GapMind for catabolism of small carbon sources

 

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

Align galactaro-1,5-lactonase (characterized)
to candidate Pf1N1B4_4510 Gluconolactonase (EC 3.1.1.17)

Query= reanno::WCS417:GFF3393
         (291 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4510 Gluconolactonase (EC
           3.1.1.17)
          Length = 297

 Score =  489 bits (1259), Expect = e-143
 Identities = 237/293 (80%), Positives = 253/293 (86%), Gaps = 4/293 (1%)

Query: 1   MNAELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIAR 60
           M  ELIVDARNAVGE PVWVP ENALYWVDIP GGLQRW+A +GHV AW APQMLACIAR
Sbjct: 1   MQVELIVDARNAVGESPVWVPEENALYWVDIPTGGLQRWNADSGHVHAWKAPQMLACIAR 60

Query: 61  TDAGNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVL 120
             AG WVAGME+GFF L PHNDGSLD+ LLA V+H R DMRLNDGRCDRQGRFWAGSMVL
Sbjct: 61  HSAGGWVAGMESGFFHLHPHNDGSLDSELLAHVDHARPDMRLNDGRCDRQGRFWAGSMVL 120

Query: 121 NMGLNAAEGTLYRYTS--GAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFD 178
           NMG NAA+GTLYRY++       A+L GFI  NGL FSPDG+TMY SDSHP VQQIWAFD
Sbjct: 121 NMGANAADGTLYRYSARQPGPLDARLSGFIVPNGLGFSPDGKTMYLSDSHPNVQQIWAFD 180

Query: 179 YDIDTGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTV 238
           YDID+GTPSNRR+FVDMH  LGRPDGAAVDA+GCYWICANDAGLIHRF+PDGRLDRSL V
Sbjct: 181 YDIDSGTPSNRRLFVDMHHFLGRPDGAAVDAEGCYWICANDAGLIHRFTPDGRLDRSLPV 240

Query: 239 PVKKPTMCAFGGSRLDTLFVTSIR--DDQSEQSLSGGVFALNPGVVGLPEPTF 289
           PVKKPTMCAFGGS+LDTLFVTSIR  DD  EQSL+GGVFALNPGV GLPEP F
Sbjct: 241 PVKKPTMCAFGGSQLDTLFVTSIRPADDHDEQSLAGGVFALNPGVKGLPEPAF 293


Lambda     K      H
   0.321    0.137    0.443 

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: 517
Number of extensions: 21
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: 291
Length of database: 297
Length adjustment: 26
Effective length of query: 265
Effective length of database: 271
Effective search space:    71815
Effective search space used:    71815
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: 48 (23.1 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