Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_012385990.1 BIND_RS15605 dihydroxy-acid dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >NCBI__GCF_000019845.1:WP_012385990.1 Length = 578 Score = 816 bits (2109), Expect = 0.0 Identities = 401/571 (70%), Positives = 476/571 (83%), Gaps = 2/571 (0%) Query: 9 KPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAE 68 KPLRSQAWFG +D+ GF +RS++KN G P D+FDGRPVIGICNTWSELTPCNAHFR +AE Sbjct: 8 KPLRSQAWFGRQDKMGFYYRSFLKNSGFPQDQFDGRPVIGICNTWSELTPCNAHFRTIAE 67 Query: 69 YVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCD 128 +V+ GV EAGG PLEFPV SLGE +RPTAMLFRNLASMDVEE+IR +P+DGV+LL+GCD Sbjct: 68 HVRYGVLEAGGFPLEFPVSSLGEVTMRPTAMLFRNLASMDVEEAIRAHPLDGVVLLMGCD 127 Query: 129 KTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEEFTE 188 KTTPALLMGAAS ++P + VSGGP L G +RG+ IGSGT + MSE++RAG +T EF E Sbjct: 128 KTTPALLMGAASADIPTIGVSGGPQLRGVYRGEIIGSGTNIISMSEQLRAGEITLAEFHE 187 Query: 189 AESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMV 248 AE+ MNRS G CMTMGTASTMASMVE+LG+GLP NAAIPA DARR ++A +AGRRIVDMV Sbjct: 188 AEAAMNRSAGSCMTMGTASTMASMVEALGIGLPENAAIPAADARRNLIARMAGRRIVDMV 247 Query: 249 REDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-ELGSNVPC 307 EDL ILTR AFENAIRT AAIGGSTNAVVHL+A+A RIGVEL+L+D+ +LG + C Sbjct: 248 HEDLKPSDILTRAAFENAIRTLAAIGGSTNAVVHLLAIAGRIGVELTLDDFDQLGRGIHC 307 Query: 308 LVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYDEKV 367 LV+L PSG +LMEDFYYAGGLPAVL+ LGE+GLLH++A TVNG+++W+NV NA ++ +V Sbjct: 308 LVDLMPSGRFLMEDFYYAGGLPAVLRTLGERGLLHRDARTVNGQSIWENVANAPCWNNEV 367 Query: 368 ITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDE 427 IT F + FK AGIA+LKGNLAP+GAVIKPSAA+ L+ H GRAVVFEN+EE+H ++DE Sbjct: 368 ITPFDKAFKADAGIAILKGNLAPDGAVIKPSAASPELMSHTGRAVVFENVEEMHHAVNDE 427 Query: 428 SLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYGAVV 487 +LDID CIMVLK GPKGYPG AEVGNMPLP K+L++G+ DM+RISD RMSGTAYG VV Sbjct: 428 TLDIDASCIMVLKNCGPKGYPGMAEVGNMPLPAKLLRQGVRDMIRISDARMSGTAYGTVV 487 Query: 488 LHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAP-EAPKRGYYK 546 LHV+PEA AGGPLA V+ GD+I LDV R LHL V+ EELA RRA W+ P RGY + Sbjct: 488 LHVAPEATAGGPLALVRNGDLITLDVPARSLHLHVSQEELAARRAVWKPPVPHADRGYAR 547 Query: 547 LYVEHVLQADQGADLDFLVGSSGAPVPRDSH 577 LY++HVLQAD+GAD DFLVG SGAPVPRD+H Sbjct: 548 LYIDHVLQADRGADFDFLVGRSGAPVPRDNH 578 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: 1076 Number of extensions: 43 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: 578 Length adjustment: 36 Effective length of query: 541 Effective length of database: 542 Effective search space: 293222 Effective search space used: 293222 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