Alignments for a candidate for xacD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Cupriavidus basilensis 4G11

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate RR42_RS18585 RR42_RS18585 dihydroxy-acid dehydratase

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



>FitnessBrowser__Cup4G11:RR42_RS18585
          Length = 577

 Score =  869 bits (2246), Expect = 0.0
 Identities = 426/579 (73%), Positives = 495/579 (85%), Gaps = 4/579 (0%)

Query: 1   MADSNQTKKPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCN 60
           M D   T    RSQAWFG  DRDGFL+RSW+KN+GIPHD+FDGRPVIGICNT+SELTPCN
Sbjct: 1   MNDDKPTPPTRRSQAWFGRLDRDGFLYRSWLKNRGIPHDQFDGRPVIGICNTYSELTPCN 60

Query: 61  AHFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDG 120
           +HFR LAE VK GV EAGG PLEFPVMSLGET LRPTAMLFRNLASMDVEESIRGNP+DG
Sbjct: 61  SHFRTLAEQVKIGVWEAGGFPLEFPVMSLGETMLRPTAMLFRNLASMDVEESIRGNPIDG 120

Query: 121 VILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGT 180
           V+LL+GCDKTTPAL+MGAASC+LP + VSGGPML+G+FRG  +GSGT VW+MSE+VRAG 
Sbjct: 121 VVLLMGCDKTTPALMMGAASCDLPTIGVSGGPMLSGKFRGGELGSGTDVWKMSEQVRAGQ 180

Query: 181 MTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLA 240
           M+QE+F EAESCM+RS GHCMTMGTASTMASMVE+LGM LP NAAIPAVD RR VLA  +
Sbjct: 181 MSQEDFFEAESCMHRSHGHCMTMGTASTMASMVEALGMSLPGNAAIPAVDGRRNVLARAS 240

Query: 241 GRRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE 300
           GRRIV+MV+++L M KILTR AFENAIR NAAIGGSTNAV+HL+A+A RIGVEL LEDW+
Sbjct: 241 GRRIVEMVKDNLVMSKILTRDAFENAIRVNAAIGGSTNAVIHLLAIAGRIGVELKLEDWD 300

Query: 301 -LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRN 359
            LG  +PCL++LQPSG +LMEDFYYAGGLPAV+++L  + +L ++ALTVNGKTLWDN ++
Sbjct: 301 ALGHELPCLLDLQPSGRHLMEDFYYAGGLPAVIREL--ESVLARDALTVNGKTLWDNCKD 358

Query: 360 AANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEE 419
           A N++ +VI  F  PFK  AGIAVL+GNL P+GAVIKPSAAT +LLKH GRAVVFEN E 
Sbjct: 359 APNWNREVIHAFGAPFKANAGIAVLRGNLCPDGAVIKPSAATPALLKHTGRAVVFENSEH 418

Query: 420 LHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMS 479
           +H ++DDESLD+DE C++VLK  GP+GYPG AE GNMPLP KVL+KGITDMVR+SD RMS
Sbjct: 419 MHQRLDDESLDVDETCVLVLKNCGPRGYPGMAEAGNMPLPPKVLRKGITDMVRVSDARMS 478

Query: 480 GTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEA 539
           GTAYG VVLHV+PEAAAGGPLA V+ GDM+ELDV  R+LHL V + EL RRRAAWQAP  
Sbjct: 479 GTAYGTVVLHVAPEAAAGGPLALVKDGDMVELDVPMRKLHLHVDEAELQRRRAAWQAPAL 538

Query: 540 P-KRGYYKLYVEHVLQADQGADLDFLVGSSGAPVPRDSH 577
           P  RG+ +LYVEHV QA+ GAD+DFLVG SGA VP+D+H
Sbjct: 539 PMARGWTRLYVEHVQQANLGADMDFLVGKSGAAVPKDNH 577


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: 1130
Number of extensions: 43
Number of successful extensions: 5
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: 577
Length adjustment: 36
Effective length of query: 541
Effective length of database: 541
Effective search space:   292681
Effective search space used:   292681
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)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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