GapMind for catabolism of small carbon sources

 

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

Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate N515DRAFT_0019 N515DRAFT_0019 Na+/H+-dicarboxylate symporter

Query= uniprot:L0GT47
         (419 letters)



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

 Score =  250 bits (638), Expect = 7e-71
 Identities = 163/442 (36%), Positives = 238/442 (53%), Gaps = 43/442 (9%)

Query: 7   LSAPLRLLVRLPLWQQILIGLALGVAAGMAFGADAQ---------------LLAPIGTLF 51
           +S P RL  R      IL GL +GV A +A  A  Q               +L P+G +F
Sbjct: 1   MSTPNRLATR------ILQGLLIGVVAAIATLAIGQFHPATLKTMQAFATAVLDPLGQVF 54

Query: 52  LNAIKMLIVPLVFVSLVAGITSMQDSAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSP 111
           L  +  +++PLVF SL +G+  +    +LG ++ +T A++      AV+IGLL   L  P
Sbjct: 55  LRLLFFVVIPLVFASLASGVAQLGRLGRLGPLAARTFALFAANMLIAVAIGLLMMNLLQP 114

Query: 112 GEGMNMVASGN-------------EQAKQAP--SLVSILVGLVPANPVTAF------AEG 150
           G  +   +                E+ +Q P  SL + +   +P N + AF      A G
Sbjct: 115 GHQLEPGSRERLLQEYGGGAHRAMERRQQQPDMSLATAVDMFMPRNLLGAFVGHDRGALG 174

Query: 151 NILQIIVFAIALGVSINLIGERGAPAVRL-FDALAETFYKLTDLVMRVAPIGVFALTAGV 209
           ++L +I+FAI +G +  L+ E     ++   D L+E    +    +R+AP+ V A+   V
Sbjct: 175 DVLPLILFAILVGAAATLLDEDKRLKLQSGLDLLSELMTGIVGFALRLAPVAVPAMIYSV 234

Query: 210 VGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARLNPLRFFQGIAPALAVAFST 269
           +   G  VLL L+       LA   H+       L LLAR +PL +F+ I P L  AFST
Sbjct: 235 IVKIGTGVLLTLSVFTAGCALALALHLFGSLSLWLRLLARRSPLAYFRQIRPVLITAFST 294

Query: 270 SSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGTAIYQGVLALFIAQAFGIDLS 329
           SSSS TLP S+  AR  L +    AGFVLP+GAT+NM GTA+++G + LF+AQAFG+DL+
Sbjct: 295 SSSSATLPASLALARDELRLRPSTAGFVLPLGATMNMSGTALFEGCVVLFVAQAFGVDLT 354

Query: 330 AGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPLEGVALIAGIDRILDMARTTV 389
            GQ  +++L A L+++  AGIPG  L ++  +L   G+P EG+ L+ G+DRILDM RTTV
Sbjct: 355 LGQQCVLMLLAVLSAVAVAGIPGGSLPLIAGLLATFGVPPEGIGLVLGVDRILDMLRTTV 414

Query: 390 NVAGDLMTTTLVGRSEQELDRA 411
           NV  DL+T T+V       D A
Sbjct: 415 NVGSDLVTATVVDAGAVRGDHA 436


Lambda     K      H
   0.324    0.140    0.386 

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: 554
Number of extensions: 30
Number of successful extensions: 2
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: 419
Length of database: 438
Length adjustment: 32
Effective length of query: 387
Effective length of database: 406
Effective search space:   157122
Effective search space used:   157122
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: 41 (22.0 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