Align 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (characterized)
to candidate Ac3H11_3522 Fumarylacetoacetate hydrolase family protein
Query= reanno::HerbieS:HSERO_RS19360 (391 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3522 Length = 405 Score = 432 bits (1112), Expect = e-126 Identities = 217/384 (56%), Positives = 283/384 (73%), Gaps = 5/384 (1%) Query: 11 LPEDHAQATLIGRIWQP--GV-GPVLVRIDADGAYDLTLIAATSSELLELDNPAAAVRSA 67 LP+D Q TL+GR+W P G+ GP +V + +G +DL+ T S LL+ PA A R+A Sbjct: 19 LPDDGLQGTLVGRVWMPLGGIPGPAVVALRPEGVFDLSAHYPTMSTLLDTLAPAEAARTA 78 Query: 68 TNMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVIEEQARGD 127 T + ++++L+ N+ RD + P LLAP DLQ VKA+GVTF AS++ERVIEEQARGD Sbjct: 79 TGQY-LCSVEDLVANSLPGARDATLPRLLAPCDLQVVKAAGVTFAASLIERVIEEQARGD 137 Query: 128 AGKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPDAEIFTKA 187 A +A+ +R + +IG+NL+ + PGSPEA LK +L ++G+WSQYLEVGIGPDAE+FTKA Sbjct: 138 ATRAQGLRSQVIGLIGENLADIRPGSPEAMELKALLQEKGLWSQYLEVGIGPDAEVFTKA 197 Query: 188 QPMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEGRSALLLG 247 ++SVG GD++GI SAWNNPEPE+VLA+NSRG++VGATLGNDVNLRD EGRSALLLG Sbjct: 198 PVLASVGCGDDIGIRSDSAWNNPEPEVVLAVNSRGQIVGATLGNDVNLRDIEGRSALLLG 257 Query: 248 KAKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGTEGFTLKGSSSMSMISRDPLQL 307 KAKDNNASCA+GPFIRLFDA+F ++ VR + +RV G +GF L+G ++M+ ISRDP L Sbjct: 258 KAKDNNASCALGPFIRLFDASFGLEQVRNETVHLRVAGADGFELRGINTMASISRDPTDL 317 Query: 308 VEHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGALVNTVNF 367 V + HQYPDG +LF+GT+FAP +DR PG GFTH++ D+V+I + LG L N V Sbjct: 318 VAQTLAA-HQYPDGFMLFMGTLFAPIEDRDQPGSGFTHKLGDLVSIQSAWLGGLHNRVAH 376 Query: 368 SDQTAPWTFGLTALFKNLADRKLI 391 S+ PW FGL A NLA R L+ Sbjct: 377 SEAAPPWRFGLRAFMANLAQRGLL 400 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: 478 Number of extensions: 22 Number of successful extensions: 4 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: 405 Length adjustment: 31 Effective length of query: 360 Effective length of database: 374 Effective search space: 134640 Effective search space used: 134640 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