Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate WP_012501687.1 CPAR_RS02225 bifunctional aldolase/short-chain dehydrogenase
Query= metacyc::BSU31220-MONOMER (689 letters) >NCBI__GCF_000020505.1:WP_012501687.1 Length = 706 Score = 337 bits (865), Expect = 9e-97 Identities = 222/708 (31%), Positives = 361/708 (50%), Gaps = 50/708 (7%) Query: 11 AAQLPKGVEELVYRSNLIGSDRTVCNWGGGNTSMKTTEKDFRGREIEVMWVKGSGSDLAT 70 AA P+ + +LVY S L+G D + GGGNTS+K+ DF G ++ V+++K SG +LA+ Sbjct: 20 AADTPEELVDLVYASRLLGKDDRLVMHGGGNTSVKSVLTDFIGNKVNVIFIKASGVNLAS 79 Query: 71 MKAHNFSGLKLDDIRPL--------------IKRDQMPDEEMVDYLSHCMID----SKHP 112 + A +F+ ++LD +R L IKR + + YL+ + S+ Sbjct: 80 VDAGDFTPVRLDPLRKLQQMYASGQRHSEDDIKRFSTREFKNFLYLNLFTLTDHMVSRSL 139 Query: 113 RPSIETLLHAFLPYKHVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLSK 172 PSIETLLHAFLP++++ HTH A++++ G ++ + G+ + VPY++PG L+K Sbjct: 140 SPSIETLLHAFLPHRYILHTHSLALLTLSNQTEGDRMCREALGDGYGMVPYIQPGLGLAK 199 Query: 173 MIAEGVANNPHAELVLMEKHGLVTWGETSETCYQKTISIIQEAEQYINDRINQHEVFGGK 232 E NP E +++ KHGLVT+G++++ Y + I + E+ I+ + +VF Sbjct: 200 SAFEAYEENPSIEGMVLHKHGLVTFGDSAKEAYDRMIDGVNRIEERISSA--ERKVFAS- 256 Query: 233 RYQPLPEDKRKQILAGIMPVIRGAVSEEK--------KMILSYDDHDDVLEFVNSVQAPA 284 +P + + P++RGA S EK +L + + +L+++ Sbjct: 257 ----VPMPASIATVEQVAPIVRGACSFEKTPGEKDYQSFVLEFRNSPALLDYLKIADLET 312 Query: 285 LSQIGAACPDHLVHTKRVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRNQQDG 344 ++ GA PD ++ TK PL + P+ D+ ++ VE + EY+AY+ R QQ Sbjct: 313 FARKGAMTPDFIIRTKNHPL-VAPAPDAADLEGFGKALRERVERYVEEYRAYYERQQQAT 371 Query: 345 D---QIFESAPRVILIPGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVSLHEN 401 + + PRV+L+PG+G+ G S +K++ + + M A ++G F S+ E Sbjct: 372 GMEVSMIDPMPRVVLVPGLGLFGLGLSAVDAKLTADIAEHSALAMLDAESIGCFESISER 431 Query: 402 ESYHVEYWPLELYKLTLAPPEAEFSRKVALITGGAGGIGSAACRRFAAEGGHVIVADLNI 461 +++ +EYW +E K+ EF+ KV ++TGGAG IG A + F +G +++ DL+ Sbjct: 432 DAFEIEYWDMEQAKVRKNRNGGEFAGKVVMVTGGAGAIGLATAKAFKQKGAELVIMDLDP 491 Query: 462 EGAQKIAGEINDAYGKGRAMAVKMDVTKEEDVQSAFERAALAYGGIDIVVNNAGLATSSP 521 K A E+ G G +A+ DVT V+SAF+ YGGIDI+V+N G+A Sbjct: 492 TALNKAAEEL----GAG-TLAIPCDVTDASVVRSAFDTICRTYGGIDIIVSNVGVALQGR 546 Query: 522 FDETSLKEWNLNMNVLGTGYFLVAREAFKQMKHQNRGGSMVFVGSKNSVYAGKNASAYSS 581 + S + + + + VA+ A K M+ Q GGS++F SK +V G + Y Sbjct: 547 IGDVSDELLRKSFEINFFSHQTVAQNAVKIMRAQKIGGSLLFNVSKQAVNPGADFGPYGL 606 Query: 582 VKALETHLARCIAAEGGEFGIRVNSVLPDAVLQGSAIWGSSWREERAAAYGIEPDQLEEH 641 KA L R A + G GIR N V D + G + + R+AA G+ E+ Sbjct: 607 PKAATLFLVRQYALDHGRDGIRANGVNADRIRSG--LLTPEMIKARSAARGLS----EKD 660 Query: 642 YRKRTALLVNIYPEDIAEAIAFFASSKAEKTTGCMITVDGGVPAAFTR 689 Y L + + ED+A+A A KTTG + TVDGG AA R Sbjct: 661 YMAGNLLGLEVTAEDVADAFVHLALE--AKTTGSITTVDGGNIAAALR 706 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: 974 Number of extensions: 44 Number of successful extensions: 6 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: 706 Length adjustment: 39 Effective length of query: 650 Effective length of database: 667 Effective search space: 433550 Effective search space used: 433550 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