GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Dyella japonica UNC79MFTsu3.2

Align 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-) (characterized)
to candidate N515DRAFT_1252 N515DRAFT_1252 2,4-diketo-3-deoxy-L-fuconate hydrolase

Query= reanno::BFirm:BPHYT_RS34210
         (282 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1252
          Length = 288

 Score =  367 bits (941), Expect = e-106
 Identities = 181/280 (64%), Positives = 217/280 (77%), Gaps = 1/280 (0%)

Query: 1   MKLLRYGPKGQEKPGLLDAQGKIRDLSKVVADIDGAALTDEGLAKLRALDPASLPLVEGN 60
           MKL+RYG  G EKPGL+D  G +RDLS+ VADID   L  EG A+L A+DPASLP VEG 
Sbjct: 1   MKLVRYGAHGNEKPGLIDKDGALRDLSEHVADIDPYVLGREGRARLAAIDPASLPEVEGT 60

Query: 61  PRMGPCVGKIGKFICIGLNYADHAAESNLPVPAEPVIFNKWTSAISGPNDDVEIPRGSKK 120
           PR G  V  + K IC+G+NYA HAAE+  PVPA+PV+F K T+AI GPNDDV IPRGS  
Sbjct: 61  PRFGAPVAPVSKIICVGMNYARHAAETGQPVPAQPVLFMKATTAIMGPNDDVVIPRGSTC 120

Query: 121 TDWEVELGVVIGKPAKYIDEANALDYVAGYCVINDVSEREWQIEKGGTWDKGKGFDTFGP 180
           TDWEVELGVVIG+ A+ +    AL +VAG+ VIND+SERE+Q+E GG W KGK  D+FGP
Sbjct: 121 TDWEVELGVVIGETARDVSVDEALAHVAGFIVINDLSEREFQLEHGGQWVKGKSCDSFGP 180

Query: 181 IGPWVVTRDEVADPQNLSLWLEVDGHRYQNGSTKTMVFGVAKLVSYVSQCMSLQPGDVIS 240
           +GPW+VT DEV DPQNL LWLEV+GHRYQ+ +T  MVFGVAKLVSY+S+ M+L PGDVIS
Sbjct: 181 LGPWLVTIDEVPDPQNLHLWLEVNGHRYQDSNTSDMVFGVAKLVSYISRYMTLLPGDVIS 240

Query: 241 TGTPPGVGMGVKPNPVFLKPGQTIRLGIEGLGEQTQKTYA 280
           TGTP GVG+G+KP P +L+PG  I LGI+GLG Q Q+  A
Sbjct: 241 TGTPAGVGLGLKP-PTYLRPGDVIELGIDGLGRQRQQVRA 279


Lambda     K      H
   0.315    0.138    0.422 

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: 363
Number of extensions: 12
Number of successful extensions: 2
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: 282
Length of database: 288
Length adjustment: 26
Effective length of query: 256
Effective length of database: 262
Effective search space:    67072
Effective search space used:    67072
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: 42 (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