GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Corynebacterium deserti GIMN1.010

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_053546284.1 CDES_RS13820 S-(hydroxymethyl)mycothiol dehydrogenase

Query= BRENDA::Q86ZV0
         (358 letters)



>NCBI__GCF_001277995.1:WP_053546284.1
          Length = 368

 Score =  134 bits (338), Expect = 3e-36
 Identities = 107/346 (30%), Positives = 166/346 (47%), Gaps = 36/346 (10%)

Query: 35  HDVLVDVRFTGICGSDVHYWEHGSIGQFVVKDPMVLGHESSGVISKVGSAVTTLKVGDHV 94
           HDV+V ++ TG+C +D+ Y +     +F    P +LGHES+GV+  VG AVT ++VGD V
Sbjct: 30  HDVIVKIQSTGVCHTDLAYRDGDISDEF----PFLLGHESAGVVETVGDAVTHVEVGDFV 85

Query: 95  AMEPGIPCRRCEPCKEGKYNLC-------EKMAFA----ATPPYD-GTLAKYYVLPEDFC 142
            +     C  C  C++G    C       +KM        TP    G+ A+  ++ E  C
Sbjct: 86  VLNWRAVCGECRACRKGDLEYCFNTHNASKKMTLTDGTELTPALGIGSFAEKTLVHEGQC 145

Query: 143 YKL-----PENINLQEAAVMEPLSVAVHIVKQANVAPGQSVVVFGAGPVGLLCCAVARAF 197
            K+     P    L    +M  L  AV+      V  G+SV VFG G VG+   A A+  
Sbjct: 146 TKVNPDADPAAAGLLGCGIMAGLGSAVNT---GEVKRGESVAVFGLGGVGMAAVAGAKIA 202

Query: 198 GSPKVIAVDIQKGRLEFAKKYAATAIFEPSKVSAL-ENAE--RIVNENDLGRGADIVIDA 254
           G+  +IAVDI   +LE+AK++ AT + + S++S   EN+E  + V E   G G D+ IDA
Sbjct: 203 GATTIIAVDIDAKKLEWAKEFGATHVIDSSQLSGEGENSEVAQKVREITDGFGTDVAIDA 262

Query: 255 SGAEPSVHTGIHVLRPGGTYVQGGMGRNEITFPIMAACTKELNVRGSFR---YG----SG 307
            G  P+     +     G  V   +G   +T  I           GS R   YG      
Sbjct: 263 VGIMPTWQQAFYSRDHAGRMVM--VGVPNLTSRIEVPAIDFYGRGGSLRPAWYGDCLPER 320

Query: 308 DYKLAVNLVASGKVSVKELITGVVSFEDAEQAFHEVKAGKGIKTLI 353
           D+   V+L   G+  + + ++  +   D E+AF  +KAG  +++++
Sbjct: 321 DFPTYVDLYLQGRFPLDKFVSERIGLGDVEEAFTTMKAGDVLRSVV 366


Lambda     K      H
   0.319    0.137    0.406 

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: 350
Number of extensions: 20
Number of successful extensions: 6
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: 358
Length of database: 368
Length adjustment: 29
Effective length of query: 329
Effective length of database: 339
Effective search space:   111531
Effective search space used:   111531
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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