Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_012334621.1 M446_RS23595 dihydroxy-acid dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >NCBI__GCF_000019365.1:WP_012334621.1 Length = 603 Score = 483 bits (1243), Expect = e-141 Identities = 271/592 (45%), Positives = 371/592 (62%), Gaps = 27/592 (4%) Query: 11 LRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEFD-GRPVIGICNTWSELTPCNAHFRELA 67 LRS+ WF D G L+ N G+ E G+P+IGI T S+L+PCN H ELA Sbjct: 14 LRSRLWFDNPDNPGMTALYLERYLNYGLTLAELQAGKPLIGIAQTGSDLSPCNRHHMELA 73 Query: 68 EYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGC 127 + V+ G+ AGG+ EFP + ET RPTA L RNLA + + E + G P+DGV+LL GC Sbjct: 74 KRVRDGITAAGGVAFEFPCHPIQETGKRPTAALDRNLAYLSLVEVLYGYPLDGVVLLTGC 133 Query: 128 DKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFT 187 DKT PA LM AA+ N+PA++++ GPMLNG RG+ GSGT VW+ E AG + ++F Sbjct: 134 DKTMPACLMAAATVNIPAISLNVGPMLNGWSRGERTGSGTVVWKARERHAAGDIDYQQFL 193 Query: 188 EAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDM 247 + + S GHC TMGTASTM ++ E+LGM LP +AAIPA R A+ G+RIV+M Sbjct: 194 DIVASSAPSTGHCNTMGTASTMNALAEALGMALPGSAAIPAPYRERGQAAYATGQRIVEM 253 Query: 248 VREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE-LGSNVP 306 V EDL ILTR+AFENAI N AIGGSTNA +H+ A+AK IGV LS +DWE +G ++P Sbjct: 254 VWEDLKPSDILTREAFENAIVANTAIGGSTNAPIHINAIAKLIGVPLSCDDWERVGYDIP 313 Query: 307 CLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEK 366 LVN+QP+G YL E++Y AGGLPAVL +L E G +H +ALT NG+T+ +N R A +D + Sbjct: 314 LLVNMQPAGAYLGEEYYRAGGLPAVLAELIEAGKIHADALTCNGRTVGENCREARTWDRE 373 Query: 367 VITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKH-----------RGRAVVFE 415 VI ++EP + +AG LKG L + A++K S + GR VVF+ Sbjct: 374 VIKPYSEPLRERAGFLNLKGTLF-DSAIMKTSVISREFYDRYLSNPGDPYAFEGRVVVFD 432 Query: 416 NIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISD 475 E+ H +IDD +LDIDE+ +++++GAGP GYPG AEV NM P ++++G+ + I D Sbjct: 433 GPEDYHHRIDDPALDIDENTVLIMRGAGPIGYPGAAEVVNMQPPGALIRRGVLSLPCIGD 492 Query: 476 GRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRA--- 532 GR SGT+ +L+ SPEAAAGG LA +Q GD + +D+ RR + + DEELARRR Sbjct: 493 GRQSGTSGTPSILNASPEAAAGGGLALLQNGDRVRIDLNTRRADILLPDEELARRREDLA 552 Query: 533 -----AWQAPEAPKRGYYKLYVEHVLQAD--QGADLDFLVGSSGAPVPRDSH 577 + A + P + + VE + + +G+D V + P PRD+H Sbjct: 553 ARGGYPFPASQTPWQAIQRAMVEQLSEGMILRGSDAFQKVAQTMGP-PRDNH 603 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: 962 Number of extensions: 60 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: 603 Length adjustment: 37 Effective length of query: 540 Effective length of database: 566 Effective search space: 305640 Effective search space used: 305640 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