Alignments for a candidate for mt2d in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for mt2d in Sinorhizobium meliloti 1021

Align Mannitol dehydrogenase DSF1; Deletion suppressor of MPT5 mutation protein 1; EC 1.1.1.67 (characterized)
to candidate SM_b20749 SM_b20749 D-mannonate oxidoreductase

Query= SwissProt::P0CX08
         (502 letters)



>FitnessBrowser__Smeli:SM_b20749
          Length = 487

 Score =  363 bits (933), Expect = e-105
 Identities = 198/489 (40%), Positives = 292/489 (59%), Gaps = 12/489 (2%)

Query: 12  LNAKTLKSFESTLPIPTYPREGVKQGIVHLGVGAFHRSHLAVFMHRLMQEHHLKDWSICG 71
           L+ KT+     T+  P Y    V  GIVHLG+GAFHR+H AV+   L+ E     W ICG
Sbjct: 3   LSRKTIDRLPRTVKRPHYDLGTVTVGIVHLGIGAFHRAHQAVYTDGLLSED--PSWGICG 60

Query: 72  VGLMKADALMRDAMKAQDCLYTLVERGIKDTNAYIVGSITAYMYAPDDPRAVIEKMANPD 131
           V L   +   RDA+  QD LYTL  +  + +   +VGS+   + APDDP AV+ +MA+P 
Sbjct: 61  VSLRSPET--RDALHPQDGLYTLAVQDGEGSELSVVGSVVELLCAPDDPEAVLRRMADPG 118

Query: 132 THIVSLTVTENGYYHSEATNSLMTDAPEIINDLNHPEKPDTLYGYLYEALLLRYKRGLTP 191
           T IVSLT+TE GY H+ AT +L    P+I++DL +P +P +  G++ EA+  R   G+ P
Sbjct: 119 TRIVSLTITEKGYCHNPATGTLDEGHPDIVHDLANPARPRSAIGFIVEAISRRVSAGIAP 178

Query: 192 FTIMSCDNMPQNGVTVKTMLVAFAKLKKDEKFAAWIEDKVTSPNSMVDRVTPRCTDKERK 251
           FT++SCDN+P NG  +K ++  FA+ + D   AA + + V SP++MVDR+ P  TD +R 
Sbjct: 179 FTLLSCDNLPGNGHVLKRIVTQFAEAR-DPALAAVVRN-VASPSTMVDRIVPATTDSDRS 236

Query: 252 YVADTWGIKDQCPVVAEPFIQWVLEDNFSDGRPPWELVGVQVVKDVDSYELMKLRLLNGG 311
            VA   G++D  P++ EPF QWV+E++F  GRP WE  G   V+DV ++E MKLRLLNG 
Sbjct: 237 AVASAMGLEDAWPIMTEPFRQWVIEEDFPLGRPAWEKAGALFVQDVSAFEFMKLRLLNGS 296

Query: 312 HSAMGYLGYLAGYTYIHEVVNDPTINKYIRVLMREEVIPLLPKVPGVDFEEYTASVLERF 371
           HS + YLGYLAG   + + +    +   +  LMR EV P LP++PG D   Y A +L+RF
Sbjct: 297 HSTLAYLGYLAGAETVADAMALAGMEALVEGLMRHEVSPTLPELPGFDLPAYRAELLQRF 356

Query: 372 SNPAIQDTVARICLMGSGKMPKYVLPSIYEQLRKPDGKYKLLAVCVAGWFRYLTGVDMNG 431
            NPA++    +I + GS K+P+ +L SI ++L+   G Y  LA+ VA W RY  G+D  G
Sbjct: 357 RNPALRHRTWQIAMDGSQKLPQRLLGSIRDRLQAGAG-YDRLALGVAAWMRYARGLDEAG 415

Query: 432 KPFEIEDPMAPTLKAAAVKGGKDPHEL----LNIEVLFSPEIRDNKEFVAQLTHSLETVY 487
           +P ++ DP A  + A   +G  +P  +    L +  +F  ++  +  F A L  +L+ + 
Sbjct: 416 RPIDVRDPHAARI-AGLARGIDEPDRIVDAFLTMTDVFGTDLPASAPFRAALIKALDGLL 474

Query: 488 DKGPIAAIK 496
             G  A ++
Sbjct: 475 RIGAAATLR 483


Lambda     K      H
   0.319    0.136    0.409 

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: 656
Number of extensions: 36
Number of successful extensions: 4
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: 502
Length of database: 487
Length adjustment: 34
Effective length of query: 468
Effective length of database: 453
Effective search space:   212004
Effective search space used:   212004
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: 52 (24.6 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
the source code
instructions for running GapMind on your computer

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