GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Oscillibacter ruminantium GH1

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_040661330.1 ON16_RS08890 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_000307265.1:WP_040661330.1
          Length = 612

 Score =  110 bits (276), Expect = 8e-29
 Identities = 102/337 (30%), Positives = 169/337 (50%), Gaps = 48/337 (14%)

Query: 54  LAQRLRANPPRVVVTCARGSSDHAATFARY----LIETKAGVLTSSAGPSVSSVYDASPN 109
           L Q    N  R+ +  A GSS H    ++Y    L+     V+ +S       + D    
Sbjct: 287 LTQEYVKNISRIFII-ACGSSYHVGMVSKYNWEKLLRRPVEVVLASEFRYCDPLVD---- 341

Query: 110 LEGALYLAISQSGKSPDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELS 169
            E +L + ISQSG++ D +AA++ AK  G   +A+VNVV S +A  AD+V+   AGPE++
Sbjct: 342 -EHSLVVVISQSGETLDTMAAMREAKRRGGRTLAIVNVVGSSIARDADDVLYTWAGPEIA 400

Query: 170 VAATKSYIAALVAVTQLIAAWTED-------AELTAA---LQDLPTALAAAW--TLDWSL 217
           VA TK+Y   L A+  ++  +  D        + TAA   +Q LP  ++A    T D   
Sbjct: 401 VATTKAYSTQL-ALMDMVGLYLGDLLGTVCKEDYTAAVEGIQRLPEQMSAFLKDTEDIKY 459

Query: 218 AVERLKTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPA 277
              R    ++++ +GR + + + +E +LK KE   +H+EA+++ E+ HG ++L++ G   
Sbjct: 460 FASRYFNHNSIFFIGRNLDYAMGMEGSLKLKEISYIHSEAYASGELKHGTISLIEPG--T 517

Query: 278 LVFAQN------DESRASVDEMAAGLRARGASVLIAGGG---------GDAPDALP-TLA 321
           LV A        D++ ++V E    ++ARGA V+               DA  A+P T+A
Sbjct: 518 LVVALGSYTPLFDKAMSNVVE----VKARGAEVMALATNSQKAKMEKTADAVIAVPDTIA 573

Query: 322 SHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNK 358
              +L+P L +      A  +++ RG D D P +L K
Sbjct: 574 ---MLQPSLGVVPLQLFAYYVALQRGCDIDKPRNLAK 607


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: 321
Number of extensions: 13
Number of successful extensions: 3
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: 612
Length adjustment: 33
Effective length of query: 330
Effective length of database: 579
Effective search space:   191070
Effective search space used:   191070
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