Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate WP_012466873.1 CLIM_RS09915 bifunctional aldolase/short-chain dehydrogenase
Query= metacyc::BSU31220-MONOMER (689 letters) >NCBI__GCF_000020465.1:WP_012466873.1 Length = 705 Score = 346 bits (888), Expect = 2e-99 Identities = 226/716 (31%), Positives = 366/716 (51%), Gaps = 67/716 (9%) Query: 11 AAQLPKGVEELVYRSNLIGSDRTVCNWGGGNTSMKTTEKDFRGREIEVMWVKGSGSDLAT 70 A +P + ELVY S L+G + ++ GGGNTS+K+ D G + V+++KGSG DLA Sbjct: 20 ADDIPAELAELVYASRLLGRESSLVMHGGGNTSVKSELHDIIGNRVNVIFIKGSGVDLAA 79 Query: 71 MKAHNFSGLKLDDIRPL----IKRDQMPDEEM---------------VDYLSHCMIDSKH 111 + AH+F+ ++++ ++ L ++ +E+M + YL+ M+++ Sbjct: 80 LDAHDFTPVRIEPLQKLQHLYATGERRSEEDMQRFSTREFKNFLYLNLFYLTDHMVNNSL 139 Query: 112 PRPSIETLLHAFLPYKHVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLS 171 PSIETLLHAFLP++ + HTH A++++ NG ++ ++ G F VPY++PG L+ Sbjct: 140 S-PSIETLLHAFLPHRFIFHTHSTALLTLSNQPNGAELCREVLGEEFGLVPYIKPGLGLA 198 Query: 172 KMIAEGVANNPHAELVLMEKHGLVTWGETSETCYQKTISIIQEAEQYINDRINQHEVFGG 231 + AE N P ++++KHGLVT +++ Y I + + E+ I G Sbjct: 199 RSAAEAYGNAPDIRGLVLQKHGLVTLADSAAAAYDCMIECVSKLEERI--------ARAG 250 Query: 232 KRYQP---LPEDKRKQILAGIMPVIRGAVSEEK--------KMILSYDDHDDVLEFVNSV 280 + P LPE +L + PVIRGAV EEK + +L + D+L++VN + Sbjct: 251 RNVFPSISLPE--TVALLEDVAPVIRGAVVEEKSPGTFEYNQFVLDFRSSPDILQYVNGI 308 Query: 281 QAPALSQIGAACPDHLVHTKRVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRN 340 + +S GA PD ++ TK PL + P+ D + VE + +EY AYF R Sbjct: 309 ELEEVSGRGAMTPDFIIRTKNRPLVVP-APDALDPEGFKSAVHEAVERYKAEYLAYFQRQ 367 Query: 341 QQ-DGDQI--FESAPRVILIPGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVS 397 QQ G Q+ + PRV+L+PG+G+ G++ + V+ + + + A ++G F S Sbjct: 368 QQASGMQVTMLDPLPRVVLVPGLGLFGLGRTAHAASVNADIAESTASAILDAQSVGTFES 427 Query: 398 LHENESYHVEYWPLELYKLTLAPPEAEFSRKVALITGGAGGIGSAACRRFAAEGGHVIVA 457 + E + +++EYW +E K+ + F+ KVAL+TG A GIG A + F G +++ Sbjct: 428 ITERDVFNIEYWEMEQAKMKKVRHDV-FAGKVALVTGAASGIGLATAKAFRQRGAELVIV 486 Query: 458 DLNIEGAQKIAGEINDAYGKGRAMAVKMDVTKEEDVQSAFERAALAYGGIDIVVNNAGLA 517 DLN E ++ + E+ G +++ DVT V+ AF+ +GG+DI+V+N G+A Sbjct: 487 DLNPEALERASAELG-----GGVLSIACDVTDRNAVKRAFDAVCRRFGGLDILVSNVGVA 541 Query: 518 TSSPF----DETSLKEWNLNMNVLGTGYFLVAREAFKQMKHQNRGGSMVFVGSKNSVYAG 573 DE + + LN + +A++A + MK Q GG ++F SK +V G Sbjct: 542 LQGRIGDVADEVLRRSFELNF----FSHQSIAQQAVRIMKLQGTGGVLLFNVSKQAVNPG 597 Query: 574 KNASAYSSVKALETHLARCIAAEGGEFGIRVNSVLPDAVLQGSAIWGSSWREERAAAYGI 633 + Y KA L R A + G GIR N + D + G + + R+ A G+ Sbjct: 598 PDFGPYGLPKAATMFLVRQYALDHGRDGIRANGINADRIRTG--LLTDEMIKTRSKARGL 655 Query: 634 EPDQLEEHYRKRTALLVNIYPEDIAEAIAFFASSKAEKTTGCMITVDGGVPAAFTR 689 E Y L V + ED+AE AF + KTTG ++TVDGG AA R Sbjct: 656 S----EREYMAGNLLQVEVTAEDVAE--AFVHQALETKTTGSIVTVDGGNIAAALR 705 Lambda K H 0.317 0.134 0.396 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: 1017 Number of extensions: 46 Number of successful extensions: 9 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: 689 Length of database: 705 Length adjustment: 39 Effective length of query: 650 Effective length of database: 666 Effective search space: 432900 Effective search space used: 432900 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