GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS16705
          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:

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:

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:

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:

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