Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_067913032.1 AQZ52_RS15535 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase
Query= reanno::Smeli:SMc02322 (699 letters) >NCBI__GCF_001519075.1:WP_067913032.1 Length = 702 Score = 831 bits (2147), Expect = 0.0 Identities = 425/690 (61%), Positives = 510/690 (73%), Gaps = 11/690 (1%) Query: 14 WDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWVKGSG 73 WDD AA ++ E LLYRSNLLGSD +TN+GGGNTSAK+ DPLTGE V VLWVKGSG Sbjct: 20 WDDAHAASLSPAELLLYRSNLLGSDLTVTNFGGGNTSAKLTGIDPLTGEAVPVLWVKGSG 79 Query: 74 GDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTPLHAY 133 GD+G++K+DGFSTLY +KL L+ Y G + +D MVGYLPHCTFNLN RAASIDTPLH+ Sbjct: 80 GDIGSMKLDGFSTLYQEKLLGLEAHYSGPDDDDTMVGYLPHCTFNLNGRAASIDTPLHSL 139 Query: 134 VPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQENPD 193 +P HVDH+HPDAIIA+AAS T I+G IGWLPWKRPGY LG+ L + + NP Sbjct: 140 LPFAHVDHVHPDAIIALAASSGGEAATRAIWGGTIGWLPWKRPGYTLGVMLRDYVRANPQ 199 Query: 194 ARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTG-PAFGGRSKPVLAAADRA 252 +GV+L HG+ W D+AK YE TI +I A G PAFGG+ V DRA Sbjct: 200 VKGVMLAGHGIICWADSAKACYEHTISLIADAARHLNAAMAGKPAFGGQI--VAPNPDRA 257 Query: 253 AIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRTKIRP 312 AIA LMP +RGL++ K+GHF D L+F S + LAALGTSCPDHFLRTKI P Sbjct: 258 AIAADLMPRLRGLMTGARRKLGHFSDDAEALEFTGSADFQRLAALGTSCPDHFLRTKIAP 317 Query: 313 LVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDPNAVVYLVPGVGM 372 L +D D A L + +A YRA YAAYYERCKRA+SPAMRDPN VV LVPGVG Sbjct: 318 LTLDPARLTDD-----AYLAQQLADYRALYAAYYERCKRANSPAMRDPNPVVVLVPGVGR 372 Query: 373 ITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEAKLQRMPKP 432 ITFA DK TAR++ EFY NAINVMRGA + Y+ L EQEAFDIEYWLLEEAKLQRMP P Sbjct: 373 ITFATDKTTARLAGEFYGNAINVMRGAEAIGDYIALDEQEAFDIEYWLLEEAKLQRMPAP 432 Query: 433 KSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTRYGKDFVRS 492 K + GRIALVTGGAGGIG ATA RL++EGACV+LAD D ALE + L+ ++GKD +R+ Sbjct: 433 KPMVGRIALVTGGAGGIGAATAVRLLKEGACVLLADRDADALEETRAGLAQQFGKDVIRA 492 Query: 493 VNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNMDILATGYF 552 +VT EAAV + F FGGLD+LV+NAG+A+SA +E+TTL+LW++N D+LA GYF Sbjct: 493 ATCDVTDEAAVAAAFAACAREFGGLDMLVANAGIASSATIEETTLSLWHRNHDVLAQGYF 552 Query: 553 LVSREAFRIFRNQK--AGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLALEGASA 610 L +R A+ + + K G +VVF+ SKN LAA+ GASAY +AKAA HLARCLALEGA Sbjct: 553 LTARAAWPLLKRMKEQGGTSVVFIGSKNALAAAAGASAYASAKAAANHLARCLALEGAPD 612 Query: 611 QIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDV-DELEAHYRERSMLKLSVFPEDIAE 669 IRVN+VNPDAV+RGS+IW G+W+++RAAA K+D +ELEAHYR RSMLK V PEDIAE Sbjct: 613 GIRVNIVNPDAVIRGSRIWDGDWRKERAAANKVDAGEELEAHYRNRSMLKRDVLPEDIAE 672 Query: 670 AIYFLASDMSAKSTGNIVNVDAGNAQSFTR 699 A +LASD+SAKSTGN++NVDAGN Q+FTR Sbjct: 673 AAAWLASDLSAKSTGNMINVDAGNVQAFTR 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: 1233 Number of extensions: 52 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