GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctP in Pseudomonas stutzeri RCH2

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate GFF4195 Psest_4268 tripartite ATP-independent periplasmic transporter solute receptor, DctP family

Query= SwissProt::Q9HU18
         (331 letters)



>lcl|FitnessBrowser__psRCH2:GFF4195 Psest_4268 tripartite
           ATP-independent periplasmic transporter solute receptor,
           DctP family
          Length = 331

 Score =  548 bits (1412), Expect = e-161
 Identities = 272/330 (82%), Positives = 299/330 (90%)

Query: 1   MLKHTAKALVCALSLTVAGIVQAADPIVIKFSHVVAEHTPKGQGALLFKKLVEERLPGKV 60
           M K TAKAL CALSL++AG+  AADPI IKFSHVVAE+TPKGQGAL+FKKLVEERL GKV
Sbjct: 1   MFKLTAKALACALSLSIAGLAHAADPITIKFSHVVAENTPKGQGALMFKKLVEERLAGKV 60

Query: 61  KVEVYPNSSLFGDGKEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQAVDRF 120
           +V+VYPNSSLFGDGKEMEALLLGDVQ+IAPSLAKFE Y+K +Q++DLPFLFD+I AVDRF
Sbjct: 61  EVQVYPNSSLFGDGKEMEALLLGDVQLIAPSLAKFEHYSKGVQVYDLPFLFDDIAAVDRF 120

Query: 121 QQSPQGKELLTSMQDKGITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASKVLEEQF 180
           Q+   G+ LL SM+DK ITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQAS VL+EQF
Sbjct: 121 QKGEAGQSLLRSMEDKNITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASAVLDEQF 180

Query: 181 KAVRANPRKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEVQKYITESDHGVLDYMVIT 240
           KAVRANPRKMSFAEVYQGLQTGVVNG ENP+SNIYSQKMHEVQKYITES+HG+LDYMVIT
Sbjct: 181 KAVRANPRKMSFAEVYQGLQTGVVNGAENPYSNIYSQKMHEVQKYITESNHGLLDYMVIT 240

Query: 241 NTKFWNGLPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRIVEAKTSEIIELTPEQRAE 300
           NTKFWNGLP DVR  L   ++EVTV VNKQA+ LNQ DKQRIV+A T+EII LTPEQR  
Sbjct: 241 NTKFWNGLPADVRSELESILNEVTVAVNKQADELNQADKQRIVDAGTTEIINLTPEQREM 300

Query: 301 WRKAMQPVWKKFEGEIGADLIKAAEAANQA 330
           WR+AM+PVWKKFEGEIGADLIKAAEAANQA
Sbjct: 301 WREAMKPVWKKFEGEIGADLIKAAEAANQA 330


Lambda     K      H
   0.316    0.132    0.376 

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: 432
Number of extensions: 8
Number of successful extensions: 1
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: 331
Length of database: 331
Length adjustment: 28
Effective length of query: 303
Effective length of database: 303
Effective search space:    91809
Effective search space used:    91809
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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