Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >FitnessBrowser__Dyella79:N515DRAFT_2488 Length = 463 Score = 224 bits (570), Expect = 6e-63 Identities = 145/449 (32%), Positives = 224/449 (49%), Gaps = 3/449 (0%) Query: 27 NPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHLRRIAAKIRADAGRIA 86 NP G + P+A+ EV +AL A+A + W R L++ A +R + A Sbjct: 7 NPYTGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESHTQYA 66 Query: 87 RTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEG-EIIASDRPG-ENIFLFRKPLGV 144 + +TLE GK+ AE EV A L+Y A+ A +L E ++S P ++ P G+ Sbjct: 67 KVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQSWVEHVPQGI 126 Query: 145 VAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPRGVFNVV 204 + + PWNFP++ I R AP L GN +++K + P F RL E LP+G F + Sbjct: 127 LLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGGFTNL 186 Query: 205 CGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIVLADADL 264 A+ P V ++ TGS GA + A A L K +ELGG +VLADADL Sbjct: 187 YATRDQLKAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFVVLADADL 246 Query: 265 ELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRYGDPLAEPEVEMG 324 + AV+ R N+GQVC ++R+ V ++ + F+E+ A +A R GDP+ EP + Sbjct: 247 DKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPM-EPSTTLA 305 Query: 325 PLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRIMREEIFG 384 P+ +R ++ + ++ A+A GA + GA G ++P +L+ D E FG Sbjct: 306 PMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVPSRGAFFRPVLLSHVSDDNPARYWEFFG 365 Query: 385 PVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYINREHFEAMQ 444 PV + D +AI +AND +GL SVFT D+ + +++ G YIN A Sbjct: 366 PVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYINHPTGVAAD 425 Query: 445 GFHAGVRKSGIGGADGKHGLYEYTHTHVV 473 GVR+SG G G+ E+ + ++ Sbjct: 426 LPFGGVRRSGYGRELTGLGIKEFVNHKLI 454 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: 492 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: 463 Length adjustment: 33 Effective length of query: 444 Effective length of database: 430 Effective search space: 190920 Effective search space used: 190920 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 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