GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctA in Pseudomonas stutzeri RCH2

Align Fumarate:H+ symporter of 442 aas and 14 established TMSs, DctA. Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate (characterized)
to candidate GFF1351 Psest_1386 Na+/H+-dicarboxylate symporters

Query= TCDB::Q1J1H5
         (442 letters)



>lcl|FitnessBrowser__psRCH2:GFF1351 Psest_1386 Na+/H+-dicarboxylate
           symporters
          Length = 409

 Score =  196 bits (497), Expect = 1e-54
 Identities = 127/409 (31%), Positives = 212/409 (51%), Gaps = 23/409 (5%)

Query: 7   SLYVQVLIAIVLGILVGFLFPSFGEGLKPLGDG-----------FIKLIKMLIAPIIFAT 55
           SL +Q+LIA  LG+ +G+L  +      P+ +G           FI L+KM++ P+IF +
Sbjct: 3   SLNLQILIAACLGVAIGWLTGTLPTDA-PVREGVLYASTLAGSIFIGLLKMVLIPLIFTS 61

Query: 56  VVSGIAHMRDTKKVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATLDTSA 115
           +V G+A+++   +V RV G AL+YF + T+ A+++ LV AN+ KPG G+     +LD  A
Sbjct: 62  IVVGVANLQAHHQVHRVWGGALVYFTLTTSAAMLVALVAANLFKPGAGL-----SLDLFA 116

Query: 116 ISKYTQAAGEQSVADFLLHIIPNTL---VSAFTEGDLLQVLLISVLFGFALTQLGTLGQK 172
            +     A + ++ +F LH   N      +A   G +L V++ ++  G AL   G   + 
Sbjct: 117 EAMNDFEARQLTLPEFFLHFFANLFQNPFAALANGSILAVVVFAMFIGIALVAGGDRYRN 176

Query: 173 VLAGIEAVNSAVFVILGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLF 232
           +L  ++     +  I+ ++MRLAP+G    +   + +  V  L+ +   +   +AT L  
Sbjct: 177 ILVVLQEFLELMMRIISWIMRLAPLGILALLIKLVAEQDVALLSAVGGFIALVFATTLFH 236

Query: 233 VFVVL-GLIARFAGFSILKFIRFIKEELLLVLGTSSSESALP-RLITKLEYAGANRSVVG 290
             VVL G++    G S L F R  +E L+    TSSS + LP  L    +       + G
Sbjct: 237 GTVVLPGILFLATGKSPLWFFRGTREALITAFATSSSAATLPISLRCAEDNLKVRPGIAG 296

Query: 291 LVVPAGYSFNLDGTSIYLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGF 350
            V+P G + N+DGT++Y   A LF+A      LSL QQ  +    ++ S GA G+  +G 
Sbjct: 297 FVLPLGATMNMDGTALYEAAAALFVANLMGIELSLAQQAVVFFTAMIASTGAPGIPSAGM 356

Query: 351 ITLAATLSAVGHVPVAGLALILGIDRFMSEARALTNFVGNGVATLVIAR 399
           +T+   L AVG +P   +A++L IDR +   R   N  G+ + ++V+ R
Sbjct: 357 VTMVMVLQAVG-LPAEAVAILLPIDRLLDTVRTAVNVEGDIIGSVVVQR 404


Lambda     K      H
   0.325    0.142    0.398 

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: 426
Number of extensions: 30
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: 442
Length of database: 409
Length adjustment: 32
Effective length of query: 410
Effective length of database: 377
Effective search space:   154570
Effective search space used:   154570
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