Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__HerbieS:HSERO_RS05645 Length = 493 Score = 313 bits (803), Expect = 6e-90 Identities = 176/468 (37%), Positives = 264/468 (56%), Gaps = 11/468 (2%) Query: 18 WRGDA---WIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRK 74 WRG A +DV +PAT V + +PDG A DAR A++AA A W A PA +RA +++ Sbjct: 22 WRGAADGRQLDVSDPATGQVFASVPDGGAADARAAVEAAVAAFAAWRATPAKQRAGIIKR 81 Query: 75 ISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGE 134 + + ++ LI E GK A+ EVA+ A Y+++ E A R G+II + G Sbjct: 82 WNDLLLAHQDDLGRLISREQGKPLAEAKGEVAYAASYVEWFGEEATRANGDIIPAPVTGR 141 Query: 135 NILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDE 194 ++ K +GV I PWNFP +IARK+APAL G T+V KP+E TP ++A ++ E Sbjct: 142 RMMALKEPVGVVAAITPWNFPAAMIARKIAPALAAGCTVVCKPAEDTPLTSLALVRLAQE 201 Query: 195 IGLPRGVFNLVLGRGETVGQEL---AGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLE 251 G+P GV N+V E + + + +V +S TGS + G+ + +A + K+ LE Sbjct: 202 AGVPVGVINIVTASRERTPEVVDVWLADGRVRKISFTGSTAVGKHLARHSADTLKKLSLE 261 Query: 252 LGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQA 311 LGG AP IV DDAD++ A+ ++ ++ N GQ C R+YVQ+ +YD FV++LG + A Sbjct: 262 LGGNAPFIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYVQEKVYDAFVDKLGARVAA 321 Query: 312 VQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGY----YYPP 367 ++ G PA +GP+INA A+ +++Q V A+ GARV GGK ++G G+ YY P Sbjct: 322 LKVG-PATDPASQIGPMINARAIAKIDQHVRDAIARGARVITGGKRLQGPGFGSDNYYAP 380 Query: 368 TLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAI 427 T+L DV M EETFGPV P+ F T ++ I+ AN + +GL + Y+ ++ + Sbjct: 381 TVLADVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFGLAAYFYSTDVRRIHRVT 440 Query: 428 KGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475 L+ G +N A G ++SG G HGL +YL T+ V Sbjct: 441 DALESGIVGVNEGALAAEAAPFGGVKESGYGREGSVHGLDDYLHTKYV 488 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: 554 Number of extensions: 30 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: 493 Length adjustment: 34 Effective length of query: 445 Effective length of database: 459 Effective search space: 204255 Effective search space used: 204255 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: 52 (24.6 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