Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate WP_110805876.1 C8J30_RS10870 bifunctional aldolase/short-chain dehydrogenase
Query= metacyc::BSU31220-MONOMER (689 letters) >NCBI__GCF_003217355.1:WP_110805876.1 Length = 677 Score = 309 bits (791), Expect = 3e-88 Identities = 222/696 (31%), Positives = 342/696 (49%), Gaps = 40/696 (5%) Query: 1 MVKHIWDSERAAQLPKGVEELVYRSNLIGSDRTVCNWGGGNTSMKTTEKDFRGREIEVMW 60 M++++W E AA + + +Y S LIGSD + GGGNTS+KT D G + V+ Sbjct: 1 MIRNLWSDEAAAAAGGDLGQRIYTSRLIGSDPELVLHGGGNTSVKTEAVDLFGETVSVLH 60 Query: 61 VKGSGSDLATMKAHNFSGLKLDDIRPLIKRDQMPDEEMVDYLSHCMIDSKHPRPSIETLL 120 VKGSG DLAT+ A ++LD + L D +PD+ +V ++D P PS+E LL Sbjct: 61 VKGSGHDLATIDAAGMPAVRLDPMLRLKDFDAVPDDVLVKLQRLNLLDPAAPNPSVEMLL 120 Query: 121 HAFLPYKHVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLSKMIAEGVAN 180 H FLP+K VDHTH + + + +++G+R VP+V+PGF L+K A Sbjct: 121 HVFLPHKFVDHTHATPFLVLANLPEAEAAIRELFGDRMALVPFVKPGFGLAKAGLATYAA 180 Query: 181 NPHAELVLMEKHGLVTWGETSETCYQKTISIIQEAEQYINDRINQHEVFGGKRYQPLPED 240 +P E +L++ HG TWG +++ Y K I+ E ++ DR + LP Sbjct: 181 HPGVEALLLKNHGHFTWGPDAKSSYFKVIAHANLVEAWLADRRPAPLLPAA----ALPVA 236 Query: 241 KRKQILAGIMPVIRGAVSEEKKM-ILSYDDHDDVLEFVNSVQAPALSQIGAACPDHLVHT 299 + +LA + + A+ EE + +L D FV+ AL++ G PDH++ T Sbjct: 237 EVAPVLAALRGALASALPEEAALPVLDLRADDATRAFVSRPDLEALAKAGVVTPDHVIRT 296 Query: 300 KRVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRNQ-QDGDQI--FESAPRVIL 356 K L + + + + +++ V + S Y+AYF N+ + G + P +I Sbjct: 297 KGEVLVL------RQAAQRPEAMRAAVTDYVSRYRAYFEANKARFGGPVAMLNPMPGLIW 350 Query: 357 IPGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVSLHENESYHVEYWPLELYKL 416 + GIG V G ++++ + ++ V A G F S+ + + + +EYWPLEL KL Sbjct: 351 LEGIGAVGAGADAKAARIAADIGDQSARVKADGLAAGGFRSIADADLFDMEYWPLELAKL 410 Query: 417 TLAPPEAEFSRKVALITGGAGGIGSAACRRFAAEGGHVIVADLNIEGAQK-IAGEINDAY 475 A A +V L+TGGAG IG A FAA+G + + D E +K +AG DA Sbjct: 411 GTAKAPA-LQGRVVLVTGGAGAIGLATAEAFAAQGASIFLVDRPGEVLEKAVAGLGRDAA 469 Query: 476 GKGRAMAVKMDVTKEEDVQSAFERAALAYGGIDIVVNNAGLATS---SPFDETSLKEWNL 532 G G D+T+ +A A +GG+DI+V+NAG A + + DE L+ + Sbjct: 470 GHG------CDITQPGAAAAAVAACAARFGGLDILVSNAGAAITGDIATLDEQVLR-GSF 522 Query: 533 NMNVLGTGYFLVAREAFKQMKHQNRG------GSMVFVGSKNSVYAGKNASAYSSVKALE 586 +N F A A + + RG G ++F SK +V GK +AY KA Sbjct: 523 ELNFFSHLAFSQAAIALYRAQAAGRGTRGAEPGQILFNVSKQAVNPGKGFAAYGLPKATS 582 Query: 587 THLARCIAAEGGEFGIRVNSVLPDAVLQGSAIWGSSWREERAAAYGIEPDQLEEHYRKRT 646 L R +A E G GIRVN + D + G + R++A GI+ Y Sbjct: 583 FFLLRQLALELGPEGIRVNGINADRIRSG--LLTPEMIAARSSARGIDAGT----YMAGN 636 Query: 647 ALLVNIYPEDIAEAIAFFASSKAEKTTGCMITVDGG 682 L V + +AE AF A ++AE+TT ++TVDGG Sbjct: 637 LLKVEVEARHVAE--AFVALARAERTTAHVMTVDGG 670 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: 978 Number of extensions: 47 Number of successful extensions: 8 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: 677 Length adjustment: 39 Effective length of query: 650 Effective length of database: 638 Effective search space: 414700 Effective search space used: 414700 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