GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Arenitalea lutea P7-3-5

Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_019386674.1 P735_RS0103765 SDR family oxidoreductase

Query= reanno::Phaeo:GFF1301
         (257 letters)



>NCBI__GCF_000283015.1:WP_019386674.1
          Length = 254

 Score =  127 bits (318), Expect = 3e-34
 Identities = 84/259 (32%), Positives = 131/259 (50%), Gaps = 14/259 (5%)

Query: 1   MKRLSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQIGAAAIAVE-- 58
           M +L+GK A+ITGA  GIG   A+   N+G  V++  I+         Q+ A  I  E  
Sbjct: 1   MSKLNGKIAVITGATGGIGFQVAKRLGNDGFTVILNGIEDEAGAERVKQLEAEGIKAEYY 60

Query: 59  -LDVTDQASIDRALSRTVECFGGLDILINNAAVFTAAPLVE-VTREAYQRTFDINVSGTL 116
             DVT + ++   +++  E +G +D+L+NNA         E +T E Y+    +N+  T 
Sbjct: 61  GFDVTSEEAVTSNINKIGEKYGKIDVLVNNAGGLGGRSRFEDMTTEFYRFVMALNLDSTF 120

Query: 117 FMMQAAAQQMITQGTGGKIINMASQAG-RRGEPLVSVYCATKAAVISLTQSAGLNLISHG 175
           F  +AA    + +G    IIN  S AG   G P   VY  +KAAV ++T++   +L  +G
Sbjct: 121 FASRAAIP-FLKKGENASIINYTSIAGWNAGGPGAGVYGTSKAAVHAITRALAKDLAEYG 179

Query: 176 INVNAIAPGVVDGEHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFL 235
           I VNA++PG +D +        F K       +  A    ++  GR+G   ++  +  FL
Sbjct: 180 IRVNAVSPGTIDTD--------FHKQIKSTKPEVFASWKNNIMLGRLGQPENVASVVSFL 231

Query: 236 ASEDADYVVAQTYNVDGGQ 254
           ASEDA ++ A+T  V GGQ
Sbjct: 232 ASEDASFITAETIQVTGGQ 250


Lambda     K      H
   0.317    0.130    0.365 

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: 144
Number of extensions: 8
Number of successful extensions: 3
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: 257
Length of database: 254
Length adjustment: 24
Effective length of query: 233
Effective length of database: 230
Effective search space:    53590
Effective search space used:    53590
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: 47 (22.7 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