Align D-galactonate dehydratase family member Dd703_0947; EC 4.2.1.-; D-gluconate dehydratase; EC 4.2.1.39; D-mannonate dehydratase; EC 4.2.1.8 (uncharacterized)
to candidate Pf1N1B4_3383 Mandelate racemase (EC 5.1.2.2)
Query= curated2:C6CBG9 (417 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3383 Length = 391 Score = 131 bits (330), Expect = 3e-35 Identities = 114/379 (30%), Positives = 176/379 (46%), Gaps = 58/379 (15%) Query: 23 VVKVETNEPGLYGLGCATFTQRIFAVKSAIDEYMAPFLIGKDPTRIEDIWQSAAVSGY-W 81 VV+VET + GL G+G R+ K ID Y+AP IG+DP E IWQ + W Sbjct: 49 VVEVET-DTGLVGIGNCALAPRV--AKEIIDTYLAPIAIGEDPFDNEYIWQKMYRQSHAW 105 Query: 82 RNGPIMNNALSGVDMALWDIKGKLAGMPVYELLGGKCRDGIPLYCHTDGGDEVEVEDNIR 141 I A+S +D+A+WDI GK PV++LLGG+ ++ I Y ++ DN+ Sbjct: 106 GRKGIGMAAISAIDIAIWDIMGKAVNKPVFKLLGGRTKEKIWTY-----ASKLYANDNLD 160 Query: 142 ARMEEGYQYVR---CQMGMYGGAGTDDLKLIATQLARAKNIQPKRSPRSKT-PGIYFDPE 197 +EE Y+ + M G G D KNI+ R+ R P I E Sbjct: 161 LFLEEAQGYLNQGFTALKMRFGYGPKD-----GPAGMRKNIEQVRALRELAGPDIDIMLE 215 Query: 198 AYAKSVPRLFEHLRNKLGFGIEFIHDVHERVTPVTAIQLAKTLEPYQLFYLEDPVAPENI 257 Y +G+ +E+ A ++ L ++ +LE+PV ++I Sbjct: 216 CY--------------MGWTLEY------------ARRMLPKLAEFEPRWLEEPVIADDI 249 Query: 258 DWLRMLRQQSSTPISMGELFVNINEWKPLIDNKLIDYIRCHVSTIGGITPAKKLAVYSEL 317 + L++ PIS GE +K L++ + ID I+ + +GGIT A+K + Sbjct: 250 EGYIELKKMGIMPISGGEHEFTSYGFKDLLERRAIDVIQYDTNRVGGITAARK------I 303 Query: 318 NGVRTAWHGPGDISPVGVCANMHLDMSSPNFGIQEYTPM------NDALREVFPGCPEID 371 N + AW P I G N HL MS+ + E+ P+ N+ VF G P+ Sbjct: 304 NALAEAWSVP-VIPHAGQMHNYHLTMSTTASPMAEFFPVFDVEVGNELFYYVFKGEPQPV 362 Query: 372 QGYAYVND-KPGLGIDINE 389 +GY ++D KPGLG++I++ Sbjct: 363 KGYIQLDDNKPGLGLEISD 381 Lambda K H 0.319 0.139 0.430 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: 453 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 391 Length adjustment: 31 Effective length of query: 386 Effective length of database: 360 Effective search space: 138960 Effective search space used: 138960 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 (21.7 bits) S2: 50 (23.9 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