Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate GFF233 Psest_0234 dihydroxy-acid dehydratase
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__psRCH2:GFF233 Length = 612 Score = 206 bits (525), Expect = 2e-57 Identities = 167/511 (32%), Positives = 248/511 (48%), Gaps = 67/511 (13%) Query: 120 DGRTQGTTGMFDSLPYRNDASMVMRRLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNI 179 DG G GM SLP R + + ++ + A A++ +++CDK P +MA A + NI Sbjct: 81 DGIAMGHDGMLYSLPSREIIADSVEYMVNA-HCADAIVCISNCDKITPGMLMA-ALRLNI 138 Query: 180 ATVLVPGGA-----TLPAKDGEDNGKVQTIGARFANGELSLQDARRAGCKACASSGGGCQ 234 V V GG T A G D I A + + + + R+ C C G C Sbjct: 139 PVVFVSGGPMEAGKTKLASHGLDLVDAMVIAADESASDEKVAEYERSACPTC----GSCS 194 Query: 235 FLGTAGTSQVVAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQK-------GITT 287 + TA + +AE LGLA+P + + ++ + R + L ++ + Sbjct: 195 GMFTANSMNCLAEALGLALPGNGSTLATHSDREQLFLRAGRTVVELCKRYYGEGDESVLP 254 Query: 288 REILTDKAIENAMTVHAAFGGSTNLLLHIPAIAHQAGCHIPTVDDWIR----INKRVPRL 343 R I + +A ENAMT+ A GGSTN +LH+ A A +A VD +R ++++VP+L Sbjct: 255 RNIASRRAFENAMTLDIAMGGSTNTILHLLAAAQEA-----EVDFDLRAIDALSRKVPQL 309 Query: 344 VSVLPNGPVYHPTVNAFMAGGVPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWEHSERR 403 V PN YH + AGG+ ++ L GLLH DV TV TL E + W+ ++ + Sbjct: 310 CKVAPNIQKYH-MEDVHRAGGIFSILGELARGGLLHTDVPTVHSRTLAEGIAQWDITQTQ 368 Query: 404 QR------------------FKQLL----LDQEQINADEVIMSPQQAKARGLTSTITFPV 441 F Q LD ++ N I S + A ++ + + Sbjct: 369 DEAVHTFFKAGPAGIPTQTAFSQSTRWDSLDDDRENG--CIRSVEHAYSQEGGLAVLY-- 424 Query: 442 GNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAGDILVIIG 501 GNIA +G V+K+ +D S I+ +G AK+Y S+ SA+ I D++KAGDI++I Sbjct: 425 GNIALDGCVVKTAGVDES------IHVFEGTAKIYESQDSAVKGILADEVKAGDIVIIRY 478 Query: 502 VGP-SGTGMEETYQVTSALKHLSYGKHVSLITDARFSGVSTGACIGHVGPEALAGGPIGK 560 GP G GM+E TS LK GK +L+TD RFSG ++G IGH PEA AGG IG Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538 Query: 561 LRTGDLIEIKIDCRELHGEVNFLGTRSDEQL 591 +R GD + I I R + +V SDE+L Sbjct: 539 VRDGDKVLIDIPNRSIQLQV------SDEEL 563 Lambda K H 0.317 0.135 0.400 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: 909 Number of extensions: 52 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 655 Length of database: 612 Length adjustment: 38 Effective length of query: 617 Effective length of database: 574 Effective search space: 354158 Effective search space used: 354158 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: 54 (25.4 bits)
This GapMind analysis is from Sep 17 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