Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate GFF612 HP15_595 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__Marino:GFF612 Length = 597 Score = 259 bits (661), Expect = 3e-73 Identities = 180/544 (33%), Positives = 277/544 (50%), Gaps = 59/544 (10%) Query: 43 GRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEFPVFSTGES-TLRPTAMMF 101 G+PII + N++++ P + HL+DL + V R + AGG EF + + + M++ Sbjct: 19 GKPIIAVANSFTQFVPGHVHLKDLGQLVCREIESAGGVAKEFNTIAVDDGIAMGHDGMLY 78 Query: 102 ----RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGK 157 R + A VE + + D +V + CDK TP +LM A ++IP I VSGGPM GK Sbjct: 79 SLPSREIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMEAGK 138 Query: 158 WRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALG 217 + + + + S E+ + E+ + GSC M TA++M + EA+G Sbjct: 139 TKLSE--HKLDLVDAMVIAADPNASDEQVEEYERNACPTCGSCSGMFTANSMNCLTEAIG 196 Query: 218 MTLSGNAAIPAVDARRRVISQLTGRRIVEMVKE-------DLKPSDILTKEAFENAIRVN 270 + L GN ++ A A R + GR+IVE + + P I + AFENA+ ++ Sbjct: 197 LALPGNGSLLATHADREQLFLKAGRQIVENARRYYEEDDASVLPLSIASMAAFENAMVMD 256 Query: 271 GAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQP-SGKYLMEEFYYAGGL 329 A+GGSTN +LHLLA A GV +L++ D+L R VP + + P S KY ME+ + AGG+ Sbjct: 257 IAMGGSTNTILHLLAAAQEGGVPFTLNEIDQLSRRVPQLCKVAPNSPKYHMEDVHRAGGI 316 Query: 330 PVVIKAVAEMGLLHNDAITVSGDTI------WNDVKG----VVNY--------------- 364 ++ + GL++ D TV T+ W+ ++ VV + Sbjct: 317 MGILGELERGGLINTDLPTVHSKTMREALETWDIMRSPPTEVVEFYKAGPAGIPTQTAFS 376 Query: 365 ------------NEDVILPREKALTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRA 412 I E A + GG+AVL GN+A G V+K + + +G+A Sbjct: 377 QSTRWPTLDGDRETGCIRSVENAYSSEGGLAVLYGNIALDGCVVKTAGVDESIFVFEGKA 436 Query: 413 VVFESIEDYHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLK-KGI-TD 470 VFES + A I +++ E +++++Y GP+G PGM E M P LK KG+ D Sbjct: 437 RVFESQDSAVAGILSDEVKPGE--VVIIRYEGPRGGPGMQE---MLYPTSYLKSKGLGKD 491 Query: 471 MIRISDARMSGTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELAR 530 ++D R SG G I H +PEAA GG + L+ENGD I +DIPNR++++ + EL R Sbjct: 492 CALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLIENGDTIRIDIPNRSINVELDQHELDR 551 Query: 531 RRAA 534 RR A Sbjct: 552 RREA 555 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: 867 Number of extensions: 48 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: 597 Length adjustment: 37 Effective length of query: 542 Effective length of database: 560 Effective search space: 303520 Effective search space used: 303520 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