Alignments for a candidate for xad in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Sinorhizobium meliloti 1021

Align xylonate dehydratase monomer (EC 4.2.1.82) (characterized)
to candidate SMa0235 SMa0235 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-20629
         (591 letters)



>FitnessBrowser__Smeli:SMa0235
          Length = 592

 Score =  935 bits (2417), Expect = 0.0
 Identities = 440/592 (74%), Positives = 513/592 (86%), Gaps = 1/592 (0%)

Query: 1   MSNRTPRRFRSRDWFDNPDHIDMTALYLERFMNYGITPEELRSGKPIIGIAQTGSDISPC 60
           M+++  RR RS+DWFDNPDHID+TALYLERFMNYG+TPEELR GKPIIGIAQ+GSD++PC
Sbjct: 1   MTDKPQRRLRSQDWFDNPDHIDLTALYLERFMNYGVTPEELRCGKPIIGIAQSGSDLTPC 60

Query: 61  NRIHLDLVQRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNLSYLGLVETLHGYPID 120
           NR+H+DL +RVRDGIRDAGGIP+EFP HPIFENC+RPTAALDRNL+YLGLVE L+GYP+D
Sbjct: 61  NRVHMDLAKRVRDGIRDAGGIPIEFPTHPIFENCKRPTAALDRNLAYLGLVEILYGYPLD 120

Query: 121 AVVLTTGCDKTTPAGIMAATTVNIPAIVLSGGPMLDGWHENELVGSGTVIWRSRRKLAAG 180
            VVLTTGCDKTTP+ +MAA+TV+IPAIVLSGGPMLDGWHE +LVGSGTVIWR RRKLAAG
Sbjct: 121 GVVLTTGCDKTTPSALMAASTVDIPAIVLSGGPMLDGWHEGDLVGSGTVIWRMRRKLAAG 180

Query: 181 EITEEEFIDRAASSAPSAGHCNTMGTASTMNAVAEALGLSLTGCAAIPAPYRERGQMAYK 240
           EI  EEF+  A  SAPS GHCNTMGTASTMNA+AEALG+SLTGC AIPA YRERGQMAY+
Sbjct: 181 EIDREEFMQAALDSAPSVGHCNTMGTASTMNAMAEALGMSLTGCGAIPAAYRERGQMAYR 240

Query: 241 TGQRIVDLAYDDVKPLDILTKQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEITADDW 300
           TG+R V+L ++D+KP DILT++AF NAI + +A GGSTNAQPH+ AMA+HAGVE+  DDW
Sbjct: 241 TGRRAVELVFEDLKPSDILTREAFLNAIRVNSAIGGSTNAQPHLAAMAKHAGVELYPDDW 300

Query: 301 RA-AYDIPLIVNMQPAGKYLGERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTMSENLQ 359
           +   +DIPL+ N+QPAG YLGER+HRAGG PA++WELL+ G+L G   TVTG+T++ENL+
Sbjct: 301 QVHGFDIPLLANIQPAGAYLGERYHRAGGTPAIMWELLKAGKLDGGCRTVTGRTVAENLE 360

Query: 360 GRETSDREVIFPYHEPLAEKAGFLVLKGNLFDFAIMKSSVIGEEFRKRYLSQPGQEGVFE 419
           GRE +DREVI P+ EPL EKAGFLVLKGNLFDFAIMK SV+ ++FRKRYL +PG+EGVFE
Sbjct: 361 GREPTDREVIRPFDEPLKEKAGFLVLKGNLFDFAIMKMSVVSDDFRKRYLQEPGREGVFE 420

Query: 420 ARAIVFDGSDDYHKRINDPALEIDERCILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGIM 479
            +A+VFDGS+DYHKRINDP L+IDE  ILVIRGAGP+GWPGSAEVVNMQPPDHLLK+GI 
Sbjct: 421 GKAVVFDGSEDYHKRINDPELDIDENTILVIRGAGPLGWPGSAEVVNMQPPDHLLKRGIR 480

Query: 480 SLPTLGDGRQSGTADSPSILNASPESAIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIA 539
           SLPT+GDGRQSGTADSPSILNASPESA GGGL+WLR+GD IRID N GRCD LV +  I 
Sbjct: 481 SLPTIGDGRQSGTADSPSILNASPESAAGGGLAWLRSGDVIRIDFNLGRCDMLVSDEDIE 540

Query: 540 ARKQDGIPAVPATMTPWQEIYRAHASQLDTGGVLEFAVKYQDLAAKLPRHNH 591
            RK DGIPAVPA  TPWQ IYR   +QL  G VLE A  ++ +A  +PRHNH
Sbjct: 541 RRKADGIPAVPADATPWQRIYRKSVTQLSDGAVLEGAADFRQIAKNMPRHNH 592


Lambda     K      H
   0.319    0.136    0.411 

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: 1211
Number of extensions: 50
Number of successful extensions: 2
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: 591
Length of database: 592
Length adjustment: 37
Effective length of query: 554
Effective length of database: 555
Effective search space:   307470
Effective search space used:   307470
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: 53 (25.0 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