Align 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (characterized)
to candidate PP_2836 PP_2836 putative 2-keto-3-deoxyxylonate dehydratase
Query= reanno::HerbieS:HSERO_RS19360 (391 letters) >FitnessBrowser__Putida:PP_2836 Length = 405 Score = 454 bits (1169), Expect = e-132 Identities = 221/371 (59%), Positives = 277/371 (74%) Query: 21 IGRIWQPGVGPVLVRIDADGAYDLTLIAATSSELLELDNPAAAVRSATNMTRIATLQELL 80 +GR+W P GP +V + A YD++ AT S LLE+D+P A +R+ + L LL Sbjct: 26 VGRVWLPEQGPAVVLVKAGAVYDISTHVATVSALLEVDDPVAYLRALPLAEPLIALPALL 85 Query: 81 DNADAAGRDTSRPWLLAPIDLQAVKASGVTFVASMLERVIEEQARGDAGKAESVRKAITA 140 N+D R +PWLLAPIDLQAVKA+GVTF S+LERV+EEQA+GD KA+++R + + Sbjct: 86 GNSDPTRRTPHQPWLLAPIDLQAVKAAGVTFATSLLERVVEEQAKGDPAKADAIRDTLAS 145 Query: 141 VIGDNLSSVVPGSPEAARLKEVLLDQGVWSQYLEVGIGPDAEIFTKAQPMSSVGLGDEVG 200 IG +LS +VPGS +A L++VL++QG+WSQYLEVGIGPDAE+FTKAQP+S+VG G ++G Sbjct: 146 RIGADLSQIVPGSAQAEALRKVLVEQGLWSQYLEVGIGPDAEVFTKAQPLSAVGHGADIG 205 Query: 201 IHPKSAWNNPEPEIVLAINSRGKVVGATLGNDVNLRDFEGRSALLLGKAKDNNASCAVGP 260 IHPKS+WNNPEPE+VLA++S G + GA LGNDVNLRDFEGRSALLL KAKDNNAS A+GP Sbjct: 206 IHPKSSWNNPEPEVVLAVSSNGSIKGAMLGNDVNLRDFEGRSALLLSKAKDNNASTALGP 265 Query: 261 FIRLFDANFSIDDVRRAELTMRVDGTEGFTLKGSSSMSMISRDPLQLVEHAIGPNHQYPD 320 +RLFD +F +DDVR AE+ +RV+G +GF L G SSM ISRDP LV+ + NHQYPD Sbjct: 266 LLRLFDESFGLDDVRAAEVDLRVEGEDGFILSGRSSMRQISRDPQDLVQQTLNENHQYPD 325 Query: 321 GLVLFLGTMFAPTQDRFGPGQGFTHQVADIVTISTPKLGALVNTVNFSDQTAPWTFGLTA 380 GLVLFLGT+FAP QDR PG GFTH+ D+V+IS P+LG L N V SD W FGL A Sbjct: 326 GLVLFLGTLFAPKQDRDQPGNGFTHKPGDVVSISNPQLGTLCNRVTTSDLAPQWDFGLRA 385 Query: 381 LFKNLADRKLI 391 L NL R L+ Sbjct: 386 LIDNLGRRGLL 396 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: 456 Number of extensions: 11 Number of successful extensions: 1 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