Aligments for a candidate for gci in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments for a candidate for gci in Sinorhizobium meliloti 1021

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate SM_b20510 SM_b20510 galactonate dehydratase

Query= BRENDA::A9CEQ8
         (378 letters)



>FitnessBrowser__Smeli:SM_b20510
          Length = 382

 Score =  163 bits (413), Expect = 6e-45
 Identities = 120/383 (31%), Positives = 185/383 (48%), Gaps = 35/383 (9%)

Query: 1   MKITAVRTHLLEHRLDTPFESASMRFDRRAHVLVEIECDDGTVGWGECL--GPARPNAAV 58
           MKIT + T+++  R                 + ++IE D+G VGWGE +  G A    A 
Sbjct: 1   MKITKLTTYIVPPRW----------------LFLKIETDEGVVGWGEPVVEGRALTVEAA 44

Query: 59  VQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYGASIS 118
           V   S +L+G+DP   E  W VLY     +G   + ++AL+GID ALWDIKGK  G  + 
Sbjct: 45  VHELSDYLVGKDPFLIEDHWNVLYRGGFYRGG-AIHMSALAGIDQALWDIKGKALGQPVH 103

Query: 119 MLLGGRWRESVRAYATGSFKRDNVDRVSDNASEMAERRAEGFHACKIK---------IGF 169
            LLGG+ R+ ++ Y+         DR SD A+   E  A GF A K+             
Sbjct: 104 SLLGGQCRDRIKVYSW-----IGGDRPSDVANNAREVVARGFKAIKLNGCEEMQIVDTNE 158

Query: 170 GVEEDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLD 229
            +++ +  I  +R+AIGP + + +D +       A  L      F + + EEPV+ E  +
Sbjct: 159 KIDKAVETIGLIRDAIGPHVGIGVDFHGRVHRPMAKVLAKELEPFKLMFIEEPVLSENRE 218

Query: 230 AYARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLH 289
           A   +      P+A GE  + R+     LS G VDI+QPDL   GG +E +KIA +A  +
Sbjct: 219 ALREIANHCSTPIALGERLYSRWDFKSVLSDGFVDIIQPDLSHAGGITECRKIAAMAEAY 278

Query: 290 GVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAV 349
            V + PH     + +AA LQ  A      ++   +   + ++  ++       +E     
Sbjct: 279 DVALAPHCPLGPIALAACLQVDAVSYNAFIQEQSLG--IHYNEANDILDYISNKEVFAYE 336

Query: 350 NGVVTIPDGPGLGIEINRDALTE 372
           +G V+IP GPGLGIE++   + E
Sbjct: 337 DGFVSIPQGPGLGIEVDEAYVME 359


Lambda     K      H
   0.321    0.138    0.431 

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: 413
Number of extensions: 22
Number of successful extensions: 5
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: 378
Length of database: 382
Length adjustment: 30
Effective length of query: 348
Effective length of database: 352
Effective search space:   122496
Effective search space used:   122496
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: 50 (23.9 bits)

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

Downloads

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

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:

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