Alignments for a candidate for xacD in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Cereibacter sphaeroides ATCC 17029

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_011841248.1 RSPH17029_RS09155 dihydroxy-acid dehydratase family protein

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



>NCBI__GCF_000015985.1:WP_011841248.1
          Length = 593

 Score =  476 bits (1224), Expect = e-138
 Identities = 273/591 (46%), Positives = 364/591 (61%), Gaps = 23/591 (3%)

Query: 7   TKKPLRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEFDG-RPVIGICNTWSELTPCNAHF 63
           T +  RSQAWF   D  G   L+    +NQG    E  G RP+IGI  + S+L PCN   
Sbjct: 6   TGRRFRSQAWFDNPDNPGMTALYVERYQNQGFTRRELQGDRPIIGIAQSGSDLAPCNKIH 65

Query: 64  RELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVIL 123
             LAE VK G+ +AGG+P+EFPV  + ET  RPTA L RNLA + + E + G P+DGV+L
Sbjct: 66  LFLAERVKAGIRDAGGVPMEFPVHPIQETGRRPTAALDRNLAYLGLVEVLHGYPIDGVVL 125

Query: 124 LVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQ 183
             GCDKTTPA LM AA+ +LP++ +SG PML+G + GK  GSGT +W+    +  G +  
Sbjct: 126 TTGCDKTTPAQLMAAATVDLPSIVLSGWPMLDGWWEGKLAGSGTIIWESRRLLAEGEIDY 185

Query: 184 EEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRR 243
            EF E       S GHC TMGTAST+ ++ E+LGM LP  +AIPA    R  +A+  GRR
Sbjct: 186 PEFMERACASAPSLGHCNTMGTASTLNALAEALGMSLPGCSAIPAPFRERMNMAYATGRR 245

Query: 244 IVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE-LG 302
           IV+MV  DL    ILTRQAFENAIR N+AIGGSTNA  HL A+A+  GVEL++EDW+ +G
Sbjct: 246 IVEMVLADLKPSDILTRQAFENAIRVNSAIGGSTNAPPHLQAIARHAGVELAVEDWQTVG 305

Query: 303 SNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAAN 362
            ++P LVN+QP+GEYL E F+ AGG+PAV+ +L   GLLH EALTV G+++  N+    +
Sbjct: 306 FDLPLLVNMQPAGEYLGESFFRAGGVPAVMGELLAAGLLHAEALTVTGESIGHNLAGERS 365

Query: 363 YDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLK-----------HRGRA 411
            D +VI +  +P + KAG  VL+GNL  + A++K S  +A               H  RA
Sbjct: 366 RDRRVIRSVEDPLREKAGFLVLRGNLF-DSALMKTSVISAEFRHRFLAQPGREGIHEARA 424

Query: 412 VVFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMV 471
           VVFE  E+ HA+I+D  L IDE  I+ ++G G  GYPG AEV NM  P  +L++G+T + 
Sbjct: 425 VVFEGPEDYHARINDPDLGIDETTILFIRGVGCVGYPGSAEVVNMQPPDGLLREGVTHLP 484

Query: 472 RISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRR 531
            + DGR SGT+    +L+ SPEAA GG LA ++TGD + LD+   RL   V + E   RR
Sbjct: 485 TVGDGRQSGTSESPSILNASPEAAVGGGLALLRTGDRVRLDLNACRLDALVDEAEWEARR 544

Query: 532 AAWQAP----EAPKRGYYKLYVEHVLQADQGA-DLDFLVGSSGAPVPRDSH 577
           AAW  P    + P +  Y+  V  +  AD G  +L          +PRD+H
Sbjct: 545 AAWTPPVLHHQTPWQEIYRRLVGQL--ADGGCLELATAYHRVARDLPRDNH 593


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: 901
Number of extensions: 44
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: 593
Length adjustment: 37
Effective length of query: 540
Effective length of database: 556
Effective search space:   300240
Effective search space used:   300240
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 Apr 10 2024. 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