Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate BPHYT_RS28240 BPHYT_RS28240 L-rhamnonate dehydratase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__BFirm:BPHYT_RS28240 Length = 392 Score = 143 bits (360), Expect = 9e-39 Identities = 108/344 (31%), Positives = 163/344 (47%), Gaps = 30/344 (8%) Query: 32 VLVEIECDDGTVGWGECLGPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQR 91 ++VEIE DGTVG+ G V + + +L GQ EK+W +Y + G++ Sbjct: 59 LVVEIEASDGTVGFAVTTGGEIGAFIVEKHLARFLEGQLVTDIEKMWDQMYFSTLYYGRK 118 Query: 92 GLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSDNASE 151 G+ L +SG+D+ALWD+ K + LLGG R+ + YATG+ D A E Sbjct: 119 GVVLNTISGVDLALWDLLAKVRKEPVYQLLGGPVRDELVFYATGA--------RPDLAKE 170 Query: 152 MAERRAEGFHACKIKIGF-------GVEEDLRVIAAVREAIGPDMRLMIDANHGYTVTEA 204 M GF K+ + G++++L +A +R +G D LM D V A Sbjct: 171 M------GFIGGKLPLQHGPAEGEAGLKQNLEKLADMRSRVGDDFWLMYDCWMSLDVPYA 224 Query: 205 ITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQP--IPVAGGETWHGRYGMWQALSAGA 262 L A +G+ W EE + P+ YA +R P + V+ GE R+G L Sbjct: 225 TRLAQAAHEYGLKWIEECLPPDDYWGYAELRRNVPRGMMVSTGEHEATRWGFRMLLEMQC 284 Query: 263 VDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVN 322 D++QPD+ CGG +E+ KI+ LA H V +VPH G+ V + F+ P Sbjct: 285 CDLIQPDVGWCGGITELIKISALADAHNVMVVPH--GSSVY---SYHFVVTRHNSPF-AE 338 Query: 323 PIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEIN 366 + + D F +L EP+ VNG + +PD PG G+ +N Sbjct: 339 FLMMAPKADEVVPMFTPLLLDEPV-PVNGRMKVPDTPGFGVRLN 381 Lambda K H 0.321 0.138 0.431 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: 425 Number of extensions: 25 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: 378 Length of database: 392 Length adjustment: 30 Effective length of query: 348 Effective length of database: 362 Effective search space: 125976 Effective search space used: 125976 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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