Alignments for a candidate for xacD in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Halomonas desiderata SP1

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_086511017.1 BZY95_RS16650 dihydroxy-acid dehydratase

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



>NCBI__GCF_002151265.1:WP_086511017.1
          Length = 599

 Score =  461 bits (1187), Expect = e-134
 Identities = 256/551 (46%), Positives = 345/551 (62%), Gaps = 16/551 (2%)

Query: 1   MADSNQTKKPLRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEF-DGRPVIGICNTWSELT 57
           M D   T + LRS+ WF   +  G   L      N GI  +E   G+P+IGIC + S+LT
Sbjct: 1   MTDRKITPEQLRSRWWFDNPESPGTTALCIERYMNYGITLEELAGGKPIIGICQSGSDLT 60

Query: 58  PCNAHFRELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNP 117
           PCN H  EL + VK+G+  AGG+P EFP+  + E   RPTA L RNLA + + E + G P
Sbjct: 61  PCNRHHIELVKRVKEGIRAAGGVPFEFPLHPIHENARRPTAALDRNLAYLGLVEVLHGYP 120

Query: 118 MDGVILLVGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVR 177
           +DGV+L  GCDKTTPA LM AA+ N+PA+ +SGGPMLNG      +GSGT +W++ + + 
Sbjct: 121 LDGVVLTTGCDKTTPASLMAAATVNIPAIVLSGGPMLNGWRGPDRVGSGTIIWELRKRLA 180

Query: 178 AGTMTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLA 237
           AG +   EF    +    S GHC TMGTASTM SM E+LGM LP +A IPA    R ++A
Sbjct: 181 AGDIDYAEFLARATDSAPSVGHCNTMGTASTMNSMAEALGMSLPGSAMIPAPYKERAMVA 240

Query: 238 HLAGRRIVDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLE 297
           +  G RIVDMV +DL    ILTRQAFENAI   +A+GGS+NA +H+ A+A+  GVEL+ +
Sbjct: 241 YDTGARIVDMVWQDLRPSDILTRQAFENAIVVCSALGGSSNAPIHINAIARHSGVELTND 300

Query: 298 DWE-LGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDN 356
           DW+ LG  +P L N+ P+G YL E+FY AGG+PAV+ +L   G LH EALTVNG+TL DN
Sbjct: 301 DWQALGHAIPLLANVMPAGAYLSEEFYRAGGVPAVVNELLGAGKLHGEALTVNGRTLADN 360

Query: 357 VRNAANYDEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKH--------- 407
                  D +VI  +  P   +AG   LKGNL  + A++K S  +A              
Sbjct: 361 CAGRETQDPEVIRRYDNPLVEQAGFLNLKGNLF-DSALMKTSVISADFRARFLSNPDDPN 419

Query: 408 --RGRAVVFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQK 465
              G+ VVF+  E+ HA+IDD +LDIDEH I+V++GAGP G+PG AEV NM  P+ ++++
Sbjct: 420 AFEGKVVVFDGSEDYHARIDDPALDIDEHTILVMRGAGPVGHPGGAEVVNMQPPEALIKR 479

Query: 466 GITDMVRISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDE 525
           GI  +  + DGR SGT+    +L+ +PEAA GG LA ++ GD + +D+    + L V D 
Sbjct: 480 GIESLPCLGDGRQSGTSGSPSILNAAPEAATGGGLALLEDGDRLRVDLNRGEVRLLVDDA 539

Query: 526 ELARRRAAWQA 536
           EL  RR   +A
Sbjct: 540 ELQARRERLEA 550


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: 969
Number of extensions: 55
Number of successful extensions: 3
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: 599
Length adjustment: 37
Effective length of query: 540
Effective length of database: 562
Effective search space:   303480
Effective search space used:   303480
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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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