GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Gracilibacillus halophilus YIM-C55.5

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_003463886.1 J416_RS02285 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_000359605.1:WP_003463886.1
          Length = 600

 Score =  119 bits (298), Expect = 2e-31
 Identities = 94/301 (31%), Positives = 146/301 (48%), Gaps = 14/301 (4%)

Query: 70  ARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLA 129
           A G+S HA    +  IE  + +       S  S Y+     E  L++ ISQSG++ D  +
Sbjct: 297 AAGTSYHAGLVGKQFIERLSNIPVEVHIASEFS-YNMPLLSEKPLFIFISQSGETADSRS 355

Query: 130 AVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIAA 189
            +   K  G  A+ L NV  S L+  AD  + LHAGPE++VA+TK+Y A  +AV  ++A 
Sbjct: 356 VLVQTKELGHPALTLTNVPGSTLSREADYTLHLHAGPEIAVASTKAYTAQ-IAVLAILAV 414

Query: 190 WTEDAE----LTAALQDLPTALAAAWTL-DWSLAVERLK-----TASNLYVLGRGVGFGV 239
            T  A+        L++L     A  +L D   A +R+      T  N + +GRG+ + V
Sbjct: 415 DTAKAKGINLSFDPLKELGIVANAMESLTDQKDAFDRIAKDLFDTTRNAFFIGRGMDYFV 474

Query: 240 ALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMAAGLRA 299
            LEAALK KE   + AE F+  E+ HG +AL++DG P +  +  +    S+      + A
Sbjct: 475 VLEAALKLKEISYIQAEGFAGGELKHGTIALIEDGTPVIAISSQENVNLSIRGNVQEVAA 534

Query: 300 RGASVLIAGGGG--DAPDALPTLASHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLN 357
           RGA+  +    G     D       H +L P++ +     +A   ++ R  D D P +L 
Sbjct: 535 RGANTCVVSMKGLEQNEDRFVLPQVHELLAPLVSVIPMQLLAYYAALHRDCDVDKPRNLA 594

Query: 358 K 358
           K
Sbjct: 595 K 595


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: 333
Number of extensions: 13
Number of successful extensions: 2
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: 600
Length adjustment: 33
Effective length of query: 330
Effective length of database: 567
Effective search space:   187110
Effective search space used:   187110
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