Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate SM_b21185 SM_b21185 succinate-semialdehyde dehydrogenase (NAD(P)+) protein
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Smeli:SM_b21185 Length = 491 Score = 329 bits (844), Expect = 1e-94 Identities = 177/448 (39%), Positives = 263/448 (58%), Gaps = 2/448 (0%) Query: 25 DVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERAS 84 DV NP+T +++ +PD +DAR AIDAA AQP W PA +R+ LR+ I E A Sbjct: 36 DVSNPSTGELLATLPDMGIDDARTAIDAAALAQPLWAGKPAKDRSIILRRWHDLIVEHAD 95 Query: 85 EISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRALG 144 +++A++ E GK A+ EV A Y+++ AE A+R GE + +L+ K+ +G Sbjct: 96 DLAAILTAEMGKPVGEAKGEVLHAASYVEWYAEEAKRVYGETFPAPANDRRMLVIKQPVG 155 Query: 145 VTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFNL 204 V I PWNFP ++ARK++PAL G TIV+KP+E TP A A + ++ G P GV NL Sbjct: 156 VVGTITPWNFPASMVARKISPALAAGCTIVLKPAEQTPLVAGAMFVLAEKAGFPEGVLNL 215 Query: 205 V-LGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDD 263 + G +G+EL GNPKV +S TGS G +M + I KV LELGG AP IV DD Sbjct: 216 LYASEGAPIGRELCGNPKVRKISFTGSTEVGRLLMRQCSDQIKKVSLELGGNAPFIVFDD 275 Query: 264 ADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDI 323 AD++ AV V ++ N+GQ C A R+YVQ ++D F + ++ + G+ D+ Sbjct: 276 ADIDEAVDGAVQAKFRNAGQTCVSANRIYVQSAVHDAFAEKFVTRVRELTVGD-GFAPDV 334 Query: 324 AMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHEE 383 A+GP+I+A A++++E VA AV +GA+V GG + G ++ PT+L + +M I EE Sbjct: 335 AIGPMIDAHAIDKIEAHVADAVAKGAQVRSGGSRIGTTGTFFEPTVLTGISHDMRIAQEE 394 Query: 384 TFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENFE 443 TFGP+ P++ F+T E ++ AND+ YGL + Y +NL + L++G IN Sbjct: 395 TFGPIAPIIRFETAEQVVAEANDTIYGLAAYFYAENLKRVWHVAEALEYGMVGINTGRMS 454 Query: 444 AMQGFHAGWRKSGIGGADGKHGLHEYLQ 471 + G ++SGIG +HGL +YL+ Sbjct: 455 SEAAPFGGIKQSGIGREGSRHGLEDYLE 482 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: 550 Number of extensions: 19 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: 491 Length adjustment: 34 Effective length of query: 445 Effective length of database: 457 Effective search space: 203365 Effective search space used: 203365 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