Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate CCNA_01555 CCNA_01555 altronate dehydratase
Query= SwissProt::P42604 (495 letters) >FitnessBrowser__Caulo:CCNA_01555 Length = 502 Score = 482 bits (1241), Expect = e-140 Identities = 253/494 (51%), Positives = 327/494 (66%), Gaps = 7/494 (1%) Query: 6 IHALD---NVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPI 62 IHA+D +VA AL DLA G VS + +R DV +GHK A + G +V+KYG PI Sbjct: 12 IHAVDPRDHVATALRDLACGESVSAHGERFIVRADVPKGHKIATRVVRSGDDVLKYGWPI 71 Query: 63 GYALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQDLPAQAAD-REVQIYRRANGDVGVR 121 G A ADIA G HVH HN T L ++ Y + P A +AD R Q +RR NG G R Sbjct: 72 GRATADIAVGDHVHVHNVITRLEGVEGYAFAP-LPPAGAPSADTRTFQGFRRKNGRAGTR 130 Query: 122 NELWILPTVGCVNGIARQIQNRFLKETNNAEGTDGVFLFSHTYGCSQLGDDHINTRTMLQ 181 NE+W+L TVGCV AR+I + A DGV+ F H +GCSQLGDD +TR ++ Sbjct: 131 NEIWVLCTVGCVANTARRIAEK--ANQRFAGRVDGVYAFPHPFGCSQLGDDLAHTRKLIA 188 Query: 182 NMVRHPNAGAVLVIGLGCENNQVAAFRETLGDIDPERVHFMICQQQDDEIEAGIEHLHQL 241 + HPNAG VL++GLGCENNQ+ A E+ DID ER+ Q +DE+E G+ + L Sbjct: 189 ALASHPNAGGVLILGLGCENNQLKALLESAPDIDRERLKGFTTQMVEDELEDGLAAVEAL 248 Query: 242 YNVMRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANGGTTVLTEVPEM 301 + D+REP +SEL GL+CGGSDG SGITANP++GR +D V GGT VLTE+PE+ Sbjct: 249 VEIAEKDRREPVPVSELVVGLKCGGSDGFSGITANPLVGRIADKVAEAGGTPVLTEIPEI 308 Query: 302 FGAEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAGGITTLEDKSLG 361 FGAE +L+ F+ V +++DFK+YFI +QPIYENPSPGN AGGIT+LE+KSLG Sbjct: 309 FGAENVLLQRAASREVFDAAVAVIDDFKRYFIEANQPIYENPSPGNIAGGITSLEEKSLG 368 Query: 362 CTQKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMVLFSTGRGTPYG 421 QK G + +V+VLRYGE + GL LL APGNDAV+++AL AG ++LF+TGRGTP G Sbjct: 369 AVQKGGRAPLVEVLRYGETVGRHGLTLLEAPGNDAVSSTALTAAGATVILFTTGRGTPLG 428 Query: 422 GFVPTVKIATNSELAAKKKHWIDFDAGQLIHGKAMPQLLEEFIDTIVEFANGKQTCNERN 481 PT+KIA+NS LA +K WIDFDAGQ++ G +M E +D ++E A+GK T E N Sbjct: 429 FPAPTLKIASNSGLAQRKPGWIDFDAGQVLEGVSMDVAAENLMDLVIETASGKTTKAELN 488 Query: 482 DFRELAIFKSGVTL 495 RE+A++KSGVTL Sbjct: 489 GEREIALWKSGVTL 502 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: 699 Number of extensions: 33 Number of successful extensions: 4 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: 502 Length adjustment: 34 Effective length of query: 461 Effective length of database: 468 Effective search space: 215748 Effective search space used: 215748 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