Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000009985.1:WP_011384974.1 Length = 479 Score = 288 bits (738), Expect = 2e-82 Identities = 177/473 (37%), Positives = 264/473 (55%), Gaps = 13/473 (2%) Query: 10 YIDGQFVT-WRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIER 68 Y+DG +V +G +DV+NPATE V R+ G A+DA +AI AA +A P W A P ER Sbjct: 8 YVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAATPLAER 67 Query: 69 ASWLRKISAGIRERASEIS-ALIVEEGGKIQQLAEVEVAFTA-DYIDYMAEWARRYEGEI 126 L K++AG R EI+ A+ +E G +++LA+ A + A+ Y E Sbjct: 68 LEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKTYAFER 127 Query: 127 IQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAI 186 Q L+ K +GV + I PWN+P IA K+APAL G +V+KPSEF P +A Sbjct: 128 RQG-----TTLVVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSEFAPYSAR 182 Query: 187 AFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNIT 246 A+I+ E G+P GVFN+V G G +G L+ +P V MVS+TGS AG +M A I Sbjct: 183 ILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMREGAATIK 242 Query: 247 KVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLG 306 KV LELGGK+ I+ D AD + A+ V + + N+GQ CN R++V D+ Sbjct: 243 KVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLDEAEGLAA 302 Query: 307 EAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGG-KAVEG--KGY 363 E ++ G+P++ + MGP+ N ++V + + +EEGA++ GG + EG KGY Sbjct: 303 ELCAQIKVGDPSDPETV-MGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERPEGLDKGY 361 Query: 364 YYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVA 423 + PT+ V M+IM EE FGPVL + + L+DA++ AND YGL+ +Y +L+ A Sbjct: 362 FVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSGYVYAGDLDEA 421 Query: 424 MKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVY 476 + L+ G ++N G G R+SG+G G+ G E+L+++ ++ Sbjct: 422 RAVARRLRTGMVHLNGA-LSHPGGPFGGIRQSGVGREWGEAGFEEFLESKTLF 473 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: 523 Number of extensions: 24 Number of successful extensions: 5 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: 479 Length adjustment: 34 Effective length of query: 445 Effective length of database: 445 Effective search space: 198025 Effective search space used: 198025 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