Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_008410930.1 DESHY_RS05080 dihydroxy-acid dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >NCBI__GCF_000315365.1:WP_008410930.1 Length = 552 Score = 363 bits (933), Expect = e-105 Identities = 222/546 (40%), Positives = 321/546 (58%), Gaps = 20/546 (3%) Query: 27 HRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAEYVKKGVHEAGGLPLEFPV 86 HRS +K G+ +E RP+IG+ N+++E+ P + H R++AE VK GV AGG PLEFPV Sbjct: 15 HRSLLKALGLLDEELS-RPLIGVVNSFNEVVPGHIHLRDIAEAVKAGVRMAGGTPLEFPV 73 Query: 87 MS------LGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCDKTTPALLMGAAS 140 ++ +G +R ++ R + + +E + +P DG++L+ CDK P +LM AA Sbjct: 74 IAVCDGIAMGHPGMR-YSLASREIIADSIEIMAQAHPFDGLVLIPNCDKVVPGMLMAAAR 132 Query: 141 CNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFTEAESCMNRSRGHC 200 N+PA+ VSGGPML GRF+ +++ S T +++ V+AG +T EE E E G C Sbjct: 133 LNIPAVVVSGGPMLAGRFQNQDV-SVTQMFEAVGAVQAGRLTPEELAELEENACPGCGSC 191 Query: 201 MTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMVREDLTMDKILTR 260 M TA++M + E+LGM LP N IPAV A R+ LA AG R V +VRE+L ILT Sbjct: 192 AGMFTANSMNCLTEALGMALPGNGTIPAVSAARRRLAKAAGLRAVALVRENLRPRDILTM 251 Query: 261 QAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLE-DWELGSNVPCLVNLQPSGEYLM 319 F N + + A+G STN V+HL A+A+ G+EL+L+ E+ P L L P+G + + Sbjct: 252 ANFRNGLAVDMALGCSTNTVLHLPAIAREAGIELNLDLINEISERTPHLCKLSPAGRHHI 311 Query: 320 EDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEKVITTFAEPFKPKA 379 +D AGG+ AV+K+L GL++ TV+G T+ + A D +VI + EP+ Sbjct: 312 QDLDAAGGIQAVMKELLNNGLINPNIKTVSGLTVGQLLEQAKVKDRQVIRSVQEPYSSTG 371 Query: 380 GIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDESLDIDEHCIMVL 439 G+AVL+GNLAPNGAV+K +A +L+H G A VF+ E I + I ++V+ Sbjct: 372 GLAVLRGNLAPNGAVVKRAAVAPEMLRHTGPARVFDGEEAAITAI--MAGQIKPGDVVVI 429 Query: 440 KGAGPKGYPGFAEVGNMPLPKKVLQ-KGI-TDMVRISDGRMSGTAYGAVVLHVSPEAAAG 497 + GPKG PG E M P VL G+ ++ ++DGR SG + GA + H+SPEAA G Sbjct: 430 RYEGPKGGPGMRE---MLAPTSVLAGMGLDKEVALLTDGRFSGASRGASIGHISPEAAEG 486 Query: 498 GPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAPK--RGYYKLYVEHVLQA 555 G +A +Q GDMIE+D+ RL + + + +R AWQ P APK GY Y + V A Sbjct: 487 GLIALLQDGDMIEIDIPNYRLAAKLDETVIKQRLEAWQ-PPAPKVTEGYLARYAKQVSSA 545 Query: 556 DQGADL 561 QGA L Sbjct: 546 GQGAVL 551 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: 787 Number of extensions: 32 Number of successful extensions: 6 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: 552 Length adjustment: 36 Effective length of query: 541 Effective length of database: 516 Effective search space: 279156 Effective search space used: 279156 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.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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:
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