GapMind for catabolism of small carbon sources

 

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

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate Pf1N1B4_1947 Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] (EC 2.6.1.16)

Query= reanno::Caulo:CCNA_00453
         (363 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1947
           Glucosamine--fructose-6-phosphate aminotransferase
           [isomerizing] (EC 2.6.1.16)
          Length = 610

 Score =  129 bits (323), Expect = 3e-34
 Identities = 102/311 (32%), Positives = 153/311 (49%), Gaps = 21/311 (6%)

Query: 66  VVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSP 125
           +V C  G+S HA   ARY +E  AG+       S    Y         L+++ISQSG++ 
Sbjct: 298 IVAC--GTSYHAGMVARYWLEELAGIPCQVEVASEFR-YRKVVVQPDTLFVSISQSGETA 354

Query: 126 DLLAAVKAAKAAGAHA-VALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVT 184
           D LAA++ AK  G  A +A+ NV  S L   +D  +   AG E+ VA+TK++   LV + 
Sbjct: 355 DTLAALRNAKELGFLASLAICNVGISSLVRESDLTLLTQAGREIGVASTKAFTTQLVGLL 414

Query: 185 QLIAAWTE---------DAELTAALQDLPTALAAAWTLDWSLA--VERLKTASNLYVLGR 233
            L  +  +         +A L   L+ LPT L  A  +D ++    E     ++   LGR
Sbjct: 415 LLTLSLGQVRGTLAEGVEATLVEELRRLPTRLGEALAMDSTVEKIAELFAEKNHTLFLGR 474

Query: 234 GVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEM 293
           G  F VA+E ALK KE   +HAEA+ A E+ HGP+ALV +  P +  A N+E    +   
Sbjct: 475 GAQFPVAMEGALKLKEISYIHAEAYPAGELKHGPLALVDNDMPVVTVAPNNELLEKLKSN 534

Query: 294 AAGLRARGASVLI-----AG-GGGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARG 347
              +RARG  +++     AG   G+    +     H +L PIL       ++  ++V +G
Sbjct: 535 LQEVRARGGELIVFADEQAGMTNGEGTHVVHMPHIHDILSPILYTIPLQLLSYYVAVLKG 594

Query: 348 YDPDSPPHLNK 358
            D D P +L K
Sbjct: 595 TDVDQPRNLAK 605


Lambda     K      H
   0.315    0.128    0.360 

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: 381
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 363
Length of database: 610
Length adjustment: 33
Effective length of query: 330
Effective length of database: 577
Effective search space:   190410
Effective search space used:   190410
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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