Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate SMc02780 SMc02780 succinate-semialdehyde dehydrogenase [NADP+] protein
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Smeli:SMc02780 Length = 484 Score = 331 bits (849), Expect = 3e-95 Identities = 174/454 (38%), Positives = 270/454 (59%), Gaps = 1/454 (0%) Query: 24 IDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERA 83 I+V NPAT +I R+P A D R AI+AA R Q EW A A ER++ LR+ + E Sbjct: 28 IEVNNPATGEIIGRVPKLGAADTRTAIEAAARVQKEWAARTAKERSAVLRRWFELMIENK 87 Query: 84 SEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRAL 143 ++ ++ E GK A E+ + A +I++ AE ARR G+++ + + IL+ K+ + Sbjct: 88 DDLGRILTMEQGKPLAEATGEIVYGASFIEWFAEEARRVYGDLVPGHQKDKRILVMKQPI 147 Query: 144 GVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFN 203 GV I PWNFP +I RK PAL G +V+KP+ TP +AIA A + + G+P+G+F+ Sbjct: 148 GVVAAITPWNFPNAMITRKAGPALAAGCAMVLKPAAQTPFSAIAIAVLAERAGMPKGLFS 207 Query: 204 LVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDD 263 ++ G +G E+ NP V ++ TGS G ++ +A I K+ LELGG AP IV DD Sbjct: 208 VITGSAREIGAEMTSNPTVRKLTFTGSTEVGAELYRQSAATIKKLGLELGGNAPFIVFDD 267 Query: 264 ADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDI 323 ADL+ AV+ + ++ N+GQ C CA R+YVQ G+Y+ F ++L +A+ ++ GN E + + Sbjct: 268 ADLDAAVEGALIAKFRNNGQTCVCANRIYVQDGVYEAFSDKLAQAVAKLKTGNGME-DGV 326 Query: 324 AMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHEE 383 +GPLI+ AL++VE+ VA A+ +GARV GG+ G +Y T+L DV Q M++ EE Sbjct: 327 ILGPLIDQPALKKVEEHVADALAKGARVVQGGRRHSLGGTFYEATVLADVTQAMAVAREE 386 Query: 384 TFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENFE 443 TFGPV P+ F D I+ AND+++GL S Y ++L + + L++G +N Sbjct: 387 TFGPVAPLFRFKDESDVIAQANDTEFGLASYFYAKDLARVFRVAEALEYGMVGVNTGLIS 446 Query: 444 AMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 + G + SG+G K+G+ E+++ + V L Sbjct: 447 TAEAPFGGVKLSGLGREGSKYGIEEFMEIKYVCL 480 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: 512 Number of extensions: 24 Number of successful extensions: 2 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