GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagB in Burkholderia phytofirmans PsJN

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate BPHYT_RS18560 BPHYT_RS18560 glucosamine--fructose-6-phosphate aminotransferase

Query= reanno::Korea:Ga0059261_1644
         (347 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS18560 BPHYT_RS18560
           glucosamine--fructose-6-phosphate aminotransferase
          Length = 605

 Score =  125 bits (315), Expect = 2e-33
 Identities = 99/310 (31%), Positives = 146/310 (47%), Gaps = 26/310 (8%)

Query: 55  ARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLA 114
           A G+S ++   AKY +E++  +PT    ++    Y   VA    L + ISQSG++ D LA
Sbjct: 295 ACGTSYYSGLTAKYWLESIAKIPT-QVEIASEYRYRESVANPKSLVVVISQSGETADTLA 353

Query: 115 TVEHQRKAG-AFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVA 173
            ++H ++ G    +A+ N   S +    +      AG E  VA+TK++   L A+  L A
Sbjct: 354 ALKHAQELGHKHTLAVCNVGTSAMVRQTEFSFLTHAGREIGVASTKAFTTQLVALFVLAA 413

Query: 174 AWA---------QDEALETAVADLPAQLERAFALD-----WSAAVTALTGASGLFVLGRG 219
                       Q+      +  LPA L    AL+     WS   +    A     LGRG
Sbjct: 414 TLGKMRGRVSDEQEAEYLKQLRHLPAALNSVLALEPQIIAWSEEFSRKEHA---LFLGRG 470

Query: 220 YGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETV 279
             Y IA E ALK KE   +HAE++ A E++HGP+A+V EA  V+  A +D   E ++  +
Sbjct: 471 LHYPIALEGALKLKEISYIHAEAYPAGELKHGPLALVTEAMPVVTVAPNDALLEKLKSNI 530

Query: 280 AEFRSRGAEVLLADPA----ARQAGLPAIAA---HPAIEPILIVQSFYKMANALALARGC 332
            E R+RG E+ +   A        GL  I     +  + PIL V     +A   A ARG 
Sbjct: 531 QEVRARGGELYVFADADTKIVNDEGLHVIRMPEHYGLLSPILHVVPLQLLAYHTACARGT 590

Query: 333 DPDSPPHLNK 342
           D D P +L K
Sbjct: 591 DVDKPRNLAK 600


Lambda     K      H
   0.317    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: 429
Number of extensions: 22
Number of successful extensions: 4
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: 347
Length of database: 605
Length adjustment: 33
Effective length of query: 314
Effective length of database: 572
Effective search space:   179608
Effective search space used:   179608
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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