GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Pseudomonas stutzeri RCH2

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate GFF2613 Psest_2664 tripartite ATP-independent periplasmic transporter solute receptor, DctP family

Query= SwissProt::Q9HU18
         (331 letters)



>FitnessBrowser__psRCH2:GFF2613
          Length = 329

 Score =  516 bits (1330), Expect = e-151
 Identities = 253/330 (76%), Positives = 289/330 (87%), Gaps = 1/330 (0%)

Query: 1   MLKHTAKALVCALSLTVAGIVQAADPIVIKFSHVVAEHTPKGQGALLFKKLVEERLPGKV 60
           ML +  KAL CALS ++AG+V A DP+ IKF+HVVA++TPKGQGALLFKKL EERLPGKV
Sbjct: 1   MLSNKLKALACALSFSIAGLVHA-DPVTIKFAHVVADNTPKGQGALLFKKLAEERLPGKV 59

Query: 61  KVEVYPNSSLFGDGKEMEALLLGDVQIIAPSLAKFEQYTKKLQIFDLPFLFDNIQAVDRF 120
           KVEVYPNSSLFGDGKEMEALLLGDV ++APSLAKFE Y K +QI+DLPFLFD++ A DRF
Sbjct: 60  KVEVYPNSSLFGDGKEMEALLLGDVHMLAPSLAKFEHYAKAIQIYDLPFLFDDLAAADRF 119

Query: 121 QQSPQGKELLTSMQDKGITGLGYWHNGMKQLSANKPLREPKDARGLKFRVQASKVLEEQF 180
           Q  PQGK LL +M+DK ITGL YWHNGMKQLSANKPLREPKDARGLKFRVQAS VL+EQF
Sbjct: 120 QSGPQGKALLRAMEDKNITGLAYWHNGMKQLSANKPLREPKDARGLKFRVQASAVLDEQF 179

Query: 181 KAVRANPRKMSFAEVYQGLQTGVVNGTENPWSNIYSQKMHEVQKYITESDHGVLDYMVIT 240
           KAVRANPRKMSFAEVYQGLQTGVVNGTEN WSN  SQK+HEVQ Y+T SDHG++DYMVIT
Sbjct: 180 KAVRANPRKMSFAEVYQGLQTGVVNGTENTWSNYESQKVHEVQPYMTASDHGLIDYMVIT 239

Query: 241 NTKFWNGLPEDVRGVLAKTMDEVTVEVNKQAEALNQGDKQRIVEAKTSEIIELTPEQRAE 300
           NTKFWNGLPED+RG L   M+EVT EVN+QA+ LNQ  +Q I  +  +EIIELTPEQRA+
Sbjct: 240 NTKFWNGLPEDLRGELETIMEEVTAEVNRQADDLNQQARQAIAASGKTEIIELTPEQRAQ 299

Query: 301 WRKAMQPVWKKFEGEIGADLIKAAEAANQA 330
           WR+AM+PVWKKFE EIGA+LI+AA+AAN++
Sbjct: 300 WREAMKPVWKKFENEIGAELIEAAQAANRS 329


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: 411
Number of extensions: 9
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: 331
Length of database: 329
Length adjustment: 28
Effective length of query: 303
Effective length of database: 301
Effective search space:    91203
Effective search space used:    91203
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.

Links

Downloads

Related tools

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