GapMind for catabolism of small carbon sources

 

Alignments 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.

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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