Align gluconate/galactonate dehydratase (EC 4.2.1.140) (characterized)
to candidate AZOBR_RS25270 AZOBR_RS25270 mandelate racemase
Query= BRENDA::Q97U27 (395 letters) >FitnessBrowser__azobra:AZOBR_RS25270 Length = 397 Score = 203 bits (517), Expect = 6e-57 Identities = 117/359 (32%), Positives = 206/359 (57%), Gaps = 10/359 (2%) Query: 22 ASIMIVTRVITENGEVGYGEAVPTL---RVISVYNAIKQVSKAYIGKEVEEVEKNYHEWY 78 A ++ R+ TE+G G+GE T +V++ Y + ++ IG+E+ + + + Sbjct: 16 AKNLLFVRIETESGIYGWGEGYVTAGKEKVVAAY--VDAIAPLLIGREIWNI-RQLAQTL 72 Query: 79 KQDFYLAR-SFESATAVSAIDIASWDIIGKELGAPIHKLLGGKTRDRVPVYANGWYQDCV 137 DF + R S + A+SA++IASWDI+GK G P+HKLLGG R+++ VYANGW+ Sbjct: 73 LDDFSIRRTSVDFLCALSAVEIASWDIVGKRAGLPVHKLLGGAVREKIRVYANGWWFGAS 132 Query: 138 TPEEFAEKAKDVVKMGYKALKFDPF-GPYYDWIDERGLREAEERVKAVREAVGDNVDILI 196 + ++ A +A VV GY ALK+DP GP+ +++D + L A E V+AVREAVG NV++LI Sbjct: 133 SIDDTANRAAAVVAQGYDALKWDPIPGPWRNYVDPKDLDHAVENVRAVREAVGPNVELLI 192 Query: 197 EHHGRFNANSAIMIAKRLEKYNPGFMEEPVHHEDVIGLRKYKASTHLRVALGERLISEKE 256 + H R + N AI + +RL ++ + EEP E++ + + +T++ + GE L ++++ Sbjct: 193 DGHRRLSPNHAIRLIERLREFGIAWYEEPCPPENLDLTAEVRRTTNVPIVSGEALYTKEQ 252 Query: 257 TAFYVEEGLVNILQPDLTNIGGVTVGRSVIKIAEANDVEVAFHNAFGSIQN-AVEIQLSA 315 E+ +I+ PD++ +GG+ + +A+ + + V+ HN I A + LSA Sbjct: 253 YLPLFEKRAADIINPDISAVGGILAMLDIAALAQPHSIAVSPHNFNSPIVGLAATVHLSA 312 Query: 316 VTQNLYLLENFYDWFPQWKRDLVYNETPVEGGHVKVPYKPGLGVSINEKIIEQLRAEPI 374 + N + E F + + R+L + G+V +P PGLGV ++ +++ + +P+ Sbjct: 313 LVTNFTIAELFVN-LVEPTRELALQGLTIADGYVDIPDTPGLGVDLDVEVLRRHPYQPL 370 Lambda K H 0.317 0.136 0.405 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: 392 Number of extensions: 18 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: 395 Length of database: 397 Length adjustment: 31 Effective length of query: 364 Effective length of database: 366 Effective search space: 133224 Effective search space used: 133224 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 (21.6 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