GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Sporolactobacillus vineae SL153

Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate WP_010632160.1 RH97_RS09630 SDR family oxidoreductase

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



>NCBI__GCF_000246965.1:WP_010632160.1
          Length = 299

 Score =  139 bits (350), Expect = 7e-38
 Identities = 85/256 (33%), Positives = 141/256 (55%), Gaps = 12/256 (4%)

Query: 3   LKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALGR 62
           +K++V I++GG  GIGRA+AVA A EGAD+ + Y+ +++ +   + AV       E LG+
Sbjct: 53  MKNQVAIISGGDSGIGRAVAVAFAKEGADLVLAYFDEHEDARETKQAV-------EQLGQ 105

Query: 63  RVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGI-CPFHAFLDMPPEVLESTVAVN 121
           R + + G++  +E  + ++  T+E FG++D+L +N  +    + F+D+  E    T   N
Sbjct: 106 RCLLLPGDLRNKEHCKYVISSTLETFGRIDILVNNLAVQFVQNHFVDISDEQWHITFDTN 165

Query: 122 LNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGGGMQTHYTPTKAGVHSLMQSCAVAL 181
           ++  FY+T+AA   M     G +I+ T+SI+A +G      YT TK  + S  ++ A  +
Sbjct: 166 IHPFFYMTKAALPHMH---AGSSIINTTSINAYIGRKDLIDYTTTKGAIVSFTRALANNI 222

Query: 182 GPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLASDRA 241
              GIR N+V PG I T L       +  K  F   +P+ R G+P ++A     LAS   
Sbjct: 223 VDQGIRVNAVAPGPIWTPLIPASFTPDMVKT-FGSNVPMKRAGQPYELAPVYVLLASSDG 281

Query: 242 RYVTGAALLVDGGLFV 257
            Y+TG  + ++GG FV
Sbjct: 282 SYITGQTIHINGGGFV 297


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: 167
Number of extensions: 10
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: 299
Length adjustment: 26
Effective length of query: 234
Effective length of database: 273
Effective search space:    63882
Effective search space used:    63882
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