Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate Echvi_3769 Echvi_3769 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >FitnessBrowser__Cola:Echvi_3769 Length = 386 Score = 490 bits (1262), Expect = e-143 Identities = 227/382 (59%), Positives = 290/382 (75%) Query: 1 MKITKLETFIVPPRWCFLKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYLIGKDPLLI 60 +KI ++E F VPPRW F+KI T G+VGWGEPV+EG+A TVAA V E+ YLIG+ I Sbjct: 5 LKIERIELFKVPPRWLFVKITTKSGLVGWGEPVIEGKADTVAACVREMEQYLIGRGAHEI 64 Query: 61 EDHWQVMYRSGFYRGGPITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKVYSWI 120 ED WQV+YR GFYRGGPI MSA++G+DQALWDIKGKH VP++ LLGG VR K+K+Y WI Sbjct: 65 EDIWQVLYRGGFYRGGPILMSALSGIDQALWDIKGKHLNVPVYELLGGAVRQKMKMYCWI 124 Query: 121 GGDRPSDVANNARAVVERGFKAVKMNGSEELQIIDTFDKVQGVINNVAAVREAVGPNIGI 180 GGD P V A+ V+ G+ AVKMN + E+ + + +V+ V+ N+ +R+ G ++ + Sbjct: 125 GGDHPEVVLEQAQEKVDAGYTAVKMNATGEMDWVSSVKEVKKVVENIKLIRQHFGDSLDV 184 Query: 181 GVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEALRDIVNQTNTPIALGERLYSR 240 G+DFHGRVHKPM K L EL P+ LFIEEPVL+EN +AL I + PIA GER++SR Sbjct: 185 GLDFHGRVHKPMVKRLIDELSPFDPLFIEEPVLAENNDALGHIYRYSAIPIATGERMFSR 244 Query: 241 WDFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAYDVALALHCPLGPIALATCLQID 300 WDFK IL G VDIIQPD SHAGGI+E R+IA+MAEAYD+ +A HCPLGPI+LA+ L +D Sbjct: 245 WDFKEILHQGVVDIIQPDLSHAGGISEVRRIATMAEAYDITIAPHCPLGPISLASALHVD 304 Query: 301 AVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDGFVSIPQGPGLGIEVNEEKVREM 360 VS NAFIQE SLGIHYNQG DLLDY+KNPEVF ++G++ + PGLG+E++EE+++E Sbjct: 305 FVSANAFIQESSLGIHYNQGFDLLDYVKNPEVFDLKEGYIDLFDRPGLGVEMDEERLKEG 364 Query: 361 AKVGHRWRNPVWRHEDGSVAEW 382 K+GH W NP+WR+ DGS AEW Sbjct: 365 QKIGHHWANPIWRNADGSFAEW 386 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: 502 Number of extensions: 19 Number of successful extensions: 1 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: 386 Length adjustment: 30 Effective length of query: 352 Effective length of database: 356 Effective search space: 125312 Effective search space used: 125312 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