Alignments for a candidate for xacD in Azorhizobium caulinodans ORS 571

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Azorhizobium caulinodans ORS 571

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_012172275.1 AZC_RS19330 dihydroxy-acid dehydratase

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



>NCBI__GCF_000010525.1:WP_012172275.1
          Length = 604

 Score =  490 bits (1262), Expect = e-143
 Identities = 272/594 (45%), Positives = 378/594 (63%), Gaps = 27/594 (4%)

Query: 9   KPLRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEFD-GRPVIGICNTWSELTPCNAHFRE 65
           + LRSQ WF   D  G   L+     N G+  +E   G+P+IGI  T S+L+PCN H  +
Sbjct: 13  RKLRSQLWFDNPDNPGMTALYLERYLNFGLTREELQSGKPIIGIAQTGSDLSPCNRHHLD 72

Query: 66  LAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLV 125
           LA+ V++G+  AGG+P EFPV  + ET  RPTA L RNLA + + E + G P+DGV+L  
Sbjct: 73  LAKRVREGIAAAGGIPFEFPVHPIQETGKRPTAALDRNLAYLGLVEVLYGYPLDGVVLTT 132

Query: 126 GCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEE 185
           GCDKTTPA +M AA+ N+PA+ +SGGPMLNG + G+  GSGT VW+   +  AG +  + 
Sbjct: 133 GCDKTTPACIMAAATVNIPAIVLSGGPMLNGWWNGERTGSGTVVWKARAQHAAGEIDYDT 192

Query: 186 FTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIV 245
           F E  +    S GHC TMGTASTM  + E+LGM LP  AAIPA    R  +++  G+RIV
Sbjct: 193 FMEIVASSAPSVGHCNTMGTASTMNGLAEALGMSLPGCAAIPAPYRERGQISYETGKRIV 252

Query: 246 DMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE-LGSN 304
           DMV EDL    ILTR+AFENAIR N+AIGGSTNA +HL A+A+ +GV L+++DW+ +G  
Sbjct: 253 DMVWEDLKPSDILTREAFENAIRVNSAIGGSTNAPIHLNAIARHVGVSLTVDDWQAVGHK 312

Query: 305 VPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYD 364
           +P LVNLQP+GEYL E+F+ AGG+PAV+ +L + G +H+ ALTVNG+++ +N R   ++D
Sbjct: 313 IPLLVNLQPAGEYLGEEFHRAGGIPAVVAELIQAGQIHEGALTVNGRSIGENCRGKFSWD 372

Query: 365 EKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKH-----------RGRAVV 413
             VI  +  P K  AG  VL+GNL  N A++K S  +                  G AVV
Sbjct: 373 RDVIRAYDAPMKADAGFIVLRGNLFEN-AIMKTSVISEEFRARFLSDPKDPNAFEGPAVV 431

Query: 414 FENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRI 473
           FE  E+ H +IDD +L IDEH ++ ++G GP GYPG AEV NM  P  ++++G+  +  I
Sbjct: 432 FEGPEDYHHRIDDPALGIDEHTLLFIRGTGPIGYPGGAEVVNMQPPAALIKRGVNALPCI 491

Query: 474 SDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAA 533
            DGR SGT+    +L+ SPEAAAGG LA ++TGD + +D+E+    + ++DEELA+RRAA
Sbjct: 492 GDGRQSGTSGSPSILNASPEAAAGGGLALLKTGDRVRIDLEKGTADILISDEELAQRRAA 551

Query: 534 WQA------PEAPKRGYYKLYVEHVLQADQGADLDFLVG----SSGAPVPRDSH 577
            +A      P++ +  + ++    V Q D+G  L   V     +    VPRD+H
Sbjct: 552 LEANGGFPIPQS-QTPWQEIQRSMVAQFDEGMVLKPAVKYQRVAQTMGVPRDNH 604


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: 1013
Number of extensions: 62
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: 604
Length adjustment: 37
Effective length of query: 540
Effective length of database: 567
Effective search space:   306180
Effective search space used:   306180
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 24 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
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