Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_047092763.1 AAV99_RS05185 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_001013305.1:WP_047092763.1 Length = 459 Score = 228 bits (580), Expect = 4e-64 Identities = 147/458 (32%), Positives = 235/458 (51%), Gaps = 7/458 (1%) Query: 24 IDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERA 83 I NPAT ++ ++A I+ A+ A +W ERA +LR+I+ +R + Sbjct: 4 IQTCNPATGETLATYDLMSEQEAFGKIEHAQSAFLDWREKSHEERAEYLRQIAKVLRGNS 63 Query: 84 SEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEW--ARRYEGEIIQSDRPGENILLFKR 141 IS L+ E GK+ + EV A +Y AE A + E S I+ F Sbjct: 64 DRISQLMTREMGKLLRDGATEVELCAGIFEYTAENGPAELADQEREYSGGEKRGIVSFA- 122 Query: 142 ALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGV 201 +G+ + PWNFP + AR +A L+ GN +++K + + + + E GLP G+ Sbjct: 123 PIGIIYSVQPWNFPLYQPARVLAANLMAGNAVILKHASICTGSGLLLRDLCLEAGLPAGL 182 Query: 202 FNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVM 261 F++VL G + ++ + + V+MTGS AG I AAKN+ K LELG +V+ Sbjct: 183 FDVVLV-GHDLSDKIIEHKLIRAVTMTGSDGAGSHIGELAAKNLKKTVLELGSNDAYLVL 241 Query: 262 DDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERN 321 DAD+ELAVK V R+ N+G+ C A+R V +YD FV+ + M+A + G+P + Sbjct: 242 ADADIELAVKTCVQGRLYNNGETCVSAKRFVVVDAVYDAFVSAFVDQMKATKMGDPND-E 300 Query: 322 DIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGK-GYYYPPTLLLDVRQEMSIM 380 D +GP+ + + + ++V ++V+ GA + GG EG+ G+YYP T+L D + Sbjct: 301 DTQLGPVSSKEQFDTLVEQVGKSVDGGATLLCGGDPEEGREGFYYPATVLADCKPGTPAY 360 Query: 381 HEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG-LKFGETYINR 439 +E FGPV V+ EDA+ +ANDS YGL I++++ + A+K + G IN Sbjct: 361 DDELFGPVASVIRAKDDEDAMRIANDSRYGLGGGIFSKDEDKAIKLARDHFDTGMVRINS 420 Query: 440 ENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 G + SG G G G+ E++ T+ ++L Sbjct: 421 FGAADPNMPFGGVKDSGYGREHGGFGMKEFVNTKAIFL 458 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: 521 Number of extensions: 35 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: 459 Length adjustment: 33 Effective length of query: 446 Effective length of database: 426 Effective search space: 189996 Effective search space used: 189996 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