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) >FitnessBrowser__Putida:PP_5128 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:
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