GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Acidovorax sp. GW101-3H11

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2257
          Length = 267

 Score =  152 bits (383), Expect = 1e-41
 Identities = 90/248 (36%), Positives = 140/248 (56%), Gaps = 8/248 (3%)

Query: 22  KVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKADVSR 81
           +V ++TG AQGIGEA V  FA++ A+ VI D+   + + +AA   E GA  + ++ DV  
Sbjct: 21  RVCIVTGGAQGIGEACVRRFAAEGAKPVIVDVDDARGQALAA---ELGA--LYVRCDVGD 75

Query: 82  QQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYGCKAVL 141
           +  + A+    +  HGRIDVLVN AG+    D L++TE D+     ++L G++   +AV 
Sbjct: 76  KAQVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNLKGSFLVGQAVA 135

Query: 142 PQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAIAPG 201
             M+  G G+I+N++S +    IP    Y V+K G+  LTR + +  A K IRVNA+APG
Sbjct: 136 RAMVTSGGGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKNIRVNAVAPG 195

Query: 202 YIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCIT 261
            I T+L              +++     P +R+GQP E+A    +LASD A ++    +T
Sbjct: 196 TIATELAA---KAVLTSDEAKRKIMSRTPMKRLGQPSEIADVVAWLASDAASYVTGEIVT 252

Query: 262 IDGGRSVM 269
           +DGGR  +
Sbjct: 253 VDGGRMTL 260


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: 145
Number of extensions: 4
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: 267
Length adjustment: 25
Effective length of query: 247
Effective length of database: 242
Effective search space:    59774
Effective search space used:    59774
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 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