Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate HSERO_RS00730 HSERO_RS00730 4-hydroxybutyrate dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__HerbieS:HSERO_RS00730 Length = 379 Score = 188 bits (478), Expect = 2e-52 Identities = 126/352 (35%), Positives = 185/352 (52%), Gaps = 22/352 (6%) Query: 32 KALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTEELVQKGFAAYQSAECDYI 91 K L+VTD + GLLD + L E + ++D+ PNP E V+ A ++ CD I Sbjct: 31 KPLVVTDMGIRNAGLLDKVLGQLKEG-VGAVVYDQTPPNPNEGAVRAAVALFRQHGCDGI 89 Query: 92 IAFGGGSPIDTAKAVKILTANPGPSTAYS----GVGKVKNAGVPLVAINTTAGTAAEMTS 147 +A GGGS ID AK V + + GP +++ G+ + P++AI TTAGT +E+ Sbjct: 90 VAVGGGSSIDLAKGVAVCGTHEGPLKSFALIEGGLANITAKTAPVIAIPTTAGTGSEVGR 149 Query: 148 NAVII-DSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMDALTHAVEAYVSVG 206 A++I D RKV II P ++P +A+ D + L +P +TAATGMDA+ H +E +++ Sbjct: 150 GAILILDDGRKVG--IISPYLVPKLAICDPELTLGLPPLMTAATGMDAIAHCLETFMAPS 207 Query: 207 AHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAFNSAGLGLVHALAH 266 +P D AL+ + + +A + + EAR M MAF GLG VH+L+H Sbjct: 208 FNPPADGIALDGLWRAWAHIERATREPGDREARLNMMSASMQGAMAFQK-GLGCVHSLSH 266 Query: 267 QPGATH-NLPHGVCNAILLPIVENFNRPNAVA----RFARIAQAMGVETRGMSDEAASQE 321 G + L HG NAI LP + FN A + AR+A AMG+ + E Sbjct: 267 SLGGINPRLHHGTLNAIFLPAIIAFNESAASMVKDNKMARMAHAMGL--------GSGAE 318 Query: 322 AINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRTASRDE 373 AIR +S+R+G+P G +LGVT+ + ALAD NPR AS + Sbjct: 319 IGPAIREMSRRLGLPAGLGELGVTESMFPQIIQGALADHSHKTNPREASEQD 370 Lambda K H 0.317 0.133 0.384 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: 397 Number of extensions: 20 Number of successful extensions: 7 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: 382 Length of database: 379 Length adjustment: 30 Effective length of query: 352 Effective length of database: 349 Effective search space: 122848 Effective search space used: 122848 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: 50 (23.9 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