Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate PP_5128 PP_5128 Dihydroxy-acid dehydratase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Putida:PP_5128 Length = 613 Score = 214 bits (546), Expect = 6e-60 Identities = 172/563 (30%), Positives = 259/563 (46%), Gaps = 71/563 (12%) Query: 35 GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94 GM E+ + +PII IA + + P + H +L Q V I AGG+ EF + + Sbjct: 26 GMKDEDFK--KPIIAIANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDDGI 83 Query: 95 RRPTAAL-----DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149 + R + + +++ + D +V + CDK TP LMAA ++P I + Sbjct: 84 AMGHDGMLYSLPSREIIADAVEYMVNAHCADAIVCISNCDKITPGMLMAALRLNIPVIFV 143 Query: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALS 209 SGGPM G K +L G L A + A E E +A P+ G C+ M TA S Sbjct: 144 SGGPMEAG--KTKLASHGLDLVDAMVIAADSTASDEKVAEYERSACPTCGSCSGMFTANS 201 Query: 210 MNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICDLVR-------QDIRPSQIMTRQ 262 MN L EALG++LPG S A + +R Q+ G+ I +L + + + P I + Sbjct: 202 MNCLTEALGLALPGNGSTLATHSDREQLFLTAGRTIVELCKRYYGENDESVLPRSIANFK 261 Query: 263 AFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMP-AGKYLG 321 AFENA+ + A+G S+N HL+A A+ V L D R+ VP L P KY Sbjct: 262 AFENAMMLDIAMGGSTNTILHLLAAAQEGEVAFDLRDIDRLSRKVPQLCKVAPNIQKYHM 321 Query: 322 EGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSNSLTSNTD------------- 368 E HRAGG+ S++ L + G LH D TV +++ E ++ + TD Sbjct: 322 EDVHRAGGIFSILGSLARGGLLHTDLPTVHSRSMEEAIAKWDITQTDDEAVHTFFKAGPA 381 Query: 369 ------------------------VIHPFDTPLKHRAGFIVLSGNF-FDSAIMKMSVVGE 403 I F+ G VL GN D ++K + V E Sbjct: 382 GIPTQTAFSQSTRWETLDDDRENGCIRSFEHAYSQEGGLAVLYGNIALDGCVVKTAGVDE 441 Query: 404 AFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSA 463 + + FE A +FE + I A ++ I++IR G G PG Sbjct: 442 SI-----------HVFEGTAKIFESQDSAVRGI--LADEVKAGDIVIIRYEGPKGGPGMQ 488 Query: 464 EVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLK 522 E+ + P + L +G+ + L DGR SG ++ SI + SPEAA GG + L++ D++ Sbjct: 489 EM--LYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVRDGDKVL 546 Query: 523 VDLNTRTVNLLIDDAEMAQRRRE 545 +D+ R++NLL+ D E+AQRR E Sbjct: 547 IDIPNRSINLLVSDEELAQRRVE 569 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: 860 Number of extensions: 35 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: 613 Length adjustment: 37 Effective length of query: 557 Effective length of database: 576 Effective search space: 320832 Effective search space used: 320832 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