Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >FitnessBrowser__SynE:Synpcc7942_0489 Length = 459 Score = 178 bits (452), Expect = 3e-49 Identities = 144/452 (31%), Positives = 212/452 (46%), Gaps = 31/452 (6%) Query: 28 PANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHLRRIAAKIRADAGRIAR 87 PA L+ + A R LA A +D A+ A A L+ +A+ +R A Sbjct: 7 PAAAETLAALQATFDRGDTRTLAFRLARLQDLAKLVADNEAELLQALASDLRKPA----- 61 Query: 88 TITLEQGKIASLAEVEVNFTADYLD----YMAEWARRLEGEIIASDRPGENIFLFRKPLG 143 + + A E+ F D + ++ W + + I +PG+ + +PLG Sbjct: 62 --------LEAYAS-EIYFVRDQIKLTCKHLRRWMQPEKQSISLMQQPGQ-AYRQAEPLG 111 Query: 144 VVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPRGVFNV 203 VV I PWN+PF L+ + A+ GN V+KPSE P RL+++ P + V Sbjct: 112 VVLIIGPWNYPFQLLITPLIGAIAAGNCAVLKPSELAPATSSLIQRLISDRFDPDYI-RV 170 Query: 204 VCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIVLADAD 263 + G V AL + P D I FTG G ++MAAAA NLT + LELGGK+P IV D D Sbjct: 171 LEGDASVSQALITQP-FDHIFFTGGTAIGRKVMAAAAENLTPVTLELGGKSPCIVDTDID 229 Query: 264 LELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRYGDPLAEPEVEM 323 L++A + I + N+GQ C + + VQR VAEPFIE + + DP + Sbjct: 230 LDVAARRIAWGKFFNAGQTCIAPDYLLVQRTVAEPFIEALIDNIQQFYGEDPQQSADYA- 288 Query: 324 GPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRIMREEIF 383 R+ ++ ++ + L G T+ GG + +R + PT++T I++EEIF Sbjct: 289 -----RIVSDRHWQRLNSLLVDG-TIRHGGQV-DRSDRYIAPTLITDVNWRDPILQEEIF 341 Query: 384 GPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYINREHFE-- 441 GP+LPI I D LDEAIA L +F+RD L E G +N + Sbjct: 342 GPLLPILIYDQLDEAIAQIRAQPKPLALYLFSRDRQVQERVLAETSAGSVCLNDTILQVG 401 Query: 442 AMQGFHAGVRKSGIGGADGKHGLYEYTHTHVV 473 GV SG+GG GK ++H +V Sbjct: 402 VPDAAFGGVGPSGMGGYHGKASFETFSHYKLV 433 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: 477 Number of extensions: 21 Number of successful extensions: 4 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: 459 Length adjustment: 33 Effective length of query: 444 Effective length of database: 426 Effective search space: 189144 Effective search space used: 189144 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