Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate HSERO_RS05395 HSERO_RS05395 succinate-semialdehyde dehdyrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__HerbieS:HSERO_RS05395 Length = 484 Score = 325 bits (832), Expect = 3e-93 Identities = 174/461 (37%), Positives = 267/461 (57%), Gaps = 1/461 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 +++GQ+ + V NPA ++ +P A + R+AI+AA A P W+ A ER+ Sbjct: 15 FVNGQWCDADQGERLAVHNPANGELLGHVPLMGAAETRRAIEAANAAWPAWKKKTAKERS 74 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 + LR+ + +++ ++ E GK A E+ + A +I++ AE +R G+ I S Sbjct: 75 AILRRWYELMLANTDDLALIMTAEQGKPLAEARGEIGYAASFIEWFAEEGKRTYGDTIPS 134 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 P I++ K A+GV I PWNFP +I RK PAL G +V+KP+E TP +A+A A Sbjct: 135 PSPSNRIVVIKEAIGVCAAITPWNFPAAMITRKAGPALAAGCPMVLKPAEATPFSALALA 194 Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249 + + G+P GVF++V G + +G E+ NP V +S TGS G+ +M +A +I K+ Sbjct: 195 VLAERAGIPAGVFSVVTGTPKGIGGEMTSNPIVRKISFTGSTGVGKLLMQQSASSIKKLS 254 Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309 LELGG AP IV DDADL+ AV+ + S+ N+GQ C CA R+YVQ G+YD F +L EA+ Sbjct: 255 LELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRIYVQDGVYDAFAAKLVEAV 314 Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369 + + G E + GPLIN A+++VEQ VA AV +GARV GGK ++ PT+ Sbjct: 315 KKFKVGQGTEEG-VTQGPLINEQAVQKVEQHVADAVAKGARVLLGGKRHALGHSFFEPTV 373 Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429 L DV M + EETFGP+ P+ F T E+ +++AND+++GL S Y++++ + +G Sbjct: 374 LADVTPAMQVAREETFGPMAPLFRFKTDEEVLALANDTEFGLASYFYSRDIGRIWRVAEG 433 Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYL 470 L+ G IN G ++SG+G +G+ +YL Sbjct: 434 LESGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYL 474 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: 538 Number of extensions: 25 Number of successful extensions: 3 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: 484 Length adjustment: 34 Effective length of query: 445 Effective length of database: 450 Effective search space: 200250 Effective search space used: 200250 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