Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate BWI76_RS24840 BWI76_RS24840 galactarate dehydratase
Query= curated2:O34673 (497 letters) >FitnessBrowser__Koxy:BWI76_RS24840 Length = 523 Score = 240 bits (612), Expect = 1e-67 Identities = 164/491 (33%), Positives = 256/491 (52%), Gaps = 23/491 (4%) Query: 4 FIKIHKQDNVLLALRD--IQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGF 61 +IK+H+ DNV + + D + G R + + + + I +GHK+AL I + I++YG Sbjct: 15 YIKVHETDNVAIIVNDRGLTAGTR---FPDGLTLVEHIPQGHKVALVDIPVHGEIIRYGE 71 Query: 62 PIGHASQDISIGEHIHVHNTKTNLSDIQLYSYTPRFDENPYSN---ENRTFKGFRRENGD 118 IG+A +DI G I + L P + P E TF+G+R +G Sbjct: 72 VIGYAVRDIPQGSWID--ESLVELPKAPPLHTLPLATKVPAPLPPLEGYTFEGYRNADGS 129 Query: 119 AGVRNELWIVPTVGCVNGIAEKMLQRFVRETGDIAP-FDNVLVLKHQYGCSQLGDDHENT 177 G +N L I +V CV G+ + +++ R+ P D V+ L H YGC + Sbjct: 130 VGTKNLLGISTSVHCVAGVVDYVVKIIERDLLPKYPNVDGVVGLNHLYGCGVAINAPAAV 189 Query: 178 KQI--LLNAIRHPNAGG-VLVLGLGCENNELARMKEALQDVNLKRVKFLESQSVTDEMEA 234 I + N +PN GG V+V+GLGCE + R+ E DV V S+ DE Sbjct: 190 VPIRTIHNLALNPNFGGEVMVIGLGCEKLQPERLLEGTDDVKGIPVDSASIVSLQDEKHV 249 Query: 235 GV-ALLKEIHEAAKGD-------KREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSDY 286 G +++ +I + A+ +RE P SEL +G++CGGSD FSG+TANP +G SD Sbjct: 250 GFKSMVDDILQVAERHLEKLNQRQRETCPASELVVGMQCGGSDAFSGVTANPAVGYASDL 309 Query: 287 LIAQGGSTVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPSP 346 L+ G + + +EV E+ A +L RA NEEV ++++ + + Y NPSP Sbjct: 310 LVRCGATVMFSEVTEVRDAIHLLTPRAINEEVGKRLLEEMAWYDNYLDMGKTDRSANPSP 369 Query: 347 GNKAGGISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAAA 406 GNK GG++ + +K+LG K+G S + +VL G+ +GL + P +D + + A+ Sbjct: 370 GNKKGGLANVVEKALGSIAKSGKSAIAEVLSPGQRPTKRGLIYAATPASDFVCGTQQVAS 429 Query: 407 GCQIVLFTTGRGTPFG-TFVPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLREF 465 G + +FTTGRGTP+G VP +K+AT TEL +D NAG +A + E V + Sbjct: 430 GITVQVFTTGRGTPYGLVAVPVIKMATRTELANRWYDLMDINAGTIATGEETIEEVGLKL 489 Query: 466 IHYMIEVASGQ 476 ++++VASG+ Sbjct: 490 FEFILDVASGR 500 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: 606 Number of extensions: 30 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: 523 Length adjustment: 34 Effective length of query: 463 Effective length of database: 489 Effective search space: 226407 Effective search space used: 226407 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