GapMind for catabolism of small carbon sources

 

Aligments for a candidate for put1 in Pedobacter sp. GW460-11-11-14-LB5

Align Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate CA265_RS11605 CA265_RS11605 proline dehydrogenase

Query= reanno::Pedo557:CA265_RS11605
         (394 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS11605 CA265_RS11605 proline
           dehydrogenase
          Length = 394

 Score =  792 bits (2045), Expect = 0.0
 Identities = 394/394 (100%), Positives = 394/394 (100%)

Query: 1   MDLSPNKQPNFDNTEVAFRQKTNGELKKAYWLFKMIGSNFLTKVGPAITNFFLNIGLPIQ 60
           MDLSPNKQPNFDNTEVAFRQKTNGELKKAYWLFKMIGSNFLTKVGPAITNFFLNIGLPIQ
Sbjct: 1   MDLSPNKQPNFDNTEVAFRQKTNGELKKAYWLFKMIGSNFLTKVGPAITNFFLNIGLPIQ 60

Query: 61  GAIKATIFQQFCGGETIAECDKAIEQLHKGGVGTILDYSVEGEEEEQVFDETCAEIIRTI 120
           GAIKATIFQQFCGGETIAECDKAIEQLHKGGVGTILDYSVEGEEEEQVFDETCAEIIRTI
Sbjct: 61  GAIKATIFQQFCGGETIAECDKAIEQLHKGGVGTILDYSVEGEEEEQVFDETCAEIIRTI 120

Query: 121 MRADGDVKIPITVFKITGIGRFALLQKLDAKETLNASEKAEYEKVKQRCEKICQTAFDKG 180
           MRADGDVKIPITVFKITGIGRFALLQKLDAKETLNASEKAEYEKVKQRCEKICQTAFDKG
Sbjct: 121 MRADGDVKIPITVFKITGIGRFALLQKLDAKETLNASEKAEYEKVKQRCEKICQTAFDKG 180

Query: 181 VPIMIDAEETWIQDTIDELALDMMRKFNRERIIVYNTYQMYRHDKLADMKADHLIAKADG 240
           VPIMIDAEETWIQDTIDELALDMMRKFNRERIIVYNTYQMYRHDKLADMKADHLIAKADG
Sbjct: 181 VPIMIDAEETWIQDTIDELALDMMRKFNRERIIVYNTYQMYRHDKLADMKADHLIAKADG 240

Query: 241 FILGVKMVRGAYMEKERKRAAEMGYPSPIQPDKAASDRDYNESLRYCVDHIEEIAIVAGT 300
           FILGVKMVRGAYMEKERKRAAEMGYPSPIQPDKAASDRDYNESLRYCVDHIEEIAIVAGT
Sbjct: 241 FILGVKMVRGAYMEKERKRAAEMGYPSPIQPDKAASDRDYNESLRYCVDHIEEIAIVAGT 300

Query: 301 HNEDSSRLLTYLLEEKNITHNHPHVYFAQLLGMSDNLSFNLADSNYNVAKYVPYGPIKAV 360
           HNEDSSRLLTYLLEEKNITHNHPHVYFAQLLGMSDNLSFNLADSNYNVAKYVPYGPIKAV
Sbjct: 301 HNEDSSRLLTYLLEEKNITHNHPHVYFAQLLGMSDNLSFNLADSNYNVAKYVPYGPIKAV 360

Query: 361 MPYLFRRAQENTSVAGQTGRELGLIERELKRRKL 394
           MPYLFRRAQENTSVAGQTGRELGLIERELKRRKL
Sbjct: 361 MPYLFRRAQENTSVAGQTGRELGLIERELKRRKL 394


Lambda     K      H
   0.319    0.136    0.394 

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: 657
Number of extensions: 11
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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