Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate CA265_RS15795 CA265_RS15795 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__Pedo557:CA265_RS15795 Length = 560 Score = 302 bits (774), Expect = 2e-86 Identities = 180/527 (34%), Positives = 297/527 (56%), Gaps = 16/527 (3%) Query: 47 IGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPT-----AMMF 101 +GI + + CN HL DLA+ VK+GV++ + F + T +++ Sbjct: 39 VGIASMGYDGNTCNMHLNDLAKDVKKGVWKNDLVGLVFNTIGVSDGMSNGTDGMRYSLVS 98 Query: 102 RNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGK 161 R++ A +E G DG++ + GCDK P +M A +D P+I+V GG + G ++G+ Sbjct: 99 RDVIADSIETICGGQYYDGIISIPGCDKNMPGAIMAMARLDRPSIMVYGGTIAPGHYKGE 158 Query: 162 DVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLS 221 ++ +A + + G +S E++ + AG+C M TA+TMAS EALGM+L Sbjct: 159 ELNIVSAFEALGQKI-CGNLSEEDYQGIIKHTCPGAGACGGMYTANTMASAIEALGMSLP 217 Query: 222 GNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVL 281 +++ PA+ ++ G+ I ++++D+KPSDI+T++AFENAIR +GGSTNAVL Sbjct: 218 YSSSNPAISEEKKQECLDAGKYIKILLEKDIKPSDIMTRKAFENAIRSIIILGGSTNAVL 277 Query: 282 HLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGL 341 H +A+ +G++++ DD+ R+ P + + +PSGKYLM++ + GG+P V+K + GL Sbjct: 278 HFIAMGKAIGIEITQDDFQRMSDVTPVLADFKPSGKYLMQDLHQYGGIPAVLKYLLNEGL 337 Query: 342 LHNDAITVSGDTIWN---DVKGVVNYNEDVILPREKALTKSGGIAVLRGNLAPRGAVLKP 398 LH D +TV+G T+ DVK +++Y++ +I + + +G + +L GNLA +G+V K Sbjct: 338 LHGDCLTVTGKTVAENLADVKSIMDYDQKIIQKLSEPIKATGHLQILYGNLAEKGSVAKI 397 Query: 399 SAASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMG 458 S + +G A VF+ D A I+ + + ++V+K GP G PGM E+ + Sbjct: 398 SGKEGE--KFEGPARVFDGEHDLIAGISSGRVQPGD--VIVIKNSGPVGAPGMPEM--LK 451 Query: 459 LPPKVLKKGITDMIR-ISDARMSGTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNR 517 ++ G+ + I+D R SG +G V+ H PE+ +GG + LVE+ D I +D N Sbjct: 452 PTSAIIGAGLGKSVALITDGRFSGGTHGFVVGHITPESYKGGLIGLVEDEDRILIDAVNN 511 Query: 518 TLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIKTVMQADAGADLD 564 ++L VSDE +A RR +V P +T G Y KTV A +G D Sbjct: 512 IINLQVSDEVIAERRKNYVQPALKVTKGVLYKYAKTVSDAASGCVTD 558 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: 931 Number of extensions: 49 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 579 Length of database: 560 Length adjustment: 36 Effective length of query: 543 Effective length of database: 524 Effective search space: 284532 Effective search space used: 284532 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