Aligments for a candidate for dgoD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for dgoD in Herbaspirillum seropedicae SmR1

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 HSERO_RS16705 HSERO_RS16705 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS16705 HSERO_RS16705
           dihydroxy-acid dehydratase
          Length = 578

 Score =  754 bits (1946), Expect = 0.0
 Identities = 369/571 (64%), Positives = 453/571 (79%), Gaps = 6/571 (1%)

Query: 12  RSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVK 71
           RSQ W+G   RD   +R W+KN+G PHD FDGRPVIGI NT+S++TPCN H R LAE+VK
Sbjct: 11  RSQAWFGRQDRDGFIYRSWVKNRGIPHDQFDGRPVIGICNTYSELTPCNSHFRALAEQVK 70

Query: 72  AGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTT 131
            G+WEAGGFPLE PV S  E   RPTAM+YRNLA++ VEE+IR  P+DG VLL+GCDKTT
Sbjct: 71  IGIWEAGGFPLEFPVMSLGETLLRPTAMLYRNLASMDVEESIRANPLDGVVLLMGCDKTT 130

Query: 132 PSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEA 191
           P+LLMGAAS D+P+I V+GGPML+G +RG  +GSGT +W+ SE V+AG+MTQ EF EAE+
Sbjct: 131 PALLMGAASVDVPTIGVSGGPMLSGKYRGRELGSGTGVWQMSEDVRAGKMTQEEFFEAES 190

Query: 192 SMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD 251
            M RS G C TMGTASTMASM EALG+ L  NAAIP VD+RR V+A+  GRRIVQMV++D
Sbjct: 191 CMHRSHGHCMTMGTASTMASMVEALGVGLPHNAAIPAVDARRNVLARNAGRRIVQMVEED 250

Query: 252 LKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVN 311
           L  S+I+T+QAFENAIR NAAIGGSTNAVIHLLAIAGR+GI L L DWD  G+ +P +++
Sbjct: 251 LVLSKILTRQAFENAIRVNAAIGGSTNAVIHLLAIAGRIGIKLDLKDWDDIGQQLPCLLD 310

Query: 312 LMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDVILP 371
           L PSGK+LME+F+YAGGLP V+++L    ++ K ALT +G+T+W+  +D  NWNE+VI  
Sbjct: 311 LQPSGKFLMEDFYYAGGLPAVIRQL--ESVIDKTALTANGKTLWENCQDAPNWNEEVIRS 368

Query: 372 AEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLD 431
            +K    + GI +L+GNLAP GAV+KPSAA+P LL H+GRAVVFE+ DD   +I+D+NLD
Sbjct: 369 FDKPFKEAAGIAILKGNLAPDGAVIKPSAATPALLKHRGRAVVFENSDDLHKRIDDENLD 428

Query: 432 IDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVLHT 491
           +DE C++V+KNCGPKGYPGMAE GNM LPPK+L+KGI DMVR+SDARMSGTAYGTVVLH 
Sbjct: 429 VDETCVLVLKNCGPKGYPGMAEAGNMPLPPKILRKGITDMVRVSDARMSGTAYGTVVLHV 488

Query: 492 SPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTS---GYAF 548
           SPEAA GGPLAVV+NGD IELDV  R+LHLD+SDEELARR A+WQ   +LP     G+  
Sbjct: 489 SPEAAAGGPLAVVQNGDFIELDVEARKLHLDVSDEELARRRAQWQ-KPELPPQMQRGWVK 547

Query: 549 LHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579
           L+  HV+ A+ GADLDFL G  G  V KD+H
Sbjct: 548 LYVDHVQQANQGADLDFLVGKSGPYVPKDNH 578


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: 1131
Number of extensions: 54
Number of successful extensions: 3
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 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, or view the source code.

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