Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate WP_086510675.1 BZY95_RS14785 mandelate racemase/muconate lactonizing enzyme family protein
Query= BRENDA::A9CEQ8 (378 letters) >NCBI__GCF_002151265.1:WP_086510675.1 Length = 378 Score = 560 bits (1443), Expect = e-164 Identities = 271/375 (72%), Positives = 312/375 (83%) Query: 1 MKITAVRTHLLEHRLDTPFESASMRFDRRAHVLVEIECDDGTVGWGECLGPARPNAAVVQ 60 MKI AV TH+L+H LDT FESASM F RR H LVEI CDDGT+GWGECLGPA+PNAAVV+ Sbjct: 1 MKIAAVHTHILDHVLDTTFESASMYFARRQHCLVEIVCDDGTIGWGECLGPAQPNAAVVK 60 Query: 61 AYSGWLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYGASISML 120 AY LIGQDP QTE++W LYN LRDQGQRGL++TALSGIDIALWDIKGK +G IS L Sbjct: 61 AYRAALIGQDPLQTERLWLELYNRLRDQGQRGLTVTALSGIDIALWDIKGKRFGVPISTL 120 Query: 121 LGGRWRESVRAYATGSFKRDNVDRVSDNASEMAERRAEGFHACKIKIGFGVEEDLRVIAA 180 LGGR+R+SVRAYATGSF+R VDRV DNA E+A R EGFHA KIKIGFGV+EDLRVI A Sbjct: 121 LGGRFRDSVRAYATGSFRRAGVDRVEDNAREVAGYRREGFHAVKIKIGFGVDEDLRVIEA 180 Query: 181 VREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPI 240 VRE+IGPDMRLMIDANHGY EA+ +G RAA FGIDWFEEPV+PE + AY VRA QPI Sbjct: 181 VRESIGPDMRLMIDANHGYDYLEAVEVGRRAAKFGIDWFEEPVLPEHVSAYRAVRADQPI 240 Query: 241 PVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGT 300 PVAGGETWHGRY M + L+ AVDI+QPD+CG GGF+EI+++A +A LHGVR+VPHVWGT Sbjct: 241 PVAGGETWHGRYAMHEPLATRAVDIIQPDICGVGGFTEIRRVADMAALHGVRLVPHVWGT 300 Query: 301 GVQIAAALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPG 360 V +AA+LQFMAA+ P+P R +PIEPI+EFDRT NPFRQAV+ P+E GVV IPDGPG Sbjct: 301 AVCLAASLQFMAALLPNPPRRDPIEPILEFDRTENPFRQAVVTTPIEHDRGVVAIPDGPG 360 Query: 361 LGIEINRDALTEFRM 375 LGIEI+R+AL F + Sbjct: 361 LGIEIDREALARFAL 375 Lambda K H 0.321 0.138 0.431 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: 603 Number of extensions: 18 Number of successful extensions: 1 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: 378 Length of database: 378 Length adjustment: 30 Effective length of query: 348 Effective length of database: 348 Effective search space: 121104 Effective search space used: 121104 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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