GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagB in Acidovorax sp. GW101-3H11

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate Ac3H11_3072 Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] (EC 2.6.1.16)

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



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3072
           Glucosamine--fructose-6-phosphate aminotransferase
           [isomerizing] (EC 2.6.1.16)
          Length = 641

 Score =  122 bits (305), Expect = 3e-32
 Identities = 101/316 (31%), Positives = 151/316 (47%), Gaps = 30/316 (9%)

Query: 51  VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNG--LCLAISQSGK 108
           V+  A G+S ++   AKY +E + G+PT    + VAS Y    +  N   L + I+QSG+
Sbjct: 327 VLILACGTSYYSGCAAKYWLEEIAGIPTQ---VEVASEYRYRTSVPNPRTLVVTITQSGE 383

Query: 109 SPDLLATVEHQRKAGA-FVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAA 167
           + D LA + H +  G    + + N   S +     +    +AG E  VA+TK++   LA 
Sbjct: 384 TADTLAALRHAQSLGMQHTLTICNVVTSAMVRECKLAYITRAGVEIGVASTKAFTTQLAG 443

Query: 168 IAALVAAWAQDE---------ALETAVADLPAQLERAFALD-----WSAAVTALTGASGL 213
           +  L  A AQ +         A   A+  LP  L+   AL+     W+     +  A   
Sbjct: 444 LFLLTLALAQSKGRLSEEQEAAHLKAMRHLPVALQAVLALEPQLISWAEDFARMENA--- 500

Query: 214 FVLGRGYGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGE 273
             LGRG  Y IA E ALK KE   +HAE++ A E++HGP+A+V  A  V+  A +D   E
Sbjct: 501 LFLGRGLHYPIALEGALKLKEISYIHAEAYPAGELKHGPLALVTSAMPVVTVAPNDALLE 560

Query: 274 SVRETVAEFRSR-GAEVLLADPAAR---QAGLPAIAA---HPAIEPILIVQSFYKMANAL 326
            ++  + E R+R G   +LAD         G+  I     + A+ P+L V     +A   
Sbjct: 561 KLKSNMQEVRARAGVLYVLADGDTHIESSEGIHVIRMPEHYGALSPLLHVVPLQLLAYHT 620

Query: 327 ALARGCDPDSPPHLNK 342
           A ARG D D P +L K
Sbjct: 621 ACARGTDVDKPRNLAK 636


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: 431
Number of extensions: 27
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: 641
Length adjustment: 33
Effective length of query: 314
Effective length of database: 608
Effective search space:   190912
Effective search space used:   190912
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 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