GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA3 in Dinoroseobacter shibae DFL-12

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate 3608645 Dshi_2038 Altronate dehydratase (RefSeq)

Query= reanno::BFirm:BPHYT_RS34230
         (431 letters)



>FitnessBrowser__Dino:3608645
          Length = 393

 Score =  161 bits (408), Expect = 3e-44
 Identities = 130/411 (31%), Positives = 196/411 (47%), Gaps = 48/411 (11%)

Query: 9   TLEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPL---DAFDDPSAEREPPVH 65
           T++GY R +GR G+RN V +  + + ++     +    +  L    A+       +  +H
Sbjct: 9   TVKGYRRENGRVGVRNHVLILPVDDISNAACEAVANNVKGTLAIPHAYGRLQFGEDLELH 68

Query: 66  LIGFPGCYPNGYAEKMLERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVEVLTI 125
                G   N             PNV +V  V +G E      + D +R +G+ V   +I
Sbjct: 69  FRTMIGTGAN-------------PNVHSV--VVIGIEPGWTKRIADGIRETGKEVAEFSI 113

Query: 126 QEKGG---TRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPA 182
           ++KG     R+      D++  A E     Q+   ++SEL + T CG SD T+G+ + P 
Sbjct: 114 EQKGDFETIRAASWAAKDFVHKATEM----QREECSISELWVSTKCGESDTTTGLGSCPT 169

Query: 183 VGRAFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACVAKAARYYSILGHG 242
           VG  +D L+  G T  F ET E+ G E   + RA    +G      + KA +   I  H 
Sbjct: 170 VGNMYDKLLPEGITGFFGETSEITGAEHICQKRAINEEVGQRWYK-MWKAYQDDVIFAHQ 228

Query: 243 SFAV-------GNADGGLTTQEEKSLGAYAKSG-ASPIVGIIKPGDIPPTG-GLYLLDVV 293
           +  +       GN +GGLTT EEK+LG   K G  S  + I++P + P +G GLY +D  
Sbjct: 229 TDDLSDSQPTKGNIEGGLTTIEEKALGNLEKIGRTSQFIDILEPAEQPKSGNGLYFMD-- 286

Query: 294 PDGEPRFGFPNISDNAEIGELIACGAHVI-LFTTGRGSVVGSAISPVIKVCANPATYRNL 352
                     + S  AE   L+A G  VI  F TG+G+VVG+ I PVIK+ ANP T R +
Sbjct: 287 ----------SSSAAAECVTLMAAGGAVIHTFPTGQGNVVGNPIVPVIKITANPRTVRTM 336

Query: 353 SGDMDVDAGRILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEFILT 403
           +  +DVD   IL    T+DE G  + E     + G  + +E LGH+EF +T
Sbjct: 337 AEHVDVDVSGILRREMTIDEAGDALIEMICRTANGRNTAAEALGHREFSMT 387


Lambda     K      H
   0.318    0.137    0.408 

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: 432
Number of extensions: 25
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: 431
Length of database: 393
Length adjustment: 31
Effective length of query: 400
Effective length of database: 362
Effective search space:   144800
Effective search space used:   144800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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