GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctA in Pseudomonas stutzeri RCH2

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate GFF1351 Psest_1386 Na+/H+-dicarboxylate symporters

Query= TCDB::Q848I3
         (444 letters)



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

 Score =  192 bits (489), Expect = 1e-53
 Identities = 126/406 (31%), Positives = 206/406 (50%), Gaps = 15/406 (3%)

Query: 10  SLYFQVIVAIAIGILLGHFYP--------QTGV--ALKPLGDGFIKLIKMVIAPIIFCTV 59
           SL  Q+++A  +G+ +G            + GV  A    G  FI L+KMV+ P+IF ++
Sbjct: 3   SLNLQILIAACLGVAIGWLTGTLPTDAPVREGVLYASTLAGSIFIGLLKMVLIPLIFTSI 62

Query: 60  VSGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKV 119
           V G+A +Q    V +  G AL+YF + ++ A+L+ LV  N+ +PG G+ +D+     +  
Sbjct: 63  VVGVANLQAHHQVHRVWGGALVYFTLTTSAAMLVALVAANLFKPGAGLSLDLFAEAMNDF 122

Query: 120 AAYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDF 179
            A       +  + F  N+  N    A ANG IL V++F++  G AL   G   + +L  
Sbjct: 123 EARQLT-LPEFFLHFFANLFQNPF-AALANGSILAVVVFAMFIGIALVAGGDRYRNILVV 180

Query: 180 IDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVV 239
           +  F  +M  II+ IM+LAP+G L  +   +    V  L  +G  +   + T +    VV
Sbjct: 181 LQEFLELMMRIISWIMRLAPLGILALLIKLVAEQDVALLSAVGGFIALVFATTLFHGTVV 240

Query: 240 L-GAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRML-IKMERLGAKKSVVGLVIP 297
           L G +  A G S L   R  RE L+    TSSS + LP  L    + L  +  + G V+P
Sbjct: 241 LPGILFLATGKSPLWFFRGTREALITAFATSSSAATLPISLRCAEDNLKVRPGIAGFVLP 300

Query: 298 TGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLA 357
            G + N+DGT++Y   AA+F+A      + +  Q  +    +++S GA G+  +G + + 
Sbjct: 301 LGATMNMDGTALYEAAAALFVANLMGIELSLAQQAVVFFTAMIASTGAPGIPSAGMVTMV 360

Query: 358 ATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKW 403
             L AVG LP   +A++L IDR +   R   N+ G+ + +VVV ++
Sbjct: 361 MVLQAVG-LPAEAVAILLPIDRLLDTVRTAVNVEGDIIGSVVVQRF 405


Lambda     K      H
   0.326    0.142    0.402 

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: 438
Number of extensions: 18
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: 409
Length adjustment: 32
Effective length of query: 412
Effective length of database: 377
Effective search space:   155324
Effective search space used:   155324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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