GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Klebsiella michiganensis M5al

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate BWI76_RS24305 BWI76_RS24305 2,5-didehydrogluconate reductase A

Query= BRENDA::C1K8Y9
         (324 letters)



>FitnessBrowser__Koxy:BWI76_RS24305
          Length = 275

 Score =  184 bits (468), Expect = 2e-51
 Identities = 116/313 (37%), Positives = 162/313 (51%), Gaps = 45/313 (14%)

Query: 3   TTPTIPTIKLNSGYEMPLVGFGCWKVNNETAADQIYNAIKTGYRLFDGAEDYGNEKEVGE 62
           T PT+  IKL+ G  MP +G G WK  NE     I+ A++ GYR FD A  Y NE     
Sbjct: 2   THPTV--IKLHDGNLMPQLGLGVWKAGNEEVVSAIHKALEVGYRSFDTAAVYQNET---- 55

Query: 63  GINRAIKEGLVKREELFITSKLWNNFHDPKNVETALNKTLSDLNLDYVDLFLIHFPIAFK 122
           G+  A+    V R+ELF+T+KLWN+  D K  + AL ++L  L LDYVDL+LIH+P    
Sbjct: 56  GVGNALSSAGVPRDELFVTTKLWND--DQKQPKEALQESLKKLKLDYVDLYLIHWP---- 109

Query: 123 FVPIEEKYPPGFYCGDGDNFHYEDVPLLDTWKALEKLVEAGKIKSIGISNFTGALIYDLI 182
            VP    +                   +D WK+L +L + G  KSIG+ NF    +  +I
Sbjct: 110 -VPATNHF-------------------VDAWKSLIELQQQGLAKSIGVCNFQVHHLQKII 149

Query: 183 RGATIKPAVLQIEHHPYLQQPKLIEYVQKAGIAITGYSSFGPQSFLELESKRALNTPTLF 242
               + P + QIE HP +QQ +L  +     I    +S              A     +F
Sbjct: 150 DETGVAPVINQIELHPLMQQRQLHAWNATHKIQTESWSPL------------AQGGEGVF 197

Query: 243 EHETIKSIADKHGKSPAQVLLRWATQRNIAVIPKSNNPERLAQNLSVVDFDLTKDDLDNI 302
           + + I+ +ADK+GK+PAQ+++RW     + VIPKS  P R+A+N +V DF L KD+L  I
Sbjct: 198 DQKIIRQLADKYGKTPAQIVIRWHLDSGLVVIPKSVTPSRIAENFNVWDFRLDKDELSEI 257

Query: 303 AKLDIGLRFN-DP 314
            KLD   R   DP
Sbjct: 258 TKLDQNKRLGPDP 270


Lambda     K      H
   0.318    0.139    0.420 

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: 273
Number of extensions: 13
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: 324
Length of database: 275
Length adjustment: 27
Effective length of query: 297
Effective length of database: 248
Effective search space:    73656
Effective search space used:    73656
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 (21.7 bits)
S2: 48 (23.1 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