Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 18321 b4297 KpLE2 phage-like element; predicted dehydratase (NCBI)
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__Keio:18321 Length = 655 Score = 194 bits (492), Expect = 1e-53 Identities = 157/481 (32%), Positives = 245/481 (50%), Gaps = 66/481 (13%) Query: 101 FRNLASMDVEESIRGNP-MDGVILLVGCDKTTPALLMG-AASCNLPALAVSGG---PMLN 155 +RN ASM + IR P VI + CDK PA +M AA N+ + V GG P + Sbjct: 135 YRNDASMVMRRLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGATLPAKD 194 Query: 156 GRFRGK--NIGS--GTGVWQMSEEVRAGTMTQEEFTEAESCMNRSRGHCMTMGTASTMAS 211 G GK IG+ G + + RAG ++C + S G C +GTA T Sbjct: 195 GEDNGKVQTIGARFANGELSLQDARRAG---------CKACAS-SGGGCQFLGTAGTSQV 244 Query: 212 MVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMVREDLTMDKILTRQAFENAIRTNA 271 + E LG+ +PH+A P+ + + +A + R +++ ++ +T +ILT +A ENA+ +A Sbjct: 245 VAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQKGITTREILTDKAIENAMTVHA 304 Query: 272 AIGGSTNAVVHLIALAKRIGVEL-SLEDW-ELGSNVPCLVNLQPSGE--YLMEDFYYAGG 327 A GGSTN ++H+ A+A + G + +++DW + VP LV++ P+G + + + AGG Sbjct: 305 AFGGSTNLLLHIPAIAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAFMAGG 364 Query: 328 LPAVLKQLGEQGLLHKEALTVNGKTLWDNV------------------RNAANYDEKVIT 369 +P V+ L GLLH++ +TV G TL +N+ + N DE +++ Sbjct: 365 VPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWEHSERRQRFKQLLLDQEQINADEVIMS 424 Query: 370 TFAEPFKPKA-----GIAVLKGNLAPNGAVIKPSAATASLLK------HRGRAVVFENIE 418 P + KA I GN+AP G+VIK +A S++ H+G A V+ + Sbjct: 425 ----PQQAKARGLTSTITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVY--LS 478 Query: 419 ELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRM 478 E A D + I I+V+ G GP G G E + K L G + I+D R Sbjct: 479 EKSAIYDIKHDKIKAGDILVIIGVGPSG-TGMEETYQVTSALKHLSYG-KHVSLITDARF 536 Query: 479 SGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDV------TDEELARRRA 532 SG + GA + HV PEA AGGP+ ++TGD+IE+ ++ R LH +V +DE+L + Sbjct: 537 SGVSTGACIGHVGPEALAGGPIGKLRTGDLIEIKIDCRELHGEVNFLGTRSDEQLPSQEE 596 Query: 533 A 533 A Sbjct: 597 A 597 Lambda K H 0.318 0.135 0.401 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: 935 Number of extensions: 51 Number of successful extensions: 4 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: 577 Length of database: 655 Length adjustment: 37 Effective length of query: 540 Effective length of database: 618 Effective search space: 333720 Effective search space used: 333720 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