Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_057508546.1 ABB28_RS10335 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >NCBI__GCF_001431535.1:WP_057508546.1 Length = 611 Score = 249 bits (636), Expect = 2e-70 Identities = 191/566 (33%), Positives = 279/566 (49%), Gaps = 60/566 (10%) Query: 21 GKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGF 80 G+N R+ + G+ F +PII I N++++ P + HL+DL + V R + +AGG Sbjct: 12 GRNMAGARALWRATGMKDGDFH-KPIIAIANSFTQFVPGHVHLKDLGQLVAREIEQAGGV 70 Query: 81 PVEFPVFSTGES-TLRPTAMMF----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLL 135 EF + + + M++ R + A VE + + D +V + CDK TP +L Sbjct: 71 AKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGML 130 Query: 136 MGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMAR 195 M A +DIP I VSGGPM GK + + + + S E+ + E+ Sbjct: 131 MAALRLDIPVIFVSGGPMEAGKTKLSE--HKLDLVDAMVIAADDSASDEKVAEYERSACP 188 Query: 196 SAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVK-----E 250 + GSC M TA++M + EALG++L GN A A R ++ + GR IVE+ E Sbjct: 189 TCGSCSGMFTANSMNCLTEALGLSLPGNGTTLATHADREMLFRRAGRVIVELCHRWYGGE 248 Query: 251 DLK--PSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPT 308 D + PS I T AF NA+ ++ A+GGSTN +LHLLA A GVD L D L R VP Sbjct: 249 DPRALPSGIATAAAFGNAMTLDIAMGGSTNTILHLLAAAQEGGVDFDLTHIDALSRRVPQ 308 Query: 309 IVNLQP-SGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGD-----------TIWN 356 + + P + +Y +E+ + AGG+ ++ + GLL TV T+ + Sbjct: 309 LCKVAPNTPQYHIEDVHRAGGVFGILGELDRAGLLDTSVPTVHSPSLADALKRWDATLTD 368 Query: 357 DVK----------GV----------------VNYNEDVILPREKALTKSGGIAVLRGNLA 390 D K G+ ++ E I + A + GG+AVLRGNLA Sbjct: 369 DAKVHEFFAAGPAGIPTQVAFSQATRWPSLDLDRAEGCIRSLQHAYSLEGGLAVLRGNLA 428 Query: 391 PRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVLKYCGPKGYPG 450 G V+K + + +G A VFES + A I + + + ++V++Y GPKG PG Sbjct: 429 VDGCVVKTAGVDESIHVFEGNARVFESQDAAVAGILADQVKPGD--VVVIRYEGPKGGPG 486 Query: 451 MAEVGNMGLPPKVLK-KGI-TDMIRISDARMSGTAYGTVILHTAPEAAEGGPLALVENGD 508 M E M P LK KG+ ++D R SG G I H +PEAA GG + LV +GD Sbjct: 487 MQE---MLYPTSYLKSKGLGKQCALLTDGRFSGGTSGLSIGHVSPEAASGGVIGLVHDGD 543 Query: 509 LIEVDIPNRTLHLHVSDEELARRRAA 534 I +DIP R + L V D LA RRAA Sbjct: 544 RIRIDIPARGITLLVDDATLAERRAA 569 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: 847 Number of extensions: 44 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: 611 Length adjustment: 37 Effective length of query: 542 Effective length of database: 574 Effective search space: 311108 Effective search space used: 311108 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 24 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