Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate AO356_24195 AO356_24195 galactonate dehydratase
Query= curated2:O34673 (497 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24195 Length = 508 Score = 290 bits (742), Expect = 8e-83 Identities = 170/492 (34%), Positives = 268/492 (54%), Gaps = 16/492 (3%) Query: 3 SFIKIHKQDNVLLALRDIQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGFP 62 S + + D+V +A DI +G+ ++A G+ + + I GHKIAL+ + ++KYG Sbjct: 6 SLLVLTPGDDVAVARGDIAEGQSVNADGIRLVARQAIPSGHKIALRPVLAGQRVLKYGQT 65 Query: 63 IGHASQDISIGEHIHVHN----TKTNLSDIQLYSYTPRFDENPYSNENRTFKGFRRENGD 118 IG A+Q I G+H+HVHN T ++ ENP TF+G+ RE+G Sbjct: 66 IGQATQAIEPGDHVHVHNLDMPANTTEHSVRNVYVPTSLSENP-----ATFEGYVREDGR 120 Query: 119 AGVRNELWIVPTVGCVNGIAEKMLQRFVRET-GDIAPFDNVLVLKHQYGCSQ--LGDDHE 175 G RN + ++ +V C + +++ F E D D V+ + H GC G+ + Sbjct: 121 VGTRNYIGVISSVNCSATVCKQIANTFSAERLKDFPNVDGVVAITHGSGCGMGAQGEGID 180 Query: 176 NTKQILLNAIRHPNAGGVLVLGLGCENNELARMKEALQDVN--LKRVKFLESQSVTDE-M 232 K+ L H N GVL++GLGCE N+L + L D + LK ++ + T E + Sbjct: 181 ILKRTLRGYADHANFAGVLLIGLGCEVNQLTPLMNELGDRSAALKASLVIQDEGGTREAV 240 Query: 233 EAGVALLKEIHEAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSDYLIAQGG 292 G+A ++ + +R + S L +GL+CGGSDG+SGITANP LG D L+ QGG Sbjct: 241 RRGIAHIEAMLPLVDQCQRTTVAASHLCVGLQCGGSDGYSGITANPALGAAVDLLVQQGG 300 Query: 293 STVLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPSPGNKAGG 352 + +L+E PE++GAE +L RAA+ ++ K++ I+ ++ Y +D + NPSPGNKAGG Sbjct: 301 TAILSETPEIYGAEHLLTARAASADIAAKLMARIHWWEAYVRHNDGDMNNNPSPGNKAGG 360 Query: 353 ISTLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAAAGCQIVL 412 I+T+ +KSLG KAG + + V +Y E + +GL + PG D ++++ A G ++ Sbjct: 361 ITTILEKSLGAVAKAGATGLMGVYQYAETVDARGLVFMDTPGYDPVSATGQVAGGANLIC 420 Query: 413 FTTGRGTPFGTF-VPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLREFIHYMIE 471 FTTGRG+ +G P++K+ATNT L++ +DFNAG + + M+ Sbjct: 421 FTTGRGSTYGCKPTPSLKIATNTRLFQRMELDMDFNAGGIVDGVESVAQAGERLFRLMLA 480 Query: 472 VASGQLVNHEKN 483 ASG E+N Sbjct: 481 TASGHRTCSEEN 492 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: 627 Number of extensions: 20 Number of successful extensions: 5 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: 508 Length adjustment: 34 Effective length of query: 463 Effective length of database: 474 Effective search space: 219462 Effective search space used: 219462 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