GapMind for catabolism of small carbon sources

 

Aligments for a candidate for galactonolactonase in Pseudomonas fluorescens FW300-N1B4

Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate Pf1N1B4_4626 3-carboxymuconate cyclase

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4626 3-carboxymuconate
           cyclase
          Length = 405

 Score =  650 bits (1677), Expect = 0.0
 Identities = 322/380 (84%), Positives = 344/380 (90%)

Query: 1   MRNLWPLLMAGSIGAMGVQVASAEDYQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQV 60
           MRN WPLLMAGS+GAMGVQ A  + Y+LLVGSYTAGQSQGIYRL FDSRTGQIDA PLQV
Sbjct: 3   MRNFWPLLMAGSVGAMGVQAAPVDSYELLVGSYTAGQSQGIYRLNFDSRTGQIDAKPLQV 62

Query: 61  IKSANPSWLTLSKDQRHLFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQSLGNEP 120
           +KSANPSWL +SKDQ  LF VNENGPGQ DPVGRVSS+AIDPKT+ LSLISQVQ+LGNEP
Sbjct: 63  VKSANPSWLVVSKDQHRLFAVNENGPGQADPVGRVSSYAIDPKTNELSLISQVQTLGNEP 122

Query: 121 THSSLSIDGSHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASA 180
           THSS+S D SH+FVSNYSVAEDPGGTLAVLPV  DGKLK VVQMSSHP+SRVNPERQ SA
Sbjct: 123 THSSVSGDASHVFVSNYSVAEDPGGTLAVLPVGTDGKLKPVVQMSSHPSSRVNPERQKSA 182

Query: 181 HVHSTIPSPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLF 240
           HVHS + SPDG+YVF+NDLGADK+F YRFDPKANPELPLT A PA VQLPPGSGPRHLLF
Sbjct: 183 HVHSVVSSPDGQYVFSNDLGADKIFVYRFDPKANPELPLTAAKPASVQLPPGSGPRHLLF 242

Query: 241 SADGKHAWLTMEMSAQVAVFDYHDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYV 300
           SADGKHAWLTMEMSAQVAVFDY DG+LEQTQ+VDLAAG P S KAAAALHASADGKFLYV
Sbjct: 243 SADGKHAWLTMEMSAQVAVFDYRDGKLEQTQLVDLAAGLPTSGKAAAALHASADGKFLYV 302

Query: 301 SNRGTANQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVE 360
           SNRGT NQLLVFAIDPATG+L ELQRR+V+GDHPREFSLDPSGKF+LIANQKSNQIVVVE
Sbjct: 303 SNRGTTNQLLVFAIDPATGNLKELQRRSVDGDHPREFSLDPSGKFVLIANQKSNQIVVVE 362

Query: 361 RDARTGLLGKTVQKLPMDAP 380
           RDA+TGLLGKTVQK     P
Sbjct: 363 RDAKTGLLGKTVQKTTDGCP 382


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: 753
Number of extensions: 30
Number of successful extensions: 3
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: 405
Length adjustment: 31
Effective length of query: 358
Effective length of database: 374
Effective search space:   133892
Effective search space used:   133892
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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