Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_093427654.1 BM272_RS04975 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_900112605.1:WP_093427654.1 Length = 454 Score = 251 bits (642), Expect = 3e-71 Identities = 153/454 (33%), Positives = 246/454 (54%), Gaps = 7/454 (1%) Query: 27 VNPAT-EAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASE 85 ++P+T E P G+AE A+ A A P W A P ERA +R I+ +R RA E Sbjct: 6 IDPSTGETFFHMEPWGEAE-REAALAAVAAATPGWAATPVAERAEAVRAIAGELRRRADE 64 Query: 86 ISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRY-EGEIIQSDRPGENILLFKRALG 144 ++ LI E GK+ + A E+ A +Y A+ + E I++D G++++ ++ LG Sbjct: 65 LATLITREVGKLHREARGEIEKCAWVCEYYADHGPGFLADEPIETDA-GKSLVAYQ-PLG 122 Query: 145 VTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFNL 204 ++PWNFPF+ + R APAL+ GNT V+K + P +A+A +++ + GLP F Sbjct: 123 TVLAVMPWNFPFWQVFRFAAPALVAGNTGVLKHASNVPQSALAIEEVIRDAGLPADTFRT 182 Query: 205 VLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDDA 264 ++ R V + +P++A V++TGS AG + + AA NI K LELGG P IV+DDA Sbjct: 183 LMIRAADV-DAVIDDPRIAAVTLTGSEPAGRAVASRAAANIKKAVLELGGSDPFIVLDDA 241 Query: 265 DLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDIA 324 D+E AV+A SR +N+GQ C A+R + GI D FV R ++A+ G+PA Sbjct: 242 DVEQAVEAAATSRFLNNGQSCIAAKRFILTPGIADDFVERFRRRVEAMTVGDPAAET-TQ 300 Query: 325 MGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHEET 384 +GP+ + + +VA +V GA+V G + G +YPP++L V + EE Sbjct: 301 LGPMARTDLRDELHTQVADSVRAGAQVVTGCTLPDSPGAFYPPSILDHVAEGQRAFEEEL 360 Query: 385 FGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENFEA 444 FGPV V+ D E A+++AN S +GL +++T + + L+ G ++N Sbjct: 361 FGPVAIVLRADDAEHAVNLANGSRFGLGGAVWTADSQRGEAIARRLECGAAFVNGIVKSD 420 Query: 445 MQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQ 478 + G + SG G +HG+ E++ + V+++ Sbjct: 421 PRLPFGGVKASGFGRELSRHGIQEFVNAKTVWVK 454 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: 471 Number of extensions: 20 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 Sep 24 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