GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Dietzia timorensis ID05-A0528

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_067475181.1 BJL86_RS04450 glutamine--fructose-6-phosphate transaminase (isomerizing)

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



>NCBI__GCF_001659785.1:WP_067475181.1
          Length = 618

 Score =  130 bits (327), Expect = 1e-34
 Identities = 106/326 (32%), Positives = 156/326 (47%), Gaps = 28/326 (8%)

Query: 56  QRLRANPPRVVVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLE-GAL 114
           Q LR      +V C  GS+ H+   A+Y IE    +       S     D  P L+   L
Sbjct: 293 QELRDIDKVFIVAC--GSAYHSGLVAKYAIEHWTRIPCEVEIASEFRYRD--PVLDRSTL 348

Query: 115 YLAISQSGKSPDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATK 174
            +AISQSG++ D L AV+ AK+  A  +A+ N   + +   AD V+  HAGPE+ VA+TK
Sbjct: 349 VVAISQSGETADTLEAVRHAKSQKARVLAVCNTNGAQIPREADAVLYTHAGPEIGVASTK 408

Query: 175 SYIAALVAVTQLIAAWTEDAELTA----------ALQDLPTALA-AAWTLDWSLAVER-L 222
           +Y+A  +A   L+      A  T           AL+ +P  +      LD    + R L
Sbjct: 409 AYLAQ-IAANYLVGLALAQARGTKFPDEVSAEFHALEQMPELIGQVVERLDQVRQIAREL 467

Query: 223 KTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQ 282
             + ++  LGR VG+  ALE ALK KE   +HAE F A E+ HGP+AL+++G P  V   
Sbjct: 468 ADSKSVLFLGRHVGYPTALEGALKLKELAYMHAEGFPAGELKHGPIALIEEGLPVFVVMP 527

Query: 283 NDESRASVDEMAAG----LRARGASVLIAGGGGD------APDALPTLASHPVLEPILMI 332
               R+ +          ++ARGA  +I    GD      A   +    +  +L+P+L  
Sbjct: 528 PLHGRSLLHSKLISNIQEIKARGARTIIISAEGDEVVKPFADYLIEIPETTTLLQPLLST 587

Query: 333 QSFYRMANALSVARGYDPDSPPHLNK 358
             +   A  ++ ARGYD D P +L K
Sbjct: 588 IPYQAFAAEVAAARGYDVDKPRNLAK 613


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: 382
Number of extensions: 16
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: 618
Length adjustment: 33
Effective length of query: 330
Effective length of database: 585
Effective search space:   193050
Effective search space used:   193050
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