Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Korea:Ga0059261_3374 Length = 474 Score = 266 bits (681), Expect = 9e-76 Identities = 168/471 (35%), Positives = 264/471 (56%), Gaps = 14/471 (2%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YI G++V G DV+NPATEA ++ I G DA KA+ AA+ A + ER Sbjct: 8 YIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVDERI 67 Query: 70 SWLRKISAGIRERASEIS-ALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128 + L I A + RA +++ A+ E G I +V ++ + +E Sbjct: 68 ALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALKAFEF---- 123 Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188 S++ G+++++ + +GV I PWN+P I K+APAL GNT+V+KPSE P +A F Sbjct: 124 SEQIGQSLVVHE-PIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSAAIF 182 Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248 A+I+D+ G+P GVFNLV G G VG L+ + V MVS TGS AG ++ AA+ + +V Sbjct: 183 AEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAETVKRV 242 Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308 ELGGK+P +++ ADL AV+ + S V+NSGQ C R+ V + + Sbjct: 243 HQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQIASGL 302 Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGG----KAVEGKGYY 364 M+AV+ G+PA+ +GP++N A E+++ + + +EEGA++ GG +E GY+ Sbjct: 303 MKAVETGDPAQEGR-HIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDGIE-TGYF 360 Query: 365 YPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAM 424 PTL VR +M+I EE FGPV+ ++ + E+A+ +AND+DYGL++ ++ V Sbjct: 361 VKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLSAVLFGSPEEVKR 420 Query: 425 KAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475 A + L+ G YIN + F G+++SG G GK GL E+++ + + Sbjct: 421 VAPR-LRAGMVYINGGQPDPSLPF-GGYKQSGNGREHGKFGLAEFMEVKAM 469 Lambda K H 0.318 0.135 0.392 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: 513 Number of extensions: 26 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: 479 Length of database: 474 Length adjustment: 33 Effective length of query: 446 Effective length of database: 441 Effective search space: 196686 Effective search space used: 196686 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: 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