GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Pedobacter sp. GW460-11-11-14-LB5

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate CA265_RS19160 CA265_RS19160 glutamine--fructose-6-phosphate transaminase (isomerizing)

Query= reanno::ANA3:7025965
         (332 letters)



>FitnessBrowser__Pedo557:CA265_RS19160
          Length = 612

 Score =  131 bits (330), Expect = 4e-35
 Identities = 96/329 (29%), Positives = 162/329 (49%), Gaps = 36/329 (10%)

Query: 28  MQQLGEKLRAFDPRFVMIVGRGSSDHAGVFAKYLFEIEAGVPTFAAAPSVASVYGKTLKL 87
           +++  EKL+  D   ++IV  G+S HAG+  +YL E  A +P      S    Y   +  
Sbjct: 286 IKEFAEKLKNIDR--IIIVACGTSWHAGLVGEYLIEEYARIPVEVEYASEFR-YRNPIIT 342

Query: 88  EGGLVIVISQSGRSPDILAQARMAKNAGAFCVALVNDETAPIKDIVDVVVPLRAGEEKAV 147
           E  +VI ISQSG + D +A   MAK  GA    + N   A I  +    V   AG E  V
Sbjct: 343 EKDVVIAISQSGETADTMAAIEMAKERGATIFGICNVAGASIPRLTHAGVYTHAGPEIGV 402

Query: 148 AATKSYLATLSAILQLASAWTQSES---------LAAAVNSLPQALQTAVDAEPQLTPAS 198
           A+TK++ A ++ +  +A    Q +          L   ++++P+ +Q A+++   +   +
Sbjct: 403 ASTKAFTAQVTVLTLMAFYMAQQKGTITTSKLIELLTELDNIPEKIQVALESNDLIKEVA 462

Query: 199 --VENVKNLVVLGRGLGYAVSKEIALKLKEVCSIHAEAFSSAEFLHGPVTLVEKKLTIVD 256
             +++  N + LGRG G+ V+ E ALKLKE+  IHAE + +AE  HGP+ L+++++ +V 
Sbjct: 463 EKIKDSTNCLFLGRGSGFPVALEGALKLKEISYIHAEGYPAAEMKHGPIALIDEEMPVVF 522

Query: 257 VCIGDESYASHIEQIENV-SQRGADLVHLNQTSTDIH-----------------PRVAPL 298
           +   + SY   I  I+ V +++G  +  + Q  T++                  P +A +
Sbjct: 523 IATQNSSYEKVISNIQEVKARKGKVIAIVTQGDTEVKKMADYCIEIPDANEAFLPLIATI 582

Query: 299 ALLQRFYIDVAAVAIARGIDPDQPAGLKK 327
            L    Y     +A+ RG + DQP  L K
Sbjct: 583 PLQLLSY----HIAVMRGCNVDQPRNLAK 607


Lambda     K      H
   0.316    0.130    0.357 

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: 418
Number of extensions: 17
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: 332
Length of database: 612
Length adjustment: 33
Effective length of query: 299
Effective length of database: 579
Effective search space:   173121
Effective search space used:   173121
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:

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