Alignments for a candidate for dgoD in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for dgoD in Sinorhizobium meliloti 1021

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate SM_b20890 SM_b20890 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Smeli:SM_b20890
          Length = 579

 Score =  904 bits (2336), Expect = 0.0
 Identities = 435/579 (75%), Positives = 507/579 (87%)

Query: 1   MKKKAEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCN 60
           MKKKAEWPRKLRSQEW+GGT ++ I HR W+KNQG P D FDGRP+IGI NTWS++TPCN
Sbjct: 1   MKKKAEWPRKLRSQEWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCN 60

Query: 61  GHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDG 120
            HLR+LAE+VK GV+EAGGFP+E PVFS  E+T RPTAMM+RNLAA+ VEE+IRG P+DG
Sbjct: 61  AHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPVDG 120

Query: 121 CVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGE 180
            VLL GCDKTTPSLLMGAAS D+P+IVV+GGPMLNG +RG+ VGSGT +W+FSEMVK+GE
Sbjct: 121 VVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGE 180

Query: 181 MTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLT 240
           M+  EF++AE  M+RS+G+C TMGTASTMASMAEALGM LSGNAAIP VD+RR+V++QLT
Sbjct: 181 MSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLT 240

Query: 241 GRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWD 300
           GRRIV+MVK+DLKPS+I+TK+AFENAIR N A+GGSTNAV+HLLA+AGRVG+DLSLDDWD
Sbjct: 241 GRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWD 300

Query: 301 RCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKD 360
           R GRDVPTIVNL PSGKYLMEEF+YAGGLPVV+K + E GLLH DA+TVSG+T+W++VK 
Sbjct: 301 RLGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKG 360

Query: 361 VVNWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDD 420
           VVN+NEDVILP EKALT SGGI VLRGNLAP+GAVLKPSAASPHL+ HKGRAVVFE I+D
Sbjct: 361 VVNYNEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIED 420

Query: 421 YKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMS 480
           Y A+IN ++LDIDE CIMV+K CGPKGYPGMAEVGNMGLPPKVLKKGI DM+RISDARMS
Sbjct: 421 YHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARMS 480

Query: 481 GTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHD 540
           GTAYGTV+LHT+PEAA GGPLA+V+NGD+IE+D+PNR LHL +SDEELARR A W     
Sbjct: 481 GTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVK 540

Query: 541 LPTSGYAFLHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579
             T GY  L+ + V  AD GADLDFL G RG+ V +DSH
Sbjct: 541 PLTGGYGGLYIKTVMQADAGADLDFLVGARGSVVERDSH 579


Lambda     K      H
   0.318    0.135    0.408 

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: 1279
Number of extensions: 63
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: 579
Length of database: 579
Length adjustment: 36
Effective length of query: 543
Effective length of database: 543
Effective search space:   294849
Effective search space used:   294849
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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.

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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
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