Alignments for a candidate for dgoD in Herbaspirillum seropedicae SmR1

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_RS05205 HSERO_RS05205 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__HerbieS:HSERO_RS05205
          Length = 585

 Score =  752 bits (1941), Expect = 0.0
 Identities = 375/584 (64%), Positives = 454/584 (77%), Gaps = 11/584 (1%)

Query: 4   KAEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHL 63
           K +  R LRS  W+G   ++   +R W+KNQG P   F G+PVIGI NTWS++TPCN H 
Sbjct: 5   KKDKSRTLRSAGWFGTADKNGFMYRSWMKNQGIPDHEFQGKPVIGICNTWSELTPCNAHF 64

Query: 64  RELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVL 123
           R++AE V+ G+ EAGGFP+E PVFS  E+  RPTAM+ RNLA++ VEE+IRG P+D  VL
Sbjct: 65  RKIAEHVRRGIIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEESIRGNPIDAVVL 124

Query: 124 LVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQ 183
           L GCDKTTP+LLMGAASCD+P+IVVTGGPMLNG  +G  +GSGT +W+ SE VKAGE+T 
Sbjct: 125 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAGEITI 184

Query: 184 AEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRR 243
            +F+ AEA MSRS+GTCNTMGTASTMA MAE+LG++L  NAAIP VD+RR V+A L+G R
Sbjct: 185 HDFMAAEAGMSRSAGTCNTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHLSGMR 244

Query: 244 IVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCG 303
           IV MV + L  S+I+T++AFENAIRTNAAIGGSTNAVIHL AIAGR+G+DL L+DW R G
Sbjct: 245 IVDMVWEGLTLSKILTRKAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLELEDWTRIG 304

Query: 304 RDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLL-HKDALTVSGETVWDEVKDVV 362
           R  PTIV+L PSG+YLMEEF+YAGGLP VL+RLGEA LL HKDALTV+G+T+WD VKD  
Sbjct: 305 RGTPTIVDLQPSGRYLMEEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQTMWDNVKDAP 364

Query: 363 NWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYK 422
            +N++V+ P  K L   GGI +LRGNLAP+GAVLKPSAA+P L+ H+GRAVVFED + YK
Sbjct: 365 IYNDEVVRPLAKPLIEDGGICILRGNLAPRGAVLKPSAATPELMKHRGRAVVFEDFNHYK 424

Query: 423 AKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGT 482
            +IND +LD+D +C++VMKN GPKGYPGMAEVGNMGLPPKVL  G+ DMVRISDARMSGT
Sbjct: 425 ERINDPDLDVDASCVLVMKNVGPKGYPGMAEVGNMGLPPKVLATGVKDMVRISDARMSGT 484

Query: 483 AYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARR-------LAEW 535
           AYGTV+LH +PEAA GGPL +V++GD IELD    +L LDIS+EE+ RR       LAE 
Sbjct: 485 AYGTVILHVAPEAAAGGPLGIVQDGDFIELDAYAGKLQLDISEEEMKRRLEARAKVLAER 544

Query: 536 QPNHDLPTSGYAFLHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579
           +P       GY  L+   V  AD G D DFL GCRG AV K SH
Sbjct: 545 KPE---MVGGYQSLYVDRVLQADEGCDFDFLVGCRGAAVPKHSH 585


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: 1155
Number of extensions: 61
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: 585
Length adjustment: 36
Effective length of query: 543
Effective length of database: 549
Effective search space:   298107
Effective search space used:   298107
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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Protein sequences (fasta format)
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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