GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Snodgrassella alvi wkB2

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_025331759.1 SALWKB2_RS11165 SDR family oxidoreductase

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>NCBI__GCF_000600005.1:WP_025331759.1
          Length = 297

 Score = 99.0 bits (245), Expect = 1e-25
 Identities = 81/268 (30%), Positives = 126/268 (47%), Gaps = 21/268 (7%)

Query: 11  PEPPKGER-------LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEK--VEKV 61
           P P  GER       L  + +L+TGA  GIG A    +A + A L I+ +  E+   ++V
Sbjct: 35  PVPDCGERSYEGHGRLHGRKILVTGADSGIGRAAAIAYAREGADLAINYLPAEEEDAKQV 94

Query: 62  AAHWREQGADVVAIKADVSRQQDLHAMARLAIELH---GRIDVLVNCAGVNVFRDPL-QM 117
           AA  +E G  VV I  D+S   D H   +L  + H   G +D L   AG     +    +
Sbjct: 95  AALAQEAGRKVVCIPGDLS---DEHFCKQLVEKAHTELGGLDGLTLVAGKQTAVERFCDI 151

Query: 118 TEEDWHRCFAIDLDGAWYGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGL 177
           + E   + F +++   ++  +  +P +      +I+  +S  +    P    Y   K G+
Sbjct: 152 STEQLKKTFEVNIFSLFWVIQTAMPHL--PAGATIVTTSSVQAYQPSPNLVDYATTKAGI 209

Query: 178 LGLTRALGIEYAPKGIRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQP 237
           +  T+AL  + A KGIRVN++APG I T L +    G   P A  +         R GQP
Sbjct: 210 VAFTQALAKQVAAKGIRVNSVAPGPIWTALEI---TGGQPPEAIPKFGQSESVLGRAGQP 266

Query: 238 IEVAMTAVFLASDEAPFINASCITIDGG 265
            E+A T VFL S+E+ ++ A    + GG
Sbjct: 267 AELASTYVFLMSEESSYVTAQVYGVTGG 294


Lambda     K      H
   0.321    0.138    0.424 

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: 169
Number of extensions: 15
Number of successful extensions: 4
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: 272
Length of database: 297
Length adjustment: 26
Effective length of query: 246
Effective length of database: 271
Effective search space:    66666
Effective search space used:    66666
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 (21.9 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