GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF1351
          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 (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