GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_1372
          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 (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