Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate PfGW456L13_3478 Altronate dehydratase (EC 4.2.1.7)
Query= SwissProt::P42604 (495 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3478 Length = 510 Score = 252 bits (643), Expect = 2e-71 Identities = 162/492 (32%), Positives = 247/492 (50%), Gaps = 13/492 (2%) Query: 4 IKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIG 63 I++ DNV VA ++ GT ++ N+++T QDV GHK A I KG V+KY IG Sbjct: 10 IRLDPADNVVVARVEIPTGTAIT--NESLTTLQDVPLGHKIAARMIEKGQPVLKYNTVIG 67 Query: 64 YALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQDLPAQAADREV--QIYRRANGDVGVR 121 YA D+ G +H+HN + D YRY D+ AD+ Q R +G V R Sbjct: 68 YASEDLPPGTWMHSHNIEFGETARD-YRYGLDYVPTDLLPADKRATFQGIIREDGRVATR 126 Query: 122 NELWILPTVGCVNGIARQIQNRFLKETNNA-EGTDGVFLFSHTYGCSQ--LGDDHINTRT 178 N L I C +AR+I N F +E A DGV F H GC G+ R Sbjct: 127 NYLGIFVVGNCGATVARKIANHFDEERLAAFPNIDGVVPFVHEIGCGMEMTGEPMNLLRR 186 Query: 179 MLQNMVRHPNAGAVLVIGLGCENNQVAAFRETLGDIDPERVHFMICQQQDD---EIEAGI 235 + ++H N L+I LGCE N + F E + + + ++ Q ++ GI Sbjct: 187 TIGGHIKHANTAGGLLIALGCERNNIYGFIEQEQLVLGDMLKSLVIQDVGGVKTAVDQGI 246 Query: 236 EHLHQLYNVMRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANGGTTVL 295 + + + +RE L G++CGGSDG SG++ANP LG D ++ +GGT +L Sbjct: 247 KMIQAMLPQANAVQRETVSAEHLIIGMQCGGSDGFSGLSANPALGAAVDILVRHGGTAIL 306 Query: 296 TEVPEMFGAEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAGGITTL 355 +E E+FG E L KL+ ++ + +Y D I SPGN AGG+ + Sbjct: 307 SETSEIFGVEHTLTARAATPEVGRKLIDRIDWWLEYNKGRDTQINGRVSPGNNAGGLANV 366 Query: 356 EDKSLGCTQKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMVLFSTG 415 +KSLG +K G++ ++DV Y + T GL + PG D V+ + G +M+ F+TG Sbjct: 367 LEKSLGGAKKGGNAPLMDVYEYAYPVTTHGLVFMDTPGYDPVSATGQIAGGANMIAFTTG 426 Query: 416 RGTPYGGF-VPTVKIATNSELAAKKKHWIDFDAGQLIHG-KAMPQLLEEFIDTIVEFANG 473 RG+ +G PT K+A+NS + + +D + GQ+I G K + Q+ +E + ++ A+G Sbjct: 427 RGSCFGSVPAPTFKLASNSPMFNRMSDDMDINCGQIIDGDKTIQQMGQEIFERLLTHASG 486 Query: 474 KQTCNERNDFRE 485 +T +E N E Sbjct: 487 DKTKSELNGLGE 498 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: 629 Number of extensions: 37 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: 495 Length of database: 510 Length adjustment: 34 Effective length of query: 461 Effective length of database: 476 Effective search space: 219436 Effective search space used: 219436 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 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