Alignments for a candidate for dgoD in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for dgoD in Rhizobium leguminosarum 3841

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 WP_011649015.1 RL_RS34110 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>NCBI__GCF_000009265.1:WP_011649015.1
          Length = 578

 Score =  511 bits (1317), Expect = e-149
 Identities = 257/558 (46%), Positives = 363/558 (65%), Gaps = 3/558 (0%)

Query: 10  KLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEK 69
           +LRS  W     +    HR      GY  + + G+P+I ++NTWSD  PC+ H RE AE 
Sbjct: 9   QLRSARWMLPDDQRSFGHRSRTMQMGYAPEDWQGKPIIAVINTWSDAQPCHMHFRERAEW 68

Query: 70  VKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDK 129
           VK G+ ++GGFP+E+P  S SEN  +PT M+YRN+ A+  EE +R  P+DG VL+ GCDK
Sbjct: 69  VKRGILQSGGFPMELPALSLSENFVKPTTMLYRNMLAMETEELLRSHPVDGAVLMGGCDK 128

Query: 130 TTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEA 189
           TTP L+MGA S  +P I +  GPML G + G+ +GSGT  +K+ +  +AG +TQ E+   
Sbjct: 129 TTPGLVMGAVSMGIPFIYLPAGPMLRGNYAGKTLGSGTDGFKYWDERRAGTITQEEWQGI 188

Query: 190 EASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVK 249
           E  ++RS G C TMGTASTM ++AEA+G+ L G ++IP  D+  + M+   GRRIV MV 
Sbjct: 189 EGGIARSYGHCMTMGTASTMTAIAEAMGLTLPGASSIPAADANHQRMSAACGRRIVDMVW 248

Query: 250 DDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTI 309
           +DL P +I+T  A +NA+    A G STNA+IHL+A+A R G+ L LDD DR GR  P +
Sbjct: 249 EDLTPEQIITSAAVDNAVTVAMATGCSTNAIIHLIAMARRAGVPLELDDLDRIGRTTPVL 308

Query: 310 VNLMPSGK-YLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDV 368
            N+ PSG  YLME+FFYAGGL  ++K+LG+   L   A+TV+G+ + D +  V  +N+DV
Sbjct: 309 ANIRPSGSTYLMEDFFYAGGLRALMKQLGDK--LDPTAITVTGKPLVDGLDQVKIYNDDV 366

Query: 369 ILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDD 428
           I P    +   G + VL+GNL P GAV+KP+A  P    H+G A+V +   + K  I+D 
Sbjct: 367 IRPLSNPVYHEGSLAVLKGNLCPDGAVIKPAACDPKFHRHRGPALVADSYAEMKKIIDDP 426

Query: 429 NLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVV 488
           +  +  + ++V++N GP+G PGM E G + +P  +LK G+ DMVRISDARMSGT++G  V
Sbjct: 427 DYPLTPDTVLVLRNAGPQGGPGMPEWGMIPMPKALLKLGLRDMVRISDARMSGTSFGACV 486

Query: 489 LHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAF 548
           LH +PE+ VGGPLA+++ GDM+ELD+P R L++ +++EE+  R A W         GY F
Sbjct: 487 LHVAPESYVGGPLALLRTGDMVELDIPARSLNMLVAEEEITARRAAWVAPTRHYERGYGF 546

Query: 549 LHQQHVEGADTGADLDFL 566
           +   H+E AD G D DFL
Sbjct: 547 MFSGHIEQADKGCDFDFL 564


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: 998
Number of extensions: 51
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: 579
Length of database: 578
Length adjustment: 36
Effective length of query: 543
Effective length of database: 542
Effective search space:   294306
Effective search space used:   294306
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 24 2021. The underlying query database was built on Sep 17 2021.

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

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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