Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate NP_662763.1 CT1886 aldehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000006985.1:NP_662763.1 Length = 460 Score = 160 bits (406), Expect = 6e-44 Identities = 128/398 (32%), Positives = 193/398 (48%), Gaps = 21/398 (5%) Query: 74 IAAKIRADAGR-IARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIASDRPG 132 IAA + AD + +A T E + S E+ F L + W R + + +P Sbjct: 44 IAAAVHADLRKPVAETWLTETAWLRS----EIRFV---LKRLHRWMRPKKVGVPLHYQPA 96 Query: 133 ENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVA 192 F+ R PLGVV I WN+P L + AL GN VVKPSE P A + Sbjct: 97 R-AFVERDPLGVVLIIGAWNYPLQLCLAPLIGALAGGNVSVVKPSEMAPATSALLASELG 155 Query: 193 ETDLPRGVFNVVCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGG 252 P+ V +V G G+ L H D I FTGS TG +M +AA +LT + LELGG Sbjct: 156 RYVDPQAV-RIVEGDGEASARLLEHC-FDHIFFTGSRRTGQAVMQSAARHLTPVTLELGG 213 Query: 253 KAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRY 312 K+P IV ADL LA + I ++ +N+GQ C + + VQ V EP + A+ Sbjct: 214 KSPVIVTEKADLRLAARRIAWAKFLNAGQTCVAPDYLLVQEGVKEPLQGLMKEALRLYYG 273 Query: 313 GDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCR 372 DP E + G +++ +++A L +G+ + GG + + + PT+L Sbjct: 274 SDP--EASADYGRIVDDRNFRRLEA----LLCEGSLVEGGG--SNKASRYIAPTILHDVP 325 Query: 373 ADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGE 432 D+ +M+EEIFGPVLP++ L+EA+++ + L +F+RD ++ + + + G Sbjct: 326 EDSDLMKEEIFGPVLPVRSFTTLEEAVSMVRALDAPLAVYLFSRDRSELRYLIEQTRSGG 385 Query: 433 TYINREHFEA-MQGFHAGVR-KSGIGGADGKHGLYEYT 468 N F+A + G G R SG+G GK G +T Sbjct: 386 VCCNDLLFQASIPGLPFGGRGMSGMGRYHGKAGFDTFT 423 Lambda K H 0.320 0.136 0.395 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: 464 Number of extensions: 24 Number of successful extensions: 3 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: 477 Length of database: 460 Length adjustment: 33 Effective length of query: 444 Effective length of database: 427 Effective search space: 189588 Effective search space used: 189588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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