GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4626
          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 (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