GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoB in Dyella japonica UNC79MFTsu3.2

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate N515DRAFT_1372 N515DRAFT_1372 phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1372 N515DRAFT_1372
           phosphoglucosamine mutase
          Length = 450

 Score =  114 bits (284), Expect = 8e-30
 Identities = 82/276 (29%), Positives = 139/276 (50%), Gaps = 17/276 (6%)

Query: 2   RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTYKSG-------KALVGRDGRTSSVMLKNA 53
           + FGT GIRG + +  ++ +  +++G A G   +        K L+G+D R S  M + A
Sbjct: 5   KYFGTDGIRGPVGQWPISADFMLRLGRAAGMALARDTREGRPKVLIGKDTRVSGYMFEAA 64

Query: 54  MISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEF 112
           + +GL++ G++V     +PTPA+A+ TR L A AG++I+ASHNP  DNG+K F+  G + 
Sbjct: 65  LEAGLVAAGVDVGLLGPMPTPAVAFLTRSLRAQAGIVISASHNPHQDNGIKFFSAIGEKL 124

Query: 113 YVEQERGLEEIIFSGNFRKARWDEIKPVRNVE-----VIPDYINAVLDFVGHETNLKVLY 167
             + E  + E+     F     + +     ++      I      ++D       L+++ 
Sbjct: 125 SDDVEAAI-ELGLDAEFTTEAPERLGKASRIDDAGGRYIEFCKRTLVDSEFTLRGLRIVL 183

Query: 168 DGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLA 227
           D ANGA   VAP +  E+GA+V+++    DG    R     +     L   V E   D+ 
Sbjct: 184 DCANGATYQVAPKVFAELGAEVIAIGHKPDGFNINRGVGSTHPQTLQLA--VLEHHADIG 241

Query: 228 IAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEE 263
           IA DGD DR+ + D +G   D D ++ + A+ +  +
Sbjct: 242 IAFDGDGDRVQLVDREGVLADGDDMLFILARAWAAQ 277


Lambda     K      H
   0.318    0.138    0.402 

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: 449
Number of extensions: 25
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 450
Length of database: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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