Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_001431535.1:WP_057507768.1 Length = 454 Score = 226 bits (577), Expect = 1e-63 Identities = 145/455 (31%), Positives = 231/455 (50%), Gaps = 5/455 (1%) Query: 24 IDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERA 83 +++VNP T V R + + AA A P W A ERA+ LR I A +RER Sbjct: 3 VEIVNPTTGRVDYRHELLDKAGIEQRLQAAAGAFPAWSATSLQERAAVLRAIGAQLRERK 62 Query: 84 SEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRY-EGEIIQSDRPGENILLFKRA 142 +I + E GK++ A EV A +Y A+ A Y + ++I D + + Sbjct: 63 DDIQGAMTREMGKLKVEALAEVEKCAAACEYYADHAADYLKPQLI--DTEAQRSYVRYEP 120 Query: 143 LGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVF 202 +G ++PWNFP + + R +APA + GN ++K + P A ++V GLP GVF Sbjct: 121 IGCVFAVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPDGVF 180 Query: 203 NLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMD 262 + VL ++ + +V V++TGS AG I A A + K +ELGG +V+D Sbjct: 181 D-VLHIDNDQAADVLRDRRVKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAFVVLD 239 Query: 263 DADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERND 322 DADL+ A+ A V SR NSGQ C A+R V + + D F R A ++G+PA+ Sbjct: 240 DADLDKAIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPADAR- 298 Query: 323 IAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHE 382 + P+ A + + ++V +V +GARV GG+ V+G YP T+L V M E Sbjct: 299 TTLAPMARADLRDELHKQVQASVAKGARVLAGGEPVDGSHAGYPATVLDQVGPGMPAYDE 358 Query: 383 ETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENF 442 E FGPV V+ +A+ +AND+ +GL S++T + + ++ G ++N Sbjct: 359 ELFGPVAAVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAFVNSIVK 418 Query: 443 EAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 ++ G ++SG G +HG+HE++ + +Y+ Sbjct: 419 SDVRLPFGGSKESGFGRELAEHGIHEFMNIKTIYV 453 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: 474 Number of extensions: 23 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: 454 Length adjustment: 33 Effective length of query: 446 Effective length of database: 421 Effective search space: 187766 Effective search space used: 187766 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 Apr 09 2024. 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