GapMind for catabolism of small carbon sources

 

Aligments 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 8501197 DvMF_1931 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= TCDB::Q9RBQ9
         (439 letters)



>lcl|FitnessBrowser__Miya:8501197 DvMF_1931 TRAP dicarboxylate
           transporter, DctM subunit (RefSeq)
          Length = 640

 Score =  203 bits (517), Expect = 1e-56
 Identities = 125/432 (28%), Positives = 232/432 (53%), Gaps = 17/432 (3%)

Query: 6   AAWLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLTPI 65
           A WLL G   + L +G+P+A+S     +  A +   G   L  L +   V++ SF +  I
Sbjct: 220 AVWLLFGYFVLFLLVGVPIAFSLGLATI--ATVLGAGTLPLEYLAQIAFVSIDSFPILAI 277

Query: 66  PLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLG 125
           P FI  G  +   GL++R +   D+++  LPG +A+  +V   FF+AISGS  AT A +G
Sbjct: 278 PFFIAAGVFMGAGGLSRRLLALGDELVGALPGGMALATIVTCMFFAAISGSGPATVAAIG 337

Query: 126 SLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGL 185
           S+ +P M+ RGY+       + + G + ++IPPS   V+ G  A  S+ KL + G++PG+
Sbjct: 338 SITIPAMVERGYDKFFAAAVVASAGCIGVMIPPSNPFVVYGVAAQASVGKLFLAGIVPGV 397

Query: 186 L--LAISFVAYIVASAK-LRPESAPREELVVLRG-WERWRELVVYVLPLSLIFVAIVAVI 241
           L  LA+  VAY ++  K  R E+  R+   V++  WE    L+V V+ L  I+       
Sbjct: 398 LCGLALMAVAYYISLKKGWRGEARHRDFRSVMQAMWEAKWALLVPVIVLGGIY------- 450

Query: 242 SGGVATPTEAAAIGCAATLAITL-MYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQ 300
            GG+ TPTEAAA+     + + L +YR + W+ +   +  +   S +I+ ++  AT F  
Sbjct: 451 -GGIMTPTEAAAVSALYGMIVGLFIYREITWRRMWDCMVESAQTSSVIIVLMAMATLFGN 509

Query: 301 VLSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSL 360
           +++     + I  ++         ++ ++   L+++G F++ ++ +++  P  +P+V  +
Sbjct: 510 IMTIEQVPDHIAAMILGVTSNKIAILLLINVFLLWVGTFMEALAAIVIITPILLPLVTQV 569

Query: 361 GIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLI 420
           G+D I FGV+ ++ + +G + PP G+ L+    ++   +++G V  +A P++ +   +L+
Sbjct: 570 GVDPIHFGVIMVVNLAIGFITPPVGVNLFVASSIS--KVSIGDVVRAAWPFLLVMIALLM 627

Query: 421 LIFFWPGIATWL 432
            I + P I+  L
Sbjct: 628 AITYIPAISLCL 639


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: 668
Number of extensions: 40
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: 640
Length adjustment: 35
Effective length of query: 404
Effective length of database: 605
Effective search space:   244420
Effective search space used:   244420
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: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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