GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Acidovorax sp. GW101-3H11

Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR

Query= reanno::BFirm:BPHYT_RS28235
         (260 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2257
          Length = 267

 Score =  147 bits (370), Expect = 3e-40
 Identities = 104/251 (41%), Positives = 142/251 (56%), Gaps = 17/251 (6%)

Query: 6   KVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGRRVI 65
           +V IVTGG++GIG A     AAEGA   I      DV   R  A+A   AE+ AL  R  
Sbjct: 21  RVCIVTGGAQGIGEACVRRFAAEGAKPVIV-----DVDDARGQALA---AELGALYVRC- 71

Query: 66  AIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVNLNGA 125
               +V  +     LV   + A G++DVL +NAGI     FL++     ++ + VNL G+
Sbjct: 72  ----DVGDKAQVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNLKGS 127

Query: 126 FYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVALGPYG 185
           F V QA A+ M   G GGAIV  SS++ ++       Y  +K GV+ L +  A+AL    
Sbjct: 128 FLVGQAVARAMVTSG-GGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKN 186

Query: 186 IRCNSVMPGTIATDLNAQDL--ADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRARY 243
           IR N+V PGTIAT+L A+ +  +DEAK+     R P+ RLG+P ++AD V +LASD A Y
Sbjct: 187 IRVNAVAPGTIATELAAKAVLTSDEAKRKIMS-RTPMKRLGQPSEIADVVAWLASDAASY 245

Query: 244 VTGAALLVDGG 254
           VTG  + VDGG
Sbjct: 246 VTGEIVTVDGG 256


Lambda     K      H
   0.319    0.134    0.386 

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: 171
Number of extensions: 12
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: 260
Length of database: 267
Length adjustment: 25
Effective length of query: 235
Effective length of database: 242
Effective search space:    56870
Effective search space used:    56870
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 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