GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Duganella sacchari Sac-22

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_072783034.1 BUA36_RS07360 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_900143065.1:WP_072783034.1
          Length = 609

 Score =  130 bits (326), Expect = 1e-34
 Identities = 113/368 (30%), Positives = 171/368 (46%), Gaps = 26/368 (7%)

Query: 13  APTGASPPSLAPASTHMFREAGEAARVAAVQLTANAPKIQAL----AQRLRANPPRVVVT 68
           A TGA+   L P   +M +E  E  RV    L      +  L    A  +     RV++ 
Sbjct: 241 AHTGAA--ELGPYRHYMQKEIFEQPRVIGDTLEGVTGIMPELFGDGAYNVFKQIDRVLIL 298

Query: 69  CARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLL 128
            A G+S ++   A+Y IE+ A +  +    S     D+ P+    L + ISQSG++ D L
Sbjct: 299 -ACGTSYYSGLTAKYWIESVAKIPVNVEIASEYRYRDSVPH-PNTLVVTISQSGETADTL 356

Query: 129 AAVKAAKAAGA-HAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLI 187
           AA+K A++ G  H + + NV  S +           AG E+ VA+TK++   L A+  L 
Sbjct: 357 AALKHARSLGMEHTLTICNVGHSAMVRECQLAYITRAGVEVGVASTKAFTTQLAALFLLT 416

Query: 188 AAWT---------EDAELTAALQDLPTALAAAWTLDWSLAV--ERLKTASNLYVLGRGVG 236
            A           E+ E   A++ LP A++A   L+  +    E      N   LGRG+ 
Sbjct: 417 LALAQVNGRLTEAEEVEHLKAMRHLPVAISAVLALEPQIIAWAEDFARKENALFLGRGMH 476

Query: 237 FGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMAAG 296
           + +ALE ALK KE   +HAEA+ A E+ HGP+ALV +  P +  A ND     +      
Sbjct: 477 YPIALEGALKLKEISYIHAEAYPAGELKHGPLALVTEEMPVVTVAPNDALIEKLKSNMQE 536

Query: 297 LRARGASVLIAGG------GGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARGYDP 350
           +RARG  + +          G+    +     + +L PIL + S   +A   +VARG D 
Sbjct: 537 VRARGGQLYVFADVDSRITSGEGVHVIRLPEHYGLLSPILHVVSLQLLAYHAAVARGTDV 596

Query: 351 DSPPHLNK 358
           D P +L K
Sbjct: 597 DKPRNLAK 604


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: 373
Number of extensions: 14
Number of successful extensions: 5
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: 363
Length of database: 609
Length adjustment: 33
Effective length of query: 330
Effective length of database: 576
Effective search space:   190080
Effective search space used:   190080
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 24 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:

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