Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate CA265_RS12250 CA265_RS12250 enolase
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >FitnessBrowser__Pedo557:CA265_RS12250 Length = 388 Score = 170 bits (430), Expect = 7e-47 Identities = 115/358 (32%), Positives = 180/358 (50%), Gaps = 30/358 (8%) Query: 20 IETDEGIVGWGEPVVEGRAHTVAAAV-----EELSDYLIGKDPLLIEDHWQVMYRS---- 70 I TD G+ G+GE + + A++ EL L+GK I W+ MY Sbjct: 38 ITTDSGLQGFGEAKAAVGSCGICASIVNCIENELKPMLLGKSVKNITRLWEEMYNGTRDH 97 Query: 71 -GFYRGGP--------ITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSWIG 121 RG +T+SA++G+D ALWD+KGK VP+ LLGG R K+ Y+ G Sbjct: 98 YALSRGRKFPILGRRGLTISAMSGIDTALWDLKGKMLNVPVADLLGGACRTKMPAYASGG 157 Query: 122 GDRPSDVANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGIG 181 ++ V +GFK VKM + ++D D VQ IN V A R A+GP+I + Sbjct: 158 WADEQNIGEQLMGYVNKGFKGVKMR----VGVMD--DTVQKSINRVKAARAALGPDIKLM 211 Query: 182 VDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSRW 241 VD HG P AK + ++ + + EEP+ +N + ++ T+ PIA GE ++ + Sbjct: 212 VDAHGTFSVPEAKQFCRGVEDCNVYWFEEPISPDNRKGTAEVRAATDIPIAAGESEFTSF 271 Query: 242 DFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPLGPIALATCLQIDA 301 D +L +D++QPDA+ GGI+E +++ +A + V LA HC + L + Sbjct: 272 DIHDLLQIRAIDVVQPDAAIIGGISEAMRVSHLASVHQVELAPHCWGSAFSFMAGLTVAF 331 Query: 302 VSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNEEKVRE 359 S +A I E SLG GN ++ + N ++ +G +S P PGLG+ N + V++ Sbjct: 332 ASASATIIEFSLG-----GNPMMYDLVNEQI-AVVNGEISAPTAPGLGLTPNWDFVKQ 383 Lambda K H 0.319 0.139 0.428 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: 358 Number of extensions: 19 Number of successful extensions: 3 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: 382 Length of database: 388 Length adjustment: 30 Effective length of query: 352 Effective length of database: 358 Effective search space: 126016 Effective search space used: 126016 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 (21.7 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