Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Marino:GFF3684 Length = 489 Score = 286 bits (733), Expect = 8e-82 Identities = 172/474 (36%), Positives = 263/474 (55%), Gaps = 10/474 (2%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 ++ G+F+ VVNPAT VI + + AI++A EW A+ AIER+ Sbjct: 11 FVHGRFLANSTGETFPVVNPATGQVIYEVEVADESVQQAAIESARAGFAEWSAMTAIERS 70 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAE-VEVAFTADYIDYMAEWARRYEGEIIQ 128 L + A +RER E++A V + GK Q AE V+V AD +++ A A EG Q Sbjct: 71 RILLRAVAILRERNDELAAAEVRDTGKPWQEAEAVDVVTGADAVEFFAGLAPSIEGN--Q 128 Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188 D G+ + LG+ GI WN+P + K APAL GN ++ KPSE TP A+ Sbjct: 129 QDLGGDFYYTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPSEETPMGAVKL 188 Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248 A+I E G+P GVFN+V G E VGQ L +P++A VS TG V+ G+K+MA A+ + V Sbjct: 189 AEIFTEAGVPAGVFNVVQGAAE-VGQWLTHHPEIAKVSFTGEVATGKKVMAAASSTLKDV 247 Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGE- 307 +ELGGK+P I+ DDADLE A+ A + G++C RV+V + +Y +F+ RL E Sbjct: 248 TMELGGKSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFIERLLER 307 Query: 308 AMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGK----GY 363 ++ G+P D G LI+A + V +A+ + EGA ++ GG+A E + GY Sbjct: 308 TRNNIKPGDPM-NPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDSKGGY 366 Query: 364 YYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVA 423 + PT+ D +M+I+ EE FGPV+ V+ F ++ I+ AN++D GL + ++T ++ A Sbjct: 367 FVEPTIFTDCTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAGVFTNDIRRA 426 Query: 424 MKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 + I ++ G +IN + G++ SGIG +G+ + Y Q + VY+ Sbjct: 427 HRVIHQIQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYV 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: 574 Number of extensions: 24 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: 489 Length adjustment: 34 Effective length of query: 445 Effective length of database: 455 Effective search space: 202475 Effective search space used: 202475 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