Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate 18321 b4297 KpLE2 phage-like element; predicted dehydratase (NCBI)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Keio:18321 Length = 655 Score = 190 bits (483), Expect = 1e-52 Identities = 164/550 (29%), Positives = 267/550 (48%), Gaps = 71/550 (12%) Query: 42 DGRPVIGILNTWSDMTPCNGHLR-ELAEKVKAGVWEAG-GFPLEVPVFSASENTFRPTAM 99 DG+PV L+ GH ++ K A V +A P V V + + T Sbjct: 77 DGKPVALALH--------QGHYELDIQMKAAAEVIKANHALPYAVYVSDPCDGRTQGTTG 128 Query: 100 M-----YRNLAALAVEEAIRGQPMDGCVL-LVGCDKTTPSLLMG-AASCDLPSIVVTGG- 151 M YRN A++ + IR P V+ + CDK P+ +M AA ++ +++V GG Sbjct: 129 MFDSLPYRNDASMVMRRLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGA 188 Query: 152 --PMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGT-CNTMGTAST 208 P +G G+ G +F+ GE++ + A SSG C +GTA T Sbjct: 189 TLPAKDGEDNGKVQTIGA---RFAN----GELSLQDARRAGCKACASSGGGCQFLGTAGT 241 Query: 209 MASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIR 268 +AE LG+A+ +A P + + +A+ + R + + + + EI+T +A ENA+ Sbjct: 242 SQVVAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQKGITTREILTDKAIENAMT 301 Query: 269 TNAAIGGSTNAVIHLLAIAGRVGIDL-SLDDWDRCGRDVPTIVNLMPSGK--YLMEEFFY 325 +AA GGSTN ++H+ AIA + G + ++DDW R + VP +V+++P+G + F Sbjct: 302 VHAAFGGSTNLLLHIPAIAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAFM 361 Query: 326 AGGLPVVLKRLGEAGLLHKDALTVSGETVWDEV------------------KDVVNWNED 367 AGG+P V+ L GLLH+D +TV+G T+ + + ++ +N +E Sbjct: 362 AGGVPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWEHSERRQRFKQLLLDQEQINADEV 421 Query: 368 VILPAE-KALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL------VHKGRAVVFEDIDD 420 ++ P + KA + I GN+AP+G+V+K +A P ++ HKG A V+ Sbjct: 422 IMSPQQAKARGLTSTITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKS 481 Query: 421 YKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMS 480 I D + + I+V+ GP G GM E + K L G + I+DAR S Sbjct: 482 AIYDIKHDKIKAGD--ILVIIGVGPSG-TGMEETYQVTSALKHLSYG-KHVSLITDARFS 537 Query: 481 GTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDI------SDEEL-----A 529 G + G + H PEA GGP+ ++ GD+IE+ + R LH ++ SDE+L A Sbjct: 538 GVSTGACIGHVGPEALAGGPIGKLRTGDLIEIKIDCRELHGEVNFLGTRSDEQLPSQEEA 597 Query: 530 RRLAEWQPNH 539 + +P+H Sbjct: 598 TAILNARPSH 607 Lambda K H 0.318 0.135 0.408 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: 969 Number of extensions: 58 Number of successful extensions: 6 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: 579 Length of database: 655 Length adjustment: 37 Effective length of query: 542 Effective length of database: 618 Effective search space: 334956 Effective search space used: 334956 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 (21.7 bits) S2: 53 (25.0 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