Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate Ac3H11_3953 D-galactarate dehydratase (EC 4.2.1.42)
Query= curated2:O34673 (497 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3953 Length = 525 Score = 239 bits (609), Expect = 2e-67 Identities = 170/497 (34%), Positives = 256/497 (51%), Gaps = 27/497 (5%) Query: 5 IKIHKQDNVLLALRD--IQKGERLH--AYGVSIEVKDDIKRGHKIALQSIKENDSIVKYG 60 I++H DNV + D + G L G I ++D + +GHK+AL + E D + +Y Sbjct: 8 IRMHPDDNVAIVANDGGLPAGTVLPPGVPGAGITLRDKVPQGHKVALSDMAEGDVVRRYN 67 Query: 61 FPIGHASQDISIGEHIHVHNTKTNLSDIQLYSYTPRFDENPYSNE---NRTFKGFRRENG 117 PIG+A + I G VH + + P P E TF+G+R +G Sbjct: 68 VPIGYALKAIPAGSW--VHERLLQMPSARALEGLPMATVKPPVLEPLTGYTFEGYRNADG 125 Query: 118 DAGVRNELWIVPTVGCVNGIAEKMLQRFVRETGDIAP-FDNVLVLKHQYGCSQLGDDHEN 176 G RN L I TV CV G+ ++R E + P D+V+ L+H YGC D + Sbjct: 126 SVGTRNILAITTTVQCVAGVVANAVRRIKDELLPLYPQVDDVIGLEHTYGCGVAIDAPDA 185 Query: 177 TKQI--LLNAIRHPNAGG-VLVLGLGCENNELARMKEALQ-DVNLKRVKFLESQSV---T 229 I L N +PN GG V+V+ LGCE + R+ A + +R L ++V Sbjct: 186 IIPIRTLRNISLNPNFGGEVMVVSLGCEKLQPDRLLPAGSFPIADERDAALGPETVCLQA 245 Query: 230 DEMEAGVALLKEIHEAAK-------GDKREDIPLSELKIGLKCGGSDGFSGITANPLLGR 282 DE +++L I ++A+ +RE I SEL +G++CGGSD FSG+TANP +G Sbjct: 246 DEHVGFMSMLDHIVQSARPHLERLNARRRETIRASELVLGVQCGGSDAFSGVTANPAVGF 305 Query: 283 FSDYLIAQGGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYE 342 +D L+ G + + +E E+ A L RAA EV IV + + +Y + Sbjct: 306 CADLLVRAGATVMFSENTEVRDAVEQLTSRAATPEVAESIVRELGWYDRYLDRGRVDRAA 365 Query: 343 NPSPGNKAGGISTLEDKSLGCTQKAGISPVTDVLKYGEVLK--TKGLTLLSAPGNDLIAS 400 N +PGNKAGG+S + +K++G K+G +P++ VL GE L+ +GL + P +D I Sbjct: 366 NTTPGNKAGGLSNIAEKAMGSIIKSGTAPISHVLAPGEKLRRDQRGLVYAATPASDFICG 425 Query: 401 SALAAAGCQIVLFTTGRGTPFG-TFVPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEE 459 + AAG + +FTTGRGTP+G P VKVAT T+L +D NAG +A+ + E Sbjct: 426 TLQLAAGMNLHVFTTGRGTPYGLAECPVVKVATRTDLARRWHDLMDINAGKIADGEASIE 485 Query: 460 YVLREFIHYMIEVASGQ 476 + E H +++VASG+ Sbjct: 486 ELGWEMFHLLLDVASGR 502 Lambda K H 0.317 0.137 0.394 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: 545 Number of extensions: 23 Number of successful extensions: 6 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: 497 Length of database: 525 Length adjustment: 35 Effective length of query: 462 Effective length of database: 490 Effective search space: 226380 Effective search space used: 226380 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 (21.6 bits) S2: 52 (24.6 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