Align 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (characterized)
to candidate BPHYT_RS28765 BPHYT_RS28765 fumarylacetoacetate hydrolase
Query= reanno::HerbieS:HSERO_RS19360 (391 letters) >FitnessBrowser__BFirm:BPHYT_RS28765 Length = 394 Score = 447 bits (1150), Expect = e-130 Identities = 225/390 (57%), Positives = 285/390 (73%), Gaps = 5/390 (1%) Query: 6 SLQAHLPEDHAQATLIGRIWQP---GVGPVLVRIDADGAYDLTLIAATSSELLELDNPAA 62 S ++LP+D A L+GR+W+ G GP +V + +D++ +A T S+L + + Sbjct: 3 SYSSYLPDDLDGALLVGRVWRQTNSGAGPCVVAVRGGEVFDISRLAPTVSDLFDRQDLVE 62 Query: 63 AVRSATNMTRIATLQELLDNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVIEE 122 VR A + + + +L++ AA R +P+LLAP DLQA+KA GVTF S+LERVIEE Sbjct: 63 LVRQAAGES-LGYVDDLIETTVAAQRKEDQPYLLAPCDLQAIKACGVTFAVSLLERVIEE 121 Query: 123 QARGDAGKAESVRKAITAVIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPDAE 182 QA GD KAE VR AIT +IG +LS + PGS A +LKE L +G WSQY+EVGIGPDAE Sbjct: 122 QAGGDPAKAEEVRAAITRLIGTDLSKIKPGSEAAVKLKEELQRRGAWSQYMEVGIGPDAE 181 Query: 183 IFTKAQPMSSVGLGDEVGIHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEGRS 242 +F+KAQPMSSVGLG ++G+ P S WNNPEPEIVLA+NS+G+VVGATLGNDVNLRD EGRS Sbjct: 182 VFSKAQPMSSVGLGADIGLLPASKWNNPEPEIVLAVNSKGEVVGATLGNDVNLRDIEGRS 241 Query: 243 ALLLGKAKDNNASCAVGPFIRLFDANFSIDDVRRAELTMRVDGT-EGFTLKGSSSMSMIS 301 ALLLGK KDNN SCA+GPFIRLFD F++D +R +++RV+GT +GF L+G S M IS Sbjct: 242 ALLLGKCKDNNGSCAIGPFIRLFDGRFTLDTIRATSVSLRVEGTDDGFVLEGVSHMQEIS 301 Query: 302 RDPLQLVEHAIGPNHQYPDGLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGAL 361 RDP+ LV G +HQYPDG +LFLGTMF+P +DR PG GFTH + D VTIS P LGAL Sbjct: 302 RDPIDLVSQTWGKHHQYPDGFMLFLGTMFSPIKDRDAPGGGFTHHLGDRVTISAPPLGAL 361 Query: 362 VNTVNFSDQTAPWTFGLTALFKNLADRKLI 391 VNTV S + APWTFG+ AL+ NLA+R L+ Sbjct: 362 VNTVRLSTEIAPWTFGVRALYANLAERSLL 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: 461 Number of extensions: 17 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: 394 Length adjustment: 31 Effective length of query: 360 Effective length of database: 363 Effective search space: 130680 Effective search space used: 130680 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