GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Pedobacter sp. GW460-11-11-14-LB5

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate CA265_RS10595 CA265_RS10595 dicarboxylate/amino acid:cation symporter

Query= TCDB::Q01857
         (444 letters)



>FitnessBrowser__Pedo557:CA265_RS10595
          Length = 458

 Score =  283 bits (725), Expect = 6e-81
 Identities = 148/374 (39%), Positives = 235/374 (62%), Gaps = 15/374 (4%)

Query: 50  LGDAFIKLVKMIIAPVIFLTVATGIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVA 109
           L D F++L+KMI+AP++F T+  G+A + D++ VGR+ GK + +FL  S ++L++G+++ 
Sbjct: 92  LSDIFLRLIKMIVAPLVFTTLVVGVAKVGDIKAVGRIGGKTLGWFLAMSLMSLVLGMVLV 151

Query: 110 NVVQPGAGMNIDPASLDPAAVATFAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFF 169
           N+ +PG  M +   SL    V T   KA   S+  F+ ++ P +I  + +  +ILQ++ F
Sbjct: 152 NLFEPGRHMKL---SLPDQLVNTGIQKA-AMSVKDFIAHVFPKSIAESMSTNEILQIVVF 207

Query: 170 SVLFGIALAMVGEKGEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSI 229
           S+ FG+A A +G+ G+ V+   +++   + K+   +M  AP+  FGAM   + K G+  +
Sbjct: 208 SLFFGVATAAIGDLGQIVIKAFDAIAHVILKMTGYVMNFAPLAVFGAMTAIVAKQGLNVL 267

Query: 230 ANLAMLIGTFYITSLLFVFIVLGAVARYNGFSIVA-----LLRYIKEELLLVLGTSSSEA 284
              A+ IG FY+        +L AV  + GF ++      L+  +KE  LL   T+SSEA
Sbjct: 268 NTYAIFIGEFYLG-----LAILWAVLIFLGFLVLKKRIFRLVNDMKEPALLAFSTASSEA 322

Query: 285 ALPGLMNKMEKAGCKRSVVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQIL 344
           A P  M  +E+ GCK  +V  V+P GYSFNLDG+ +YMT A+LFIAQA GIHL +  QI 
Sbjct: 323 AYPKTMMLLERFGCKDKIVSFVLPLGYSFNLDGSMMYMTFASLFIAQAYGIHLGFEQQIS 382

Query: 345 LLLVAMLSSKGAAGITGAGFITLAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGN 404
           +LL+ ML+SKG AG+  A  + +A T++   ++P AG+AL++GID  +   R+ TN+VGN
Sbjct: 383 MLLILMLTSKGIAGVPRASLVVIAGTIASF-NIPEAGLALLIGIDPLLDMGRSATNVVGN 441

Query: 405 AVATIVVARWENEL 418
           ++AT VV++WE EL
Sbjct: 442 SIATAVVSKWEGEL 455


Lambda     K      H
   0.324    0.139    0.393 

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: 475
Number of extensions: 24
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: 444
Length of database: 458
Length adjustment: 33
Effective length of query: 411
Effective length of database: 425
Effective search space:   174675
Effective search space used:   174675
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: 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