GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctA in Dyella japonica UNC79MFTsu3.2

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate N515DRAFT_0019 N515DRAFT_0019 Na+/H+-dicarboxylate symporter

Query= TCDB::Q01857
         (444 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0019 N515DRAFT_0019
           Na+/H+-dicarboxylate symporter
          Length = 438

 Score =  162 bits (409), Expect = 3e-44
 Identities = 120/412 (29%), Positives = 206/412 (50%), Gaps = 31/412 (7%)

Query: 27  LVAIAAGILLGHFYPE-LGTQ-------LKPLGDAFIKLVKMIIAPVIFLTVATGIAGMS 78
           +VA  A + +G F+P  L T        L PLG  F++L+  ++ P++F ++A+G+A + 
Sbjct: 19  VVAAIATLAIGQFHPATLKTMQAFATAVLDPLGQVFLRLLFFVVIPLVFASLASGVAQLG 78

Query: 79  DLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFAAKAH 138
            L ++G +A +    F     +A+ IGL++ N++QPG    ++P S +   +  +   AH
Sbjct: 79  RLGRLGPLAARTFALFAANMLIAVAIGLLMMNLLQPGH--QLEPGSRE-RLLQEYGGGAH 135

Query: 139 ----------EQSIVGFLTNIIPTTIVGAF------ADGDILQVLFFSVLFGIALAMVGE 182
                     + S+   +   +P  ++GAF      A GD+L ++ F++L G A  ++ E
Sbjct: 136 RAMERRQQQPDMSLATAVDMFMPRNLLGAFVGHDRGALGDVLPLILFAILVGAAATLLDE 195

Query: 183 -KGEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYI 241
            K  ++ + L+ L+  +  +V   ++ AP+     +   I K G G +  L++      +
Sbjct: 196 DKRLKLQSGLDLLSELMTGIVGFALRLAPVAVPAMIYSVIVKIGTGVLLTLSVFTAGCAL 255

Query: 242 TSLLFVFIVLGAVARYNGF-SIVALLRYIKEELLLVLGTSSSEAALPG-LMNKMEKAGCK 299
              L +F  L    R     S +A  R I+  L+    TSSS A LP  L    ++   +
Sbjct: 256 ALALHLFGSLSLWLRLLARRSPLAYFRQIRPVLITAFSTSSSSATLPASLALARDELRLR 315

Query: 300 RSVVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGI 359
            S  G V+P G + N+ GT ++     LF+AQA G+ L+ G Q +L+L+A+LS+   AGI
Sbjct: 316 PSTAGFVLPLGATMNMSGTALFEGCVVLFVAQAFGVDLTLGQQCVLMLLAVLSAVAVAGI 375

Query: 360 TGAGFITLAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVV 411
            G G + L A L     VP  G+ L+LG+DR +   R   N+  + V   VV
Sbjct: 376 PG-GSLPLIAGLLATFGVPPEGIGLVLGVDRILDMLRTTVNVGSDLVTATVV 426


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: 472
Number of extensions: 26
Number of successful extensions: 5
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: 438
Length adjustment: 32
Effective length of query: 412
Effective length of database: 406
Effective search space:   167272
Effective search space used:   167272
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 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