Align Altronate dehydratase; EC 4.2.1.7; D-altronate hydro-lyase (uncharacterized)
to candidate BPHYT_RS28730 BPHYT_RS28730 galactarate dehydratase
Query= curated2:O34673 (497 letters) >FitnessBrowser__BFirm:BPHYT_RS28730 Length = 503 Score = 287 bits (735), Expect = 5e-82 Identities = 167/492 (33%), Positives = 268/492 (54%), Gaps = 14/492 (2%) Query: 5 IKIHKQDNVLLALRDIQKGERLHAYGVSIEVKDDIKRGHKIALQSIKENDSIVKYGFPIG 64 ++++ D+V++AL + G + V+ V I GHK+A + I++ +++ +YG IG Sbjct: 1 MRLNPADDVVIALEQLMSGTVIDKEAVT--VSGLIPPGHKVATRDIRQGEAVHRYGQVIG 58 Query: 65 HASQDISIGEHIHVHNTKTNLSDIQLYSYTPRFDENPYSNENRTFKGFRRENGDAGVRNE 124 ASQ I G+H+H HN + Y++ SN TF+G R +G RN Sbjct: 59 FASQPIRAGQHVHTHNLAMG-DFARDYAFGQAARPTLPSNRPATFQGIVRADGRVATRNY 117 Query: 125 LWIVPTVGCVNGIAEKMLQRFVR-----ETGDIAPFDNVLVLKHQYGCS--QLGDDHENT 177 + I+ +V C +A + F R E + D V+ L H GC+ GD Sbjct: 118 IGILTSVNCSATVARAIADHFRRDIHPEELAEFPNVDGVIALTHGSGCAIDSEGDGLAIL 177 Query: 178 KQILLNAIRHPNAGGVLVLGLGCENNELARMKEAL---QDVNLKRVKFLESQSVTDEMEA 234 ++ + HPN VLV+GLGCE N++ R+ E + L+ +S T + Sbjct: 178 QRTIGGYACHPNFASVLVVGLGCETNQIPRLLETQGLREHDRLRTFTIQDSGGTTSTIAK 237 Query: 235 GVALLKEIHEAAKGDKREDIPLSELKIGLKCGGSDGFSGITANPLLGRFSDYLIAQGGST 294 G+ L++ + A +RE + S L +GL+CGGSDG+SGITANP+LG D L+ GG+ Sbjct: 238 GIELVRRMLPEANDVRREAVSASHLTVGLQCGGSDGYSGITANPVLGAAVDLLVRHGGTA 297 Query: 295 VLTEVPEMFGAETILMQRAANEEVFHKIVDLINDFKQYFIKHDQPVYENPSPGNKAGGIS 354 +L+E PE++GAE +L +RAA EV K++D I ++ Y +H + NPS GNKAGG++ Sbjct: 298 ILSETPEIYGAEHLLTRRAATPEVGRKLLDRIRWWEAYANRHGAQMNNNPSAGNKAGGLT 357 Query: 355 TLEDKSLGCTQKAGISPVTDVLKYGEVLKTKGLTLLSAPGNDLIASSALAAAGCQIVLFT 414 T+ +KSLG KAG + +T+V +Y + + +GL + PG D ++++ A G ++ FT Sbjct: 358 TVLEKSLGGIAKAGSTNLTEVYEYAQPVTARGLVFMDTPGYDPVSATGQVAGGANLICFT 417 Query: 415 TGRGTPFGTF-VPTVKVATNTELYEAKPHWIDFNAGLLAEDDVHEEYVLREFIHYMIEVA 473 TGRG+ +G P+VK+ATNT L++ + +D N G + E E + ++EVA Sbjct: 418 TGRGSAYGCAPTPSVKLATNTALWQRQSDDMDLNCGEVLEGRTTIEQLGGVLFELLLEVA 477 Query: 474 SGQLVNHEKNDF 485 SG E++ + Sbjct: 478 SGNRTRSEQHGY 489 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: 593 Number of extensions: 27 Number of successful extensions: 7 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: 503 Length adjustment: 34 Effective length of query: 463 Effective length of database: 469 Effective search space: 217147 Effective search space used: 217147 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