Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate SM_b21015 SM_b21015 short-chain dehydrogenase
Query= metacyc::BSU31220-MONOMER (689 letters) >FitnessBrowser__Smeli:SM_b21015 Length = 416 Score = 187 bits (475), Expect = 9e-52 Identities = 126/429 (29%), Positives = 202/429 (47%), Gaps = 33/429 (7%) Query: 6 WDSERAAQL-----PKGVEEL----VYRSNLIGSDRTVCNWGGGNTSMKTTEKDFRGREI 56 W+ E AA+ +G E +Y S LIGSD + GGGNTS+K + Sbjct: 5 WNDEDAARFVEAARAEGQSEALGLRIYTSRLIGSDPDLVLHGGGNTSVKIRSDEGE---- 60 Query: 57 EVMWVKGSGSDLATMKAHNFSGLKLDDIRPLIKRDQMPDEEMVDYLSHCMIDSKHPRPSI 116 ++M +KGSG DL T++A ++L + ++ D +MV L +I+ P PS+ Sbjct: 61 QLMHIKGSGWDLDTIEAPGLPAVRLASLLEARNTPKLSDPDMVLLLRASLIEKDAPNPSV 120 Query: 117 ETLLHAFLPYKHVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLSKMIAE 176 E LLHAF+P+ +VDHTH A++++ N + IYG+R +VPYV PGF LS Sbjct: 121 EALLHAFIPFDYVDHTHATAVLALADQPNMRDAIRRIYGDRLAYVPYVMPGFDLSIAADR 180 Query: 177 GVANNPHAELVLMEKHGLVTWGETSETCYQKTISIIQEAEQYI---NDRINQHEVFGGKR 233 ++ E + +E HGL ++ + Y I + AEQ + ++ + G+R Sbjct: 181 IYRSHSDCEGLWLENHGLFSFANDARASYDLMIEFVTLAEQELARAGVALSGPQPNDGER 240 Query: 234 YQPLPEDKRKQILAGIMPVIRGAVSEEKKMILSYDDHDDVLEFVNSVQAPALSQIGAACP 293 L K ++ P +G + L Y + + E + +S G P Sbjct: 241 DAALAARLEKALMRERSPFAKG-------VFLDYRSTEAIRELTSKPNVETISLRGTVTP 293 Query: 294 DHLVHTKRVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRN---QQDGDQIFES 350 DH++ K P+ I + + I+S + + Y+AYF RN + +I + Sbjct: 294 DHVIRIKPWPMIIGADAD-------EPAIESALAAYADRYRAYFERNATRANEKKRILDV 346 Query: 351 APRVILIPGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVSLHENESYHVEYWP 410 PRV+L+ G GM G + +K+ G L +A + A A G F + E + + +EYW Sbjct: 347 YPRVVLVLGKGMFAIGANAKAAKIGGDLCEQAARAINAAEAYGCFTPISEADLFDMEYWS 406 Query: 411 LELYKLTLA 419 LE KL +A Sbjct: 407 LEQAKLKIA 415 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: 552 Number of extensions: 24 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: 689 Length of database: 416 Length adjustment: 35 Effective length of query: 654 Effective length of database: 381 Effective search space: 249174 Effective search space used: 249174 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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