GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glucosaminate-lyase in Pseudomonas fluorescens FW300-N1B4

Align Glucosaminate ammonia-lyase; EC 4.3.1.9; D-glucosaminate dehydratase alpha-subunit; GlcNA-DH alpha subunit; GlcNADH-alpha (uncharacterized)
to candidate Pf1N1B4_1046 Thioredoxin reductase (EC 1.8.1.9)

Query= curated2:Q93HX6
         (320 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1046 Thioredoxin reductase
           (EC 1.8.1.9)
          Length = 318

 Score =  612 bits (1578), Expect = e-180
 Identities = 307/318 (96%), Positives = 312/318 (98%)

Query: 1   MVEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL 60
           M EVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL
Sbjct: 1   MSEVRHSRVIILGSGPAGYSAAVYAARANLKPLLITGMQAGGQLTTTTEVDNWPGDVHGL 60

Query: 61  TGPALMERMREHAERFETEIVFDHINAVDFAAKPYTLTGDSATYTCDALIIATGASARYL 120
           TGPALMERM+EHAERFETEIVFDHINAVDFAAKPYTL GDSATYTCDALIIATGASARYL
Sbjct: 61  TGPALMERMKEHAERFETEIVFDHINAVDFAAKPYTLIGDSATYTCDALIIATGASARYL 120

Query: 121 GLPSEEAFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET 180
           GLPSEE FMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET
Sbjct: 121 GLPSEETFMGKGVSACATCDGFFYRNKPVAVVGGGNTAVEEALYLANIASTVTLIHRRET 180

Query: 181 FRAEKILIDKLNARVAEGKIILKLNANLDEVLGDNMGVTGARLKNNDGSFDELKVDGVFI 240
           FRAEKILIDKLNARVAEGKI+LKLN+ LDEVLGDNMGVTGARLKNNDGSFDELKVDGVFI
Sbjct: 181 FRAEKILIDKLNARVAEGKIVLKLNSTLDEVLGDNMGVTGARLKNNDGSFDELKVDGVFI 240

Query: 241 AIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATSVEGIFAAGDVADHVYRQAITSAGA 300
           AIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATAT++EGIFAAGDVADHVYRQAITSAGA
Sbjct: 241 AIGHTPNTSLFEGQLTLKDGYLVVQGGRDGNATATNLEGIFAAGDVADHVYRQAITSAGA 300

Query: 301 GCMAALDTERYLDGLQNA 318
           GCMAALD ERYLD LQNA
Sbjct: 301 GCMAALDAERYLDDLQNA 318


Lambda     K      H
   0.318    0.135    0.386 

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: 495
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: 320
Length of database: 318
Length adjustment: 28
Effective length of query: 292
Effective length of database: 290
Effective search space:    84680
Effective search space used:    84680
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 (21.7 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