Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate WP_011384917.1 AMB_RS12770 dihydroxy-acid dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >NCBI__GCF_000009985.1:WP_011384917.1 Length = 616 Score = 198 bits (504), Expect = 5e-55 Identities = 160/570 (28%), Positives = 259/570 (45%), Gaps = 85/570 (14%) Query: 35 GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94 GMT + G+PII IA + + P + H +L Q V I AGG+ EF I + Sbjct: 26 GMTDADF--GKPIIAIANSFTQFVPGHVHLKDLGQMVAREIEKAGGVAKEFDTIAIDDGI 83 Query: 95 RRPTAAL-----DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149 A + R L + +++ + D +V + CDK TP LMA+ ++P I + Sbjct: 84 AMGHAGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRLNIPTIFI 143 Query: 150 SGGPMLDGH--HKGELIGSGTVLWHARNLMAA------GEIDYEGFMEMTTAASPSVGHC 201 SGGPM G ++GE HA +L+ A + E + + P+ G C Sbjct: 144 SGGPMEAGKVTYQGET--------HAVDLIDAMIKGADQNVSDEEALAFEKESCPTCGSC 195 Query: 202 NTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICDLVRQ-------DIR 254 + M TA SMN L EALG+ LPG ++ A + +R ++ G+RI DL R+ + Sbjct: 196 SGMFTANSMNCLIEALGLGLPGNGTVVATHADRKELFLEAGRRIVDLARRAYEGDDASVL 255 Query: 255 PSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCM 314 P I T QAFENA+ + A+G S+N HL+A A+ GV + D R+ VP L Sbjct: 256 PRSIATFQAFENAMTLDIAMGGSTNTVLHLLAAAQEAGVAFGMSDIDRLSRRVPCLCKVA 315 Query: 315 PAGKYLG-EGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSNSLTSNTD----- 368 P + E HRAGG+ ++ +L + G ++ +C T+ +T+ E + S ++ Sbjct: 316 PNVPDVHIEDVHRAGGIMGILGQLDRGGLINRECGTIHARTLAEGLDRWDISRSNDPKVV 375 Query: 369 --------------------------------VIHPFDTPLKHRAGFIVLSGNF-FDSAI 395 VI D G VL GN D I Sbjct: 376 EFYKAAPGGVRTTEAFSQSKRWAEVDKDRTAGVIRSVDNAFSKDGGLAVLFGNLALDGCI 435 Query: 396 MKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVG 455 +K + V + +F A++ E ++ A+I + + ++++R G Sbjct: 436 VKTAGVDD-----------KNLTFSGPAVICESQDEAVAKILGGQVKSGD--VVIVRYEG 482 Query: 456 TVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLAL 514 G PG E+ + P + L G+ + DGR SG ++ SI ++SPEAA GG + L Sbjct: 483 PRGGPGMQEM--LYPTSYLKSMGLGKECALITDGRFSGGTSGLSIGHVSPEAAEGGAIGL 540 Query: 515 LKTNDRLKVDLNTRTVNLLIDDAEMAQRRR 544 ++ D + + + R++ + + DAE+ +RR+ Sbjct: 541 IQAGDIIDIHIPNRSIAIRVSDAELEKRRQ 570 Lambda K H 0.319 0.135 0.407 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: 871 Number of extensions: 45 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 594 Length of database: 616 Length adjustment: 37 Effective length of query: 557 Effective length of database: 579 Effective search space: 322503 Effective search space used: 322503 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: 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