GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_0019
          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 (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