Alignments for a candidate for fucD in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for fucD in Sinorhizobium meliloti 1021

Align L-fuconate dehydratase; EC 4.2.1.68 (characterized, see rationale)
to candidate SM_b21113 SM_b21113 hypothetical protein

Query= uniprot:D8J108
         (425 letters)



>FitnessBrowser__Smeli:SM_b21113
          Length = 425

 Score =  681 bits (1758), Expect = 0.0
 Identities = 320/425 (75%), Positives = 368/425 (86%)

Query: 1   MTKITALRVLDVRFPTSQSLDGSDAMNPDPDYSAAYVILDTDNAALKGHGLTFTIGRGNE 60
           MT+IT LRV D+RFPTS SLDGSDAMNPDPDYSAAYVILDTD   L GHGLTFTIGRGN+
Sbjct: 1   MTRITDLRVFDLRFPTSASLDGSDAMNPDPDYSAAYVILDTDRPGLAGHGLTFTIGRGND 60

Query: 61  ICCAAIRAMEHLVVGLELEWIAADMGRFWRHVTSDSQLRWIGPDKGAIHLATGAVVNAAW 120
           ICC AI AM HLVVG ++  I    GRFWRH+TSDSQLRWIGP+KGAIHLATGA+VNA W
Sbjct: 61  ICCMAIEAMRHLVVGQDISNILKHPGRFWRHLTSDSQLRWIGPEKGAIHLATGAIVNAVW 120

Query: 121 DLWAKAEGKPVWKLVADMSPEELVRTIDFRYITDCITPDEALALLREKEAGKAERLRVLE 180
           DL AK  GKPVW+LVADM  EE+   +D+RY+TD +T D+A+ +LR  E GKAER+  LE
Sbjct: 121 DLLAKHAGKPVWRLVADMPAEEIADIVDYRYLTDVLTRDDAVEILRRAEPGKAERIATLE 180

Query: 181 QEGYPCYTTSAGWLGYEDAKLRRLCQEAIDQGFNHVKLKVGRDLADDKRRVTIAREVLGP 240
           +EGYPCYTTSAGWLGY+DAKLRRL QEA+D GF+H+K+KVGRDL DD RR+ IAREV+GP
Sbjct: 181 KEGYPCYTTSAGWLGYDDAKLRRLAQEAVDAGFDHIKMKVGRDLDDDIRRLRIAREVIGP 240

Query: 241 ERKLMIDANQVWEVHQAIDWVNQLAFAQPWFIEEPTSPDDVEGHRKIREGIGAVKVATGE 300
           +R LMIDANQVWEV +AI+WV +LAFA+P+FIEEPTSPDDV GHRKIRE IG VKVATGE
Sbjct: 241 DRYLMIDANQVWEVGEAIEWVQKLAFAKPFFIEEPTSPDDVAGHRKIREAIGPVKVATGE 300

Query: 301 MCQNRVLFKQFIMRDAIDVVQIDSCRLGGVNEILAVMLMAAKYGKVVCPHAGGVGLCEYV 360
           MCQNR++FKQFI   AID+VQIDSCR+GG+NE+LAV+L+AAKYG  V PHAGGVGLCEYV
Sbjct: 301 MCQNRIMFKQFIAEGAIDIVQIDSCRMGGLNEVLAVLLIAAKYGLPVWPHAGGVGLCEYV 360

Query: 361 QHLSMIDYLCISGSKEGRVTEYVDHLHEHFVDPCVVKNAAYMPPSRPGFSIEMKPQSLEQ 420
           QHLSMIDY+ +SG+K+GRV EYVDHLHEHF+DPCV++NAAYMPP RPGFSIEMK QS+E 
Sbjct: 361 QHLSMIDYVAVSGTKDGRVIEYVDHLHEHFLDPCVIRNAAYMPPERPGFSIEMKQQSIED 420

Query: 421 YRFRG 425
           YRF G
Sbjct: 421 YRFDG 425


Lambda     K      H
   0.322    0.137    0.429 

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: 710
Number of extensions: 28
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: 425
Length of database: 425
Length adjustment: 32
Effective length of query: 393
Effective length of database: 393
Effective search space:   154449
Effective search space used:   154449
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 (21.9 bits)
S2: 51 (24.3 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources