Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011809870.1 VEIS_RS10335 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase
Query= reanno::Smeli:SMc02322 (699 letters) >NCBI__GCF_000015565.1:WP_011809870.1 Length = 702 Score = 857 bits (2214), Expect = 0.0 Identities = 428/690 (62%), Positives = 522/690 (75%), Gaps = 4/690 (0%) Query: 14 WDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWVKGSG 73 WD AA + LLYRSNLLGSD RITNYGGGNTSAK+ + DPLTG+ V+VLWVKGSG Sbjct: 13 WDANHAATLDAARLLLYRSNLLGSDLRITNYGGGNTSAKIWQADPLTGQQVQVLWVKGSG 72 Query: 74 GDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTPLHAY 133 GD+G++ +DGFSTLYMDKL AL+ IYRG EDEMVGYLPHCTFNLNPR ASIDTPLHAY Sbjct: 73 GDLGSMALDGFSTLYMDKLLALQAIYRGPGHEDEMVGYLPHCTFNLNPRVASIDTPLHAY 132 Query: 134 VPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQENPD 193 +P HVDHMHPDA+IAIAA +S +LT +IF +GWLPW+RPG+ELGL L+++ +P Sbjct: 133 LPFAHVDHMHPDAVIAIAAMADSEKLTQQIFAGTVGWLPWRRPGFELGLMLQRYQAAHPG 192 Query: 194 ARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTG---PAFGGRSKPVLAAAD 250 RG+VL HGLF+WGD A+ Y+ T+ +I A W + E P+FGG ++ L+ + Sbjct: 193 QRGLVLAGHGLFSWGDDARACYDNTVGLIASAQNWLDRERVVRQVPSFGGPARQALSQDE 252 Query: 251 RAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRTKI 310 + A +++PV+RGL S K+ H + AVL+FV S L PLAALGTSCPDHFLRTKI Sbjct: 253 QDATLARVLPVLRGLASKTGPKLLHVERQAAVLEFVNSRDLAPLAALGTSCPDHFLRTKI 312 Query: 311 RPLVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDPNAVVYLVPGV 370 RPL+++ L E +A YRADY AYY+RC+RADSPA+RD N V+ L+PG+ Sbjct: 313 RPLILEPAVYMLQGAALAQALQERLAAYRADYGAYYQRCRRADSPALRDANPVIVLLPGI 372 Query: 371 GMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEAKLQRMP 430 GM+ AKDKATARI+AEFYVNAINVMR A + YVGLPEQEAFDIEYW LEEAKLQR P Sbjct: 373 GMVAMAKDKATARIAAEFYVNAINVMREAHAIDRYVGLPEQEAFDIEYWWLEEAKLQRSP 432 Query: 431 KPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTRYGKDFV 490 PK LAG++ALVTGGAGGIG+A A R++ EGACVVL DID+ AL EL+ +G D V Sbjct: 433 PPKPLAGKVALVTGGAGGIGRAIARRVLAEGACVVLVDIDQGALATVTAELAQAHGPDHV 492 Query: 491 RSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNMDILATG 550 R + +VTSEA+V + F A L FGGLDI VSNAG+A +A +EDT++ LWN + +LATG Sbjct: 493 RGLQCDVTSEASVIAAFRHAALEFGGLDIAVSNAGIAAAAPLEDTSIELWNHSQGVLATG 552 Query: 551 YFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLALEGASA 610 YFLV REAFR+ + Q AGG++V +ASKNG+ ASP ASAYC AKAAEI L+R ALEGA Sbjct: 553 YFLVGREAFRLMKAQGAGGSIVVIASKNGMVASPQASAYCAAKAAEIQLSRSFALEGAPW 612 Query: 611 QIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLKLSVFPEDIAEA 670 IR NVVNPDAV+RGS+IW+G+W +RAAA K+ +LEA YR+RSMLK SV PEDIAEA Sbjct: 613 GIRSNVVNPDAVIRGSRIWSGKWSAERAAANKIAEQDLEAFYRDRSMLKRSVLPEDIAEA 672 Query: 671 IYFLASD-MSAKSTGNIVNVDAGNAQSFTR 699 YF A++ +SAKSTGNI+NVDAGN +FTR Sbjct: 673 AYFFAAERLSAKSTGNILNVDAGNLAAFTR 702 Lambda K H 0.317 0.133 0.393 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: 1231 Number of extensions: 36 Number of successful extensions: 5 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: 699 Length of database: 702 Length adjustment: 39 Effective length of query: 660 Effective length of database: 663 Effective search space: 437580 Effective search space used: 437580 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 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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