Align Lactaldehyde dehydrogenase (EC 1.2.1.22); Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) (characterized)
to candidate Echvi_1572 Echvi_1572 rhamnulose-1-phosphate aldolase/alcohol dehydrogenase
Query= reanno::Cola:Echvi_1572 (702 letters) >FitnessBrowser__Cola:Echvi_1572 Length = 702 Score = 1408 bits (3644), Expect = 0.0 Identities = 702/702 (100%), Positives = 702/702 (100%) Query: 1 MSTAERTFKHVNYLWDEQKAQELEGDEVALLIYRSNILGADLRITNYGGGNTSCKTTEVD 60 MSTAERTFKHVNYLWDEQKAQELEGDEVALLIYRSNILGADLRITNYGGGNTSCKTTEVD Sbjct: 1 MSTAERTFKHVNYLWDEQKAQELEGDEVALLIYRSNILGADLRITNYGGGNTSCKTTEVD 60 Query: 61 PLTKEETEVMWVKGSGGDIGTLKRSGLAGLYVEKLHSLKNVYRGLEFEDEMVGLFNHCIY 120 PLTKEETEVMWVKGSGGDIGTLKRSGLAGLYVEKLHSLKNVYRGLEFEDEMVGLFNHCIY Sbjct: 61 PLTKEETEVMWVKGSGGDIGTLKRSGLAGLYVEKLHSLKNVYRGLEFEDEMVGLFNHCIY 120 Query: 121 DLDSKAPSIDTPLHAFLPFKHIDHLHPDAAIAIAASKDGEKITEELFEGQIAWVPWQRPG 180 DLDSKAPSIDTPLHAFLPFKHIDHLHPDAAIAIAASKDGEKITEELFEGQIAWVPWQRPG Sbjct: 121 DLDSKAPSIDTPLHAFLPFKHIDHLHPDAAIAIAASKDGEKITEELFEGQIAWVPWQRPG 180 Query: 181 FDLALQLEKALNENPGIRGIMLGGHGLFTWGDTAYECYINSLEVIDKASEYLEQNYGKDR 240 FDLALQLEKALNENPGIRGIMLGGHGLFTWGDTAYECYINSLEVIDKASEYLEQNYGKDR Sbjct: 181 FDLALQLEKALNENPGIRGIMLGGHGLFTWGDTAYECYINSLEVIDKASEYLEQNYGKDR 240 Query: 241 PVFGGQKIESLAPEQRQEQASIIAPVLRGLASGYNRMVGHFTDDERVLQFANSHDLEKLA 300 PVFGGQKIESLAPEQRQEQASIIAPVLRGLASGYNRMVGHFTDDERVLQFANSHDLEKLA Sbjct: 241 PVFGGQKIESLAPEQRQEQASIIAPVLRGLASGYNRMVGHFTDDERVLQFANSHDLEKLA 300 Query: 301 PLGTSCPDHFLRTKIRPLVLDFPADVDLSKADEIKEKLDKDFEEYRAYYKKYYEDHKRDN 360 PLGTSCPDHFLRTKIRPLVLDFPADVDLSKADEIKEKLDKDFEEYRAYYKKYYEDHKRDN Sbjct: 301 PLGTSCPDHFLRTKIRPLVLDFPADVDLSKADEIKEKLDKDFEEYRAYYKKYYEDHKRDN 360 Query: 361 SPAMRDPNPVVIIWPGVGMFSYAKNKQTARVASEFYINAINVMRGAEAVSEYVALPLQEA 420 SPAMRDPNPVVIIWPGVGMFSYAKNKQTARVASEFYINAINVMRGAEAVSEYVALPLQEA Sbjct: 361 SPAMRDPNPVVIIWPGVGMFSYAKNKQTARVASEFYINAINVMRGAEAVSEYVALPLQEA 420 Query: 421 FDIEYWLLEEAKLQRMPKEQPLSRKVALVTGGAGGIGKAIADKLASEGACVFITDINQER 480 FDIEYWLLEEAKLQRMPKEQPLSRKVALVTGGAGGIGKAIADKLASEGACVFITDINQER Sbjct: 421 FDIEYWLLEEAKLQRMPKEQPLSRKVALVTGGAGGIGKAIADKLASEGACVFITDINQER 480 Query: 481 LDGAVATYSKDVGGGAVMDVTKGDDIIKAYKAAALKFGGVDIIVNCAGLAISKPIEQTSE 540 LDGAVATYSKDVGGGAVMDVTKGDDIIKAYKAAALKFGGVDIIVNCAGLAISKPIEQTSE Sbjct: 481 LDGAVATYSKDVGGGAVMDVTKGDDIIKAYKAAALKFGGVDIIVNCAGLAISKPIEQTSE 540 Query: 541 QDWDLLQDILVKGQFAVSKAGVETLRAQNLGGDIINIASKNALVSGPNNVGYGTAKAAQV 600 QDWDLLQDILVKGQFAVSKAGVETLRAQNLGGDIINIASKNALVSGPNNVGYGTAKAAQV Sbjct: 541 QDWDLLQDILVKGQFAVSKAGVETLRAQNLGGDIINIASKNALVSGPNNVGYGTAKAAQV 600 Query: 601 HMSRLLAAELGKDKIRVNVVNPDAVIEGSKIWEGEWAKGRAKAYGITVEELPAFYAKRTI 660 HMSRLLAAELGKDKIRVNVVNPDAVIEGSKIWEGEWAKGRAKAYGITVEELPAFYAKRTI Sbjct: 601 HMSRLLAAELGKDKIRVNVVNPDAVIEGSKIWEGEWAKGRAKAYGITVEELPAFYAKRTI 660 Query: 661 LNEIIGVDDIANGVFAFVGGHLSKCTGNILNVDGGVAAAFVR 702 LNEIIGVDDIANGVFAFVGGHLSKCTGNILNVDGGVAAAFVR Sbjct: 661 LNEIIGVDDIANGVFAFVGGHLSKCTGNILNVDGGVAAAFVR 702 Lambda K H 0.317 0.136 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: 1726 Number of extensions: 57 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: 702 Length of database: 702 Length adjustment: 39 Effective length of query: 663 Effective length of database: 663 Effective search space: 439569 Effective search space used: 439569 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: 54 (25.4 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