Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate AZOBR_RS31430 AZOBR_RS31430 galactarate dehydratase
Query= SwissProt::P42604 (495 letters) >FitnessBrowser__azobra:AZOBR_RS31430 Length = 507 Score = 292 bits (747), Expect = 2e-83 Identities = 188/490 (38%), Positives = 259/490 (52%), Gaps = 12/490 (2%) Query: 4 IKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIG 63 I++H DNV VA ADL EGT ++ + V R + GHK A+ IA G V KY IG Sbjct: 6 IRLHPADNVVVAGADLPEGT--TLPDTGVVARTTIPSGHKVAVQAIAVGEPVRKYNQVIG 63 Query: 64 YALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQ--DLPAQAADREVQIYRRANGDVGVR 121 +A A IA G HVH HN S Y + D DL +A Q R +G V R Sbjct: 64 FATAPIAPGDHVHVHNIGVGDSFERDYAFSADVHPTDLVPEAERATFQGIVRPDGRVATR 123 Query: 122 NELWILPTVGCVNGIARQIQNRFLKETNNA-EGTDGVFLFSHTYGCSQ--LGDDHINTRT 178 N + IL TV C AR I ++F + A DGV +H+YGC GD R Sbjct: 124 NYIGILTTVNCSATAARMIADQFRGDALAAYPNIDGVVALTHSYGCGMGSQGDAIDALRR 183 Query: 179 MLQNMVRHPNAGAVLVIGLGCENNQVAAFRETLGDIDPERVHFMICQQQDDE---IEAGI 235 + RHPN AVLV+GLGCE NQ+ E G + + + Q+ + A + Sbjct: 184 TIAGYARHPNFAAVLVLGLGCEVNQIDKLVEVEGLTIGDTLQTLAIQESGGTAATVRASV 243 Query: 236 EHLHQLYNVMRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANGGTTVL 295 E + L + + KRE S L L+CGGSDG SGITANP LG D +I NGGT VL Sbjct: 244 ERIRALLPRVNDVKRETVPASHLILALQCGGSDGYSGITANPALGHAVDLLIRNGGTAVL 303 Query: 296 TEVPEMFGAEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAGGITTL 355 +E PE++GAE LL + A E LV + ++ Y + NPSPGNK GG+TT+ Sbjct: 304 SETPEVYGAEHLLTRRSVNPAVGETLVERIRWWEDYTSRTGGEMNNNPSPGNKKGGLTTI 363 Query: 356 EDKSLGCTQKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMVLFSTG 415 +KSLG KAG++ +V+V+RY E + PGL + PG D V+ + G +++ F+TG Sbjct: 364 LEKSLGAVAKAGTTNLVEVVRYAEPITGPGLVFMDTPGYDPVSATGQVAGGANVLCFTTG 423 Query: 416 RGTPYG-GFVPTVKIATNSELAAKKKHWIDFDAGQLIHGKA-MPQLLEEFIDTIVEFANG 473 RG+ +G P++K+ATN+ L K +D D G + G A + ++ I++ A+G Sbjct: 424 RGSVFGCKPTPSLKLATNTALFRKMPDDMDIDCGPIATGDATIEEVGRTIFQLILDTASG 483 Query: 474 KQTCNERNDF 483 K+T +E F Sbjct: 484 KKTKSEELGF 493 Lambda K H 0.319 0.136 0.403 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: 632 Number of extensions: 31 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: 495 Length of database: 507 Length adjustment: 34 Effective length of query: 461 Effective length of database: 473 Effective search space: 218053 Effective search space used: 218053 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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