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLIL 421
           ID +  GV+ ++ + +G+L PP G+ L     +A   I +  +  + +P + +    L+L
Sbjct: 357 IDLVHLGVIVVVNLAIGMLTPPLGVCLVVSCSIA--RIPLSAISRAIVPMLVVLIVDLLL 414

Query: 422 IFFWPGIATWL 432
           + F+P +  WL
Sbjct: 415 VTFFPPLVLWL 425


Lambda     K      H
   0.329    0.143    0.433 

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: 486
Number of extensions: 23
Number of successful extensions: 4
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: 439
Length of database: 427
Length adjustment: 32
Effective length of query: 407
Effective length of database: 395
Effective search space:   160765
Effective search space used:   160765
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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