Alignments for a candidate for xacD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Herbaspirillum seropedicae SmR1

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate HSERO_RS16705 HSERO_RS16705 dihydroxy-acid dehydratase

Query= reanno::BFirm:BPHYT_RS19730
         (577 letters)



>FitnessBrowser__HerbieS:HSERO_RS16705
          Length = 578

 Score =  890 bits (2300), Expect = 0.0
 Identities = 434/579 (74%), Positives = 509/579 (87%), Gaps = 7/579 (1%)

Query: 4   SNQTKKPLR-SQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAH 62
           ++ TKK  R SQAWFG +DRDGF++RSW+KN+GIPHD+FDGRPVIGICNT+SELTPCN+H
Sbjct: 2   TDDTKKSTRRSQAWFGRQDRDGFIYRSWVKNRGIPHDQFDGRPVIGICNTYSELTPCNSH 61

Query: 63  FRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVI 122
           FR LAE VK G+ EAGG PLEFPVMSLGET LRPTAML+RNLASMDVEESIR NP+DGV+
Sbjct: 62  FRALAEQVKIGIWEAGGFPLEFPVMSLGETLLRPTAMLYRNLASMDVEESIRANPLDGVV 121

Query: 123 LLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMT 182
           LL+GCDKTTPALLMGAAS ++P + VSGGPML+G++RG+ +GSGTGVWQMSE+VRAG MT
Sbjct: 122 LLMGCDKTTPALLMGAASVDVPTIGVSGGPMLSGKYRGRELGSGTGVWQMSEDVRAGKMT 181

Query: 183 QEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGR 242
           QEEF EAESCM+RS GHCMTMGTASTMASMVE+LG+GLPHNAAIPAVDARR VLA  AGR
Sbjct: 182 QEEFFEAESCMHRSHGHCMTMGTASTMASMVEALGVGLPHNAAIPAVDARRNVLARNAGR 241

Query: 243 RIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-EL 301
           RIV MV EDL + KILTRQAFENAIR NAAIGGSTNAV+HL+A+A RIG++L L+DW ++
Sbjct: 242 RIVQMVEEDLVLSKILTRQAFENAIRVNAAIGGSTNAVIHLLAIAGRIGIKLDLKDWDDI 301

Query: 302 GSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAA 361
           G  +PCL++LQPSG++LMEDFYYAGGLPAV++QL  + ++ K ALT NGKTLW+N ++A 
Sbjct: 302 GQQLPCLLDLQPSGKFLMEDFYYAGGLPAVIRQL--ESVIDKTALTANGKTLWENCQDAP 359

Query: 362 NYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELH 421
           N++E+VI +F +PFK  AGIA+LKGNLAP+GAVIKPSAAT +LLKHRGRAVVFEN ++LH
Sbjct: 360 NWNEEVIRSFDKPFKEAAGIAILKGNLAPDGAVIKPSAATPALLKHRGRAVVFENSDDLH 419

Query: 422 AKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGT 481
            +IDDE+LD+DE C++VLK  GPKGYPG AE GNMPLP K+L+KGITDMVR+SD RMSGT
Sbjct: 420 KRIDDENLDVDETCVLVLKNCGPKGYPGMAEAGNMPLPPKILRKGITDMVRVSDARMSGT 479

Query: 482 AYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAP- 540
           AYG VVLHVSPEAAAGGPLA VQ GD IELDVE R+LHLDV+DEELARRRA WQ PE P 
Sbjct: 480 AYGTVVLHVSPEAAAGGPLAVVQNGDFIELDVEARKLHLDVSDEELARRRAQWQKPELPP 539

Query: 541 --KRGYYKLYVEHVLQADQGADLDFLVGSSGAPVPRDSH 577
             +RG+ KLYV+HV QA+QGADLDFLVG SG  VP+D+H
Sbjct: 540 QMQRGWVKLYVDHVQQANQGADLDFLVGKSGPYVPKDNH 578


Lambda     K      H
   0.318    0.135    0.401 

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: 1118
Number of extensions: 34
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: 577
Length of database: 578
Length adjustment: 36
Effective length of query: 541
Effective length of database: 542
Effective search space:   293222
Effective search space used:   293222
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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