Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate YP_001328358.1 Smed_2693 short chain dehydrogenase
Query= metacyc::BSU31220-MONOMER (689 letters) >NCBI__GCF_000017145.1:YP_001328358.1 Length = 682 Score = 337 bits (865), Expect = 9e-97 Identities = 224/696 (32%), Positives = 355/696 (51%), Gaps = 47/696 (6%) Query: 12 AQLPKGVEE----LVYRSNLIGSDRTVCNWGGGNTSMKTTEKDFRGREIEVMWVKGSGSD 67 A + KGV Y + L+GSD + GGGNTS+KTT + G E++V+ VKGSG D Sbjct: 16 AYVAKGVNRDLAIRTYTTRLLGSDPELVLHGGGNTSVKTTFTEMDGSEVDVLCVKGSGWD 75 Query: 68 LATMKAHNFSGLKLDDIRPLIKRDQMPDEEMVDYLSHCMIDSKHPRPSIETLLHAFLPYK 127 + T++ ++L ++ +I + + D++MV ++D P PS+E +LHA LP+K Sbjct: 76 MGTIEPQGLPAVRLQPLQAMIDFETLSDDDMVMLQRRLLVDPAAPNPSVEAILHAILPFK 135 Query: 128 HVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLSKMIAEGVANNPHAELV 187 H+DHTH +AI+S+ +G+ + +++ + + VPYV PGF L+K +P + + Sbjct: 136 HIDHTHANAIVSLTNQPHGEDLIRELFPDAII-VPYVMPGFDLAKACDTAFKADPKGDGM 194 Query: 188 LMEKHGLVTWGETSETCYQKTISIIQEAEQYINDRINQHEVFGGKRYQPLPEDKRKQILA 247 ++ KHG+ TW E Y+ I+ I +AE+ R++Q K ++ + A Sbjct: 195 ILLKHGIFTWSEDPREAYEDMIAKIDKAER----RLSQGR---AKPFRSIAVPAGLAAAA 247 Query: 248 GIMPVIRGAVSEE-------KKMILSYDDHDDVLEFVNSVQAPALSQIGAACPDHLVHTK 300 I P++RGA++ + K+ +L + + +L+F N+ +L + G A P+H++H K Sbjct: 248 DIAPILRGALAIDTGIEGAPKRFVLEHRTSEKILDFCNAENIESLVRRGNATPEHVIHIK 307 Query: 301 RVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRNQQ---DGDQIFESAPRVILI 357 R + + PE + + A + V + ++YQAYF RN G ++ + PRV + Sbjct: 308 RFGVALP-APEKNRLGEWAVRAREAVAAYQADYQAYFERNNARVGGGKRMLDPKPRVFYV 366 Query: 358 PGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVSLHENESYHVEYWPLELYKLT 417 GIG+ G + + V + I V+ A + F +L E + + +EYW LE KLT Sbjct: 367 AGIGLFAAGAARKNATVGADVAEATIDVITKAEGIEAFEALSERDLFDIEYWSLEQVKLT 426 Query: 418 LAPPEAEFSRKVALITGGAGGIGSAACRRFAAEGGHVIVADLNIEGAQKIAGEINDAYGK 477 E +R+VA++TG A G+G A AEG + + D++ + +N A K Sbjct: 427 KV-QEKPLTRQVAIVTGAASGLGFAVAEALKAEGAELALFDISEDA-------LNAAAKK 478 Query: 478 GRAMAVKMDVTKEEDVQSAFERAALAYGGIDIVVNNAGLATS----SPFDETSLKEWNLN 533 A+ V DVT E V +A R A YGG+DI+++NAG A S + T K ++LN Sbjct: 479 LGALPVLCDVTSSEAVDAAVARVAQHYGGVDILISNAGAAFQGKLLSVDEATFRKAFDLN 538 Query: 534 MNVLGTGYFLVAREAFKQMKHQNRGGSMVFVGSKNSVYAGKNASAYSSVKALETHLARCI 593 + VAR + M+ Q GGS+VF SK +V G + Y + KA L R Sbjct: 539 F----WSHHYVARAVVRVMEQQKSGGSLVFNVSKQAVNPGADFGPYGTSKAALMALMRQY 594 Query: 594 AAEGGEFGIRVNSVLPDAVLQGSAIWGSSWREERAAAYGIEPDQLEEHYRKRTALLVNIY 653 A E G GI N+V D + G + EER+ A G+ P E Y + L + Sbjct: 595 AIEHGGSGITSNAVNADRIRTG--LMTDKMVEERSMARGLTP----EDYMRGNMLRREVT 648 Query: 654 PEDIAEAIAFFASSKAEKTTGCMITVDGGVPAAFTR 689 D+A A A KA +TG ++TVDGG AA R Sbjct: 649 GADVAAAFVHLA--KARTSTGAVVTVDGGNVAAMMR 682 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: 955 Number of extensions: 38 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: 682 Length adjustment: 39 Effective length of query: 650 Effective length of database: 643 Effective search space: 417950 Effective search space used: 417950 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