Align Lactaldehyde dehydrogenase (EC 1.2.1.22); Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) (characterized)
to candidate CA265_RS02630 CA265_RS02630 short-chain dehydrogenase
Query= reanno::Cola:Echvi_1572 (702 letters) >FitnessBrowser__Pedo557:CA265_RS02630 Length = 706 Score = 1006 bits (2601), Expect = 0.0 Identities = 495/706 (70%), Positives = 583/706 (82%), Gaps = 4/706 (0%) Query: 1 MSTAERTFKHVNYLWDEQKAQELEGDEVALLIYRSNILGADLRITNYGGGNTSCKTTEVD 60 MS +++KHV+YLWDE++A +L GDEVALLIYRSN+LGADLR+TNYGGGNTSCK E D Sbjct: 1 MSIDTKSYKHVSYLWDEEEAAKLAGDEVALLIYRSNLLGADLRLTNYGGGNTSCKVLEKD 60 Query: 61 PLTKEETEVMWVKGSGGDIGTLKRSGLAGLYVEKLHSLKNVYRGLEFEDEMVGLFNHCIY 120 PLT ETEVMWVKGSGGD+GTLK+SGLA LYV++L SLKN+YRG+E EDEMV LFNHCI+ Sbjct: 61 PLTGLETEVMWVKGSGGDLGTLKKSGLAALYVDRLRSLKNIYRGVEHEDEMVELFNHCIF 120 Query: 121 DLDSKAPSIDTPLHAFLPFKHIDHLHPDAAIAIAASKDGEKITEELFEGQIAWVPWQRPG 180 DL SKAPSIDTPLH FLPF HIDHLHPDAAIAIAA+KDG+KITEELF G I WV W++PG Sbjct: 121 DLSSKAPSIDTPLHGFLPFAHIDHLHPDAAIAIAAAKDGKKITEELFGGTIGWVEWKKPG 180 Query: 181 FDLALQLEKALNENPGIRGIMLGGHGLFTWGDTAYECYINSLEVIDKASEYLEQNYGKDR 240 F+L LQL++ L+ENPGIRGIMLG HGLFTWGDTAYE Y+N+LEVI+ S+YL QNYGK Sbjct: 181 FELGLQLKQCLDENPGIRGIMLGSHGLFTWGDTAYESYLNTLEVIEICSDYLNQNYGKKG 240 Query: 241 PVFGGQKIESLAPEQRQEQASIIAPVLRGLASGYNRMVGHFTDDERVLQFANSHDLEKLA 300 PVFGGQKIES A +QR++QA+ +APVLRGL S M+GHFTDD RVL+F NS+DL++LA Sbjct: 241 PVFGGQKIESAAADQRKKQAAALAPVLRGLCSSKQHMIGHFTDDARVLEFINSNDLDRLA 300 Query: 301 PLGTSCPDHFLRTKIRPLVLDFPADVDLSKADEIKEKLDKDFEEYRAYYKKYYEDHKRDN 360 P+GTSCPDHFLRTKI PLVL +D DLS +KE L+ FE YRA Y YYE K N Sbjct: 301 PMGTSCPDHFLRTKISPLVLTLTSDADLSDVKALKETLEPAFEAYRAMYTAYYEACKHPN 360 Query: 361 SPAMRDPNPVVIIWPGVGMFSYAKNKQTARVASEFYINAINVMRGAEAVSEYVALPLQEA 420 SPA+RD NPVVI++PG+GMF+++K+KQTARVA+EFYINAINVM+GAEAVS Y +LP QEA Sbjct: 361 SPAIRDTNPVVILYPGIGMFTFSKDKQTARVAAEFYINAINVMKGAEAVSAYTSLPHQEA 420 Query: 421 FDIEYWLLEEAKLQRMPKEQPLSRKVALVTGGAGGIGKAIADKLASEGACVFITDINQER 480 F+IEYWLLEEAKLQRMPK +PL+ K+AL+TG AGGIGKAIA K +EG V + D+N ER Sbjct: 421 FNIEYWLLEEAKLQRMPKPKPLTGKIALITGSAGGIGKAIAKKFVAEGGVVILNDMNAER 480 Query: 481 LDGA----VATYSKDVGGGAVMDVTKGDDIIKAYKAAALKFGGVDIIVNCAGLAISKPIE 536 L+ A + KD AV++VT +DI +A+ +AAL FGGVDIIVN AGL+ISK I Sbjct: 481 LEEAAKEFAGLFGKDSYSTAVLNVTSEEDIKQAFDSAALAFGGVDIIVNNAGLSISKTIA 540 Query: 537 QTSEQDWDLLQDILVKGQFAVSKAGVETLRAQNLGGDIINIASKNALVSGPNNVGYGTAK 596 +E+DWDLL D+LVKGQF +++A T++ Q++GGDIINI SKNALVSGPNN GYG+AK Sbjct: 541 DHTEKDWDLLYDVLVKGQFFITQAATNTMQKQDIGGDIINIVSKNALVSGPNNAGYGSAK 600 Query: 597 AAQVHMSRLLAAELGKDKIRVNVVNPDAVIEGSKIWEGEWAKGRAKAYGITVEELPAFYA 656 AAQ+H+SRL AAELG D IRVNVVNPDAVI S IW G WA+GRAKAYGITV ELPA+YA Sbjct: 601 AAQLHLSRLNAAELGADNIRVNVVNPDAVISDSNIWAGGWAEGRAKAYGITVAELPAYYA 660 Query: 657 KRTILNEIIGVDDIANGVFAFVGGHLSKCTGNILNVDGGVAAAFVR 702 KRT+LN+II DDIAN FAFVGG L K TGN+LNVDGGVA AFVR Sbjct: 661 KRTLLNQIILPDDIANACFAFVGGLLHKSTGNVLNVDGGVAMAFVR 706 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: 1409 Number of extensions: 58 Number of successful extensions: 2 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: 706 Length adjustment: 39 Effective length of query: 663 Effective length of database: 667 Effective search space: 442221 Effective search space used: 442221 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