Align 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (characterized)
to candidate Pf6N2E2_1667 Fumarylacetoacetate hydrolase family protein
Query= reanno::HerbieS:HSERO_RS19360 (391 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1667 Length = 393 Score = 459 bits (1182), Expect = e-134 Identities = 234/383 (61%), Positives = 291/383 (75%), Gaps = 4/383 (1%) Query: 11 LPEDHAQATLIGRIWQPG--VGPVLVRIDADGAYDLTLIAATSSELLELDNPAAAVRSAT 68 LP D TLIGR W PG GP + + +DG +DL+ AT S+LLE ++P AAVR T Sbjct: 11 LPVDGVAGTLIGRAWVPGRIAGPSPIALRSDGVFDLSDRFATLSDLLETESPLAAVRQ-T 69 Query: 69 NMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVIEEQARGDA 128 T IA+++ LL N D S+P LL P+DLQ +KA+GVTF ASM+ERVIEEQA GDA Sbjct: 70 PGTFIASVEALLANT-GPDADPSKPSLLPPLDLQVIKAAGVTFAASMIERVIEEQAGGDA 128 Query: 129 GKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPDAEIFTKAQ 188 KAE+VR + +VIGDNL ++VPGS +A RLK +L++QG+WSQYLEVGIGPDAEIFTKA Sbjct: 129 AKAEAVRATVHSVIGDNLRTIVPGSEQAMRLKALLIEQGMWSQYLEVGIGPDAEIFTKAP 188 Query: 189 PMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEGRSALLLGK 248 +++VG G +GIHP S WNNPEPE+VLA+NSRG+++GA+LGNDVNLRDFEGRSALLL K Sbjct: 189 VLAAVGSGSRIGIHPGSQWNNPEPEVVLAVNSRGQILGASLGNDVNLRDFEGRSALLLSK 248 Query: 249 AKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGTEGFTLKGSSSMSMISRDPLQLV 308 AKDNNASCA+GPFIRLFD +FS+DDVR + ++V G +G+ L GSSSM+ ISRDP L Sbjct: 249 AKDNNASCAIGPFIRLFDEHFSLDDVRECVVDLQVHGEDGYRLHGSSSMNQISRDPQDLA 308 Query: 309 EHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGALVNTVNFS 368 + NHQYPDG VLFLGT+FAPT+DR G GFTH+ D+V+IS+P LG+L N V S Sbjct: 309 GQTLNANHQYPDGFVLFLGTLFAPTEDRDHAGSGFTHKRGDVVSISSPLLGSLHNQVTHS 368 Query: 369 DQTAPWTFGLTALFKNLADRKLI 391 APWTFG++AL +NLA R L+ Sbjct: 369 CDAAPWTFGVSALLRNLAARGLL 391 Lambda K H 0.317 0.134 0.387 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: 472 Number of extensions: 17 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: 391 Length of database: 393 Length adjustment: 31 Effective length of query: 360 Effective length of database: 362 Effective search space: 130320 Effective search space used: 130320 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: 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