GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Sinorhizobium meliloti 1021

Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate SM_b20510 SM_b20510 galactonate dehydratase

Query= reanno::BFirm:BPHYT_RS16405
         (382 letters)



>FitnessBrowser__Smeli:SM_b20510
          Length = 382

 Score =  645 bits (1665), Expect = 0.0
 Identities = 303/382 (79%), Positives = 338/382 (88%)

Query: 1   MKITKLETFIVPPRWCFLKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYLIGKDPLLI 60
           MKITKL T+IVPPRW FLKIETDEG+VGWGEPVVEGRA TV AAV ELSDYL+GKDP LI
Sbjct: 1   MKITKLTTYIVPPRWLFLKIETDEGVVGWGEPVVEGRALTVEAAVHELSDYLVGKDPFLI 60

Query: 61  EDHWQVMYRSGFYRGGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSWI 120
           EDHW V+YR GFYRGG I MSA+AG+DQALWDIKGK  G P+H+LLGGQ RD+IKVYSWI
Sbjct: 61  EDHWNVLYRGGFYRGGAIHMSALAGIDQALWDIKGKALGQPVHSLLGGQCRDRIKVYSWI 120

Query: 121 GGDRPSDVANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGI 180
           GGDRPSDVANNAR VV RGFKA+K+NG EE+QI+DT +K+   +  +  +R+A+GP++GI
Sbjct: 121 GGDRPSDVANNAREVVARGFKAIKLNGCEEMQIVDTNEKIDKAVETIGLIRDAIGPHVGI 180

Query: 181 GVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSR 240
           GVDFHGRVH+PMAKVLAKEL+P+KL+FIEEPVLSEN EALR+I N  +TPIALGERLYSR
Sbjct: 181 GVDFHGRVHRPMAKVLAKELEPFKLMFIEEPVLSENREALREIANHCSTPIALGERLYSR 240

Query: 241 WDFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPLGPIALATCLQID 300
           WDFK +LS G+VDIIQPD SHAGGITECRKIA+MAEAYDVALA HCPLGPIALA CLQ+D
Sbjct: 241 WDFKSVLSDGFVDIIQPDLSHAGGITECRKIAAMAEAYDVALAPHCPLGPIALAACLQVD 300

Query: 301 AVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNEEKVREM 360
           AVSYNAFIQEQSLGIHYN+ ND+LDYI N EVF YEDGFVSIPQGPGLGIEV+E  V E 
Sbjct: 301 AVSYNAFIQEQSLGIHYNEANDILDYISNKEVFAYEDGFVSIPQGPGLGIEVDEAYVMER 360

Query: 361 AKVGHRWRNPVWRHEDGSVAEW 382
           AK GHRWRNPVWRH DGSVAEW
Sbjct: 361 AKEGHRWRNPVWRHSDGSVAEW 382


Lambda     K      H
   0.319    0.139    0.428 

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: 619
Number of extensions: 15
Number of successful extensions: 1
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 (21.7 bits)
S2: 50 (23.9 bits)

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

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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