GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Salinicoccus carnicancri Crm

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate WP_017549643.1 C792_RS0111725 aldo/keto reductase

Query= BRENDA::C5J3R6
         (320 letters)



>NCBI__GCF_000330705.1:WP_017549643.1
          Length = 277

 Score =  181 bits (459), Expect = 2e-50
 Identities = 103/306 (33%), Positives = 159/306 (51%), Gaps = 43/306 (14%)

Query: 5   TIKLNSGYDMPLVGFGLWKVNRETCADQVYEAIKAGYRLFDGACDYGNEVEAGQGVARAI 64
           T +LN+G  MP++GFG++K+  E  A  +  A++AGYR FD A  Y NE   G      +
Sbjct: 8   TYELNNGVKMPVIGFGVYKIPEEQMAATIGTALEAGYRHFDTAAFYENERALGD----VL 63

Query: 65  KEGIVKREDLFIVSKLWNTFHEADKVEPIARKQLADWGLDYFDLYLIHFPIALKYVDPAE 124
           K+  V RE+LFI +K+WN     ++        L    +DY DLYLIH+PI  KY     
Sbjct: 64  KKSDVSREELFITTKVWNDDLGYEETLKAFETSLEKLQMDYLDLYLIHWPIEGKYT---- 119

Query: 125 IYPPGWTGTKKEVEFSNATIQETWQAMETLVDKKLTRSIGISNFSAQLIMDLLRYARIRP 184
                                E+W+A+E L      R+IG+SNF +Q + ++ R+A + P
Sbjct: 120 ---------------------ESWRALEKLYKDGRVRAIGVSNFHSQHLEEIFRFATVTP 158

Query: 185 ATLQIEHHPYLTQQALVEYVQKEGIAVTAYSSFGPLSFLELGHQVAKDTPLLFEHSTVKS 244
              Q+E+HP L Q+ +  +  + GI + A++     +F              F    ++ 
Sbjct: 159 MVNQLEYHPQLAQKEMRAFCDEHGIQLEAWAPLKRGAF--------------FGDPVIRE 204

Query: 245 IAEKHGKTPAQVLLRWATQRNIAVIPKSNNPGRLAQNLDVTAWDLEPADIEALSALNKNL 304
           +AEK+GKTPAQ++LRW  Q  ++ IPKS  PGR+ QN+D+  ++L   D+E L  L+ + 
Sbjct: 205 LAEKYGKTPAQIVLRWDIQTGVSTIPKSVTPGRIRQNIDIFDFELTEGDMERLDTLDTHE 264

Query: 305 RFNNPP 310
           R    P
Sbjct: 265 RLGKDP 270


Lambda     K      H
   0.319    0.136    0.411 

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: 263
Number of extensions: 15
Number of successful extensions: 5
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: 320
Length of database: 277
Length adjustment: 26
Effective length of query: 294
Effective length of database: 251
Effective search space:    73794
Effective search space used:    73794
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 (21.8 bits)
S2: 48 (23.1 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