GapMind for catabolism of small carbon sources

 

Aligments for a candidate for galactonolactonase in Pseudomonas fluorescens FW300-N2E3

Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate AO353_23650 AO353_23650 3-carboxymuconate cyclase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314
         (389 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_23650 AO353_23650
           3-carboxymuconate cyclase
          Length = 391

 Score =  644 bits (1662), Expect = 0.0
 Identities = 315/389 (80%), Positives = 349/389 (89%)

Query: 1   MRNLWPLLMAGSIGAMGVQVASAEDYQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQV 60
           MR LWPLLMAGS+GAMG+  ASAE +QLLVG+YT GQSQGIYRL FDS++GQ+DA+PLQV
Sbjct: 3   MRKLWPLLMAGSVGAMGLSSASAESFQLLVGTYTQGQSQGIYRLKFDSQSGQLDATPLQV 62

Query: 61  IKSANPSWLTLSKDQRHLFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQSLGNEP 120
           +KSANPSWLTLS DQR LFVVNENGPGQ DPVGRVSSFA++P THALSLI+QVQSLGNEP
Sbjct: 63  VKSANPSWLTLSSDQRRLFVVNENGPGQADPVGRVSSFAVEPNTHALSLINQVQSLGNEP 122

Query: 121 THSSLSIDGSHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASA 180
           THSSLS DG +LFVSNYSVAEDPGG LA LPV+ DGKL   VQ+SSH  SRVNPERQ SA
Sbjct: 123 THSSLSADGKYLFVSNYSVAEDPGGNLAALPVSTDGKLAPPVQLSSHQPSRVNPERQMSA 182

Query: 181 HVHSTIPSPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLF 240
           HVHST+ SPDG+YVFANDLGADKVF YR+DPKANPE PLT ATPA VQLPPGSGPRHLLF
Sbjct: 183 HVHSTVSSPDGQYVFANDLGADKVFVYRYDPKANPERPLTAATPASVQLPPGSGPRHLLF 242

Query: 241 SADGKHAWLTMEMSAQVAVFDYHDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYV 300
           SADGKHA+LT+EMSAQVAVFDY  G+L Q QMVDLAAG+P + KAAAALHAS+DGKFLYV
Sbjct: 243 SADGKHAYLTLEMSAQVAVFDYQAGKLTQRQMVDLAAGKPAAQKAAAALHASSDGKFLYV 302

Query: 301 SNRGTANQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVE 360
           SNRGT N+LLVFAIDPA+G L ELQRR VEGDHPREFSLDPSGKF+L+ANQKSNQIV++ 
Sbjct: 303 SNRGTTNELLVFAIDPASGELKELQRRPVEGDHPREFSLDPSGKFVLVANQKSNQIVIIA 362

Query: 361 RDARTGLLGKTVQKLPMDAPSDLRFLLRQ 389
           RD +TGLLGKTVQKLP D+PSD++F LRQ
Sbjct: 363 RDVKTGLLGKTVQKLPFDSPSDIKFFLRQ 391


Lambda     K      H
   0.316    0.132    0.382 

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: 691
Number of extensions: 31
Number of successful extensions: 7
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: 389
Length of database: 391
Length adjustment: 31
Effective length of query: 358
Effective length of database: 360
Effective search space:   128880
Effective search space used:   128880
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: 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