Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate Ga0059261_2974 Ga0059261_2974 Altronate dehydratase
Query= SwissProt::P42604 (495 letters) >FitnessBrowser__Korea:Ga0059261_2974 Length = 490 Score = 443 bits (1139), Expect = e-129 Identities = 240/492 (48%), Positives = 316/492 (64%), Gaps = 7/492 (1%) Query: 4 IKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIG 63 ++IH D VA AL +L G V VTL + R HKFAL A G V+K+G PIG Sbjct: 6 LRIHGADTVATALRNLVAGEVVL----GVTLSDAIPRAHKFALVAHAPGDPVLKFGFPIG 61 Query: 64 YALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQDLPAQAADREVQIYRRANGDVGVRNE 123 A A IA G HVH HN T L+ Y + PA A+ + + Y RA+G G RNE Sbjct: 62 RATAAIAPGDHVHVHNVATALAGEAAYGGGAGAERAPAAASAIKWRGYPRADGRAGTRNE 121 Query: 124 LWILPTVGCVNGIARQIQNRFLKETNNAEGTDGVFLFSHTYGCSQLGDDHINTRTMLQNM 183 +WILPTVGCV A++I + E G DGV F+H +GCSQL DD TR +L + Sbjct: 122 IWILPTVGCVGRTAQKIAVK--AEALLPAGVDGVHAFAHPFGCSQLSDDLDGTRNILSAL 179 Query: 184 VRHPNAGAVLVIGLGCENNQVAAFRETLGDIDPERVHFMICQQQDDEIEAGIEHLHQLYN 243 +HPNAG VL++GLGCE+NQ++A ETL + RV + Q DEI G+ + +L Sbjct: 180 AQHPNAGGVLLVGLGCESNQLSALLETLPEDVRMRVRTVGAQSSPDEIGEGVGKVLELAQ 239 Query: 244 VMRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANGGTTVLTEVPEMFG 303 + +RE L L G++CGGSDGLSG+TANP++G +D + GG+ +LTE+PE+FG Sbjct: 240 LAATAQREEMGLDRLVLGVKCGGSDGLSGLTANPLVGIMADRITDAGGSAILTEIPEIFG 299 Query: 304 AEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAGGITTLEDKSLGCT 363 AEQLLM D TF+ + +VN FK+YFI H +P+ ENPSPGN AGGITTLE+KSLG Sbjct: 300 AEQLLMARAADADTFDAIGALVNRFKRYFIDHGEPVSENPSPGNIAGGITTLEEKSLGAV 359 Query: 364 QKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMVLFSTGRGTPYGGF 423 QK G ++V DV+ YG+R+K GL LL APGNDAV+++AL+ AG ++LF+TGRGTP G Sbjct: 360 QKGGQAIVTDVIDYGDRVKRTGLTLLEAPGNDAVSSTALSAAGATVILFTTGRGTPLGFP 419 Query: 424 VPTVKIATNSELAAKKKHWIDFDAGQLIHGKAMPQLLEEFIDTIVEFANGKQTCNERNDF 483 PT+KIA+NS+LAA+K WIDFDAGQ++ M + + I A+G++ ERN Sbjct: 420 APTLKIASNSDLAARKPGWIDFDAGQVL-TDGMDVAADALLARIAAIASGEEAAAERNGE 478 Query: 484 RELAIFKSGVTL 495 RE+AI+K GVTL Sbjct: 479 REIAIWKRGVTL 490 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: 687 Number of extensions: 22 Number of successful extensions: 3 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: 490 Length adjustment: 34 Effective length of query: 461 Effective length of database: 456 Effective search space: 210216 Effective search space used: 210216 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