GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Streptacidiphilus oryzae TH49

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_037569004.1 BS73_RS03225 SDR family oxidoreductase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>NCBI__GCF_000744815.1:WP_037569004.1
          Length = 252

 Score =  137 bits (345), Expect = 2e-37
 Identities = 83/255 (32%), Positives = 128/255 (50%), Gaps = 11/255 (4%)

Query: 16  GERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHAL 75
           G     +  L+TGA  GIG A    FA   A + + DI A+     A   RE G +  A+
Sbjct: 3   GAAAPRRAGLVTGAGSGIGRATALRFARDGAAVAVLDIDADAAAETAESIREDGGEALAV 62

Query: 76  KADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAW 134
             D+++++ + A     V   G +D  VN AG+      L EM  E++ R   ++L G +
Sbjct: 63  TVDIADERAVAAAVERTVASFGGLDFAVNNAGLASHHRRLDEMAPEEFERVVRVNLTGTF 122

Query: 135 YGCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVR 194
           +  +  LP +  +G G+I+N+AS    + IP    Y  AKHG++GLT+   ++YAP+G+R
Sbjct: 123 HCMRYELPALRARGGGAIVNVASNGGLYAIPTAPAYVAAKHGIVGLTKVAAVDYAPQGIR 182

Query: 195 VNAIAPGYIETQLNVDYWNGFADPYAERQ---RALDLHPPRRIGQPIEVAMTAVFLASDE 251
           VNA+ PG   T        GF    A          + P  R+  P E A  AV+L SD+
Sbjct: 183 VNAVCPGPTRTP-------GFEAVAAGTDMIAMQASITPLGRLATPEEAAAAAVWLCSDD 235

Query: 252 APFINASCITIDGGR 266
           A ++    +++DGGR
Sbjct: 236 ASYVTGIALSVDGGR 250


Lambda     K      H
   0.321    0.137    0.419 

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: 160
Number of extensions: 9
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: 272
Length of database: 252
Length adjustment: 25
Effective length of query: 247
Effective length of database: 227
Effective search space:    56069
Effective search space used:    56069
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: 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