Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate PP_5128 PP_5128 Dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >lcl|FitnessBrowser__Putida:PP_5128 PP_5128 Dihydroxy-acid dehydratase Length = 613 Score = 264 bits (675), Expect = 7e-75 Identities = 191/564 (33%), Positives = 281/564 (49%), Gaps = 60/564 (10%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 G+N R+ + G+ + F +PII I N++++ P + HL+DL + V R + AGG Sbjct: 12 GRNMAGARALWRATGMKDEDFK-KPIIAIANSFTQFVPGHVHLKDLGQLVAREIERAGGV 70 Query: 81 PVEFPVFSTGES-TLRPTAMMF----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLL 135 EF + + + M++ R + A VE + + D +V + CDK TP +L Sbjct: 71 AKEFNTIAVDDGIAMGHDGMLYSLPSREIIADAVEYMVNAHCADAIVCISNCDKITPGML 130 Query: 136 MGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMAR 195 M A ++IP I VSGGPM GK K G + + S E+ + E+ Sbjct: 131 MAALRLNIPVIFVSGGPMEAGKT--KLASHGLDLVDAMVIAADSTASDEKVAEYERSACP 188 Query: 196 SAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVK------ 249 + GSC M TA++M + EALG+ L GN + A + R + GR IVE+ K Sbjct: 189 TCGSCSGMFTANSMNCLTEALGLALPGNGSTLATHSDREQLFLTAGRTIVELCKRYYGEN 248 Query: 250 -EDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPT 308 E + P I +AFENA+ ++ A+GGSTN +LHLLA A V L D DRL R VP Sbjct: 249 DESVLPRSIANFKAFENAMMLDIAMGGSTNTILHLLAAAQEGEVAFDLRDIDRLSRKVPQ 308 Query: 309 IVNLQPS-GKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSG----------DTIWND 357 + + P+ KY ME+ + AGG+ ++ ++A GLLH D TV D D Sbjct: 309 LCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSRSMEEAIAKWDITQTD 368 Query: 358 VKGVVNY---------------------------NEDVILPREKALTKSGGIAVLRGNLA 390 + V + I E A ++ GG+AVL GN+A Sbjct: 369 DEAVHTFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSFEHAYSQEGGLAVLYGNIA 428 Query: 391 PRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVLKYCGPKGYPG 450 G V+K + + +G A +FES + I +++ + I++++Y GPKG PG Sbjct: 429 LDGCVVKTAGVDESIHVFEGTAKIFESQDSAVRGILADEVKAGD--IVIIRYEGPKGGPG 486 Query: 451 MAEVGNMGLPPKVLK-KGITDMIR-ISDARMSGTAYGTVILHTAPEAAEGGPLALVENGD 508 M E M P LK KG+ ++D R SG G I H +PEAA GG + LV +GD Sbjct: 487 MQE---MLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVRDGD 543 Query: 509 LIEVDIPNRTLHLHVSDEELARRR 532 + +DIPNR+++L VSDEELA+RR Sbjct: 544 KVLIDIPNRSINLLVSDEELAQRR 567 Lambda K H 0.318 0.135 0.402 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: 846 Number of extensions: 31 Number of successful extensions: 8 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: 579 Length of database: 613 Length adjustment: 37 Effective length of query: 542 Effective length of database: 576 Effective search space: 312192 Effective search space used: 312192 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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