Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Phaeo:GFF2918 Length = 491 Score = 303 bits (775), Expect = 1e-86 Identities = 171/467 (36%), Positives = 249/467 (53%), Gaps = 3/467 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YI G FV D V NPA VI+ + D AI AE AQ +W ERA Sbjct: 23 YIGGAFVDG-ADGTFAVKNPARGDVIANVADVSRSQVAGAIAQAEVAQKDWAKWTGKERA 81 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 + LRK + E +++ ++ E GK + E+ + A +I++ AE A+R GE I Sbjct: 82 NVLRKWFDLMMENQEDLAVILTAEMGKPLAESRGEIGYGASFIEFFAEEAKRIYGETIPG 141 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 + + I + K+ +GV I PWNFP +I RK PAL G V +P+E TP +A A A Sbjct: 142 HQRDKRITVLKQPIGVAASITPWNFPNAMITRKAGPALAAGCAFVARPAELTPLSATALA 201 Query: 190 KIVDEIGLPRGVFNLVL-GRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248 + D G+P GVFN+V G+E N V ++ TGS G +M AA + K Sbjct: 202 VLADRAGIPAGVFNVVTSSNASETGKEFCENNAVRKLTFTGSTEVGRILMRQAADTVMKC 261 Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308 +ELGG AP IV DDADL+ AV+ + + N+GQ C CA R+YVQ G+YD F +L EA Sbjct: 262 SMELGGNAPFIVFDDADLDAAVEGAIMCKFRNNGQTCVCANRIYVQAGVYDAFAAKLKEA 321 Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPT 368 + + G+ GPLIN A+E+V+ +A A E+GA V GG E G ++ PT Sbjct: 322 VAKMTVGDGLAEG-TQFGPLINEKAVEKVQAHIADAKEKGAEVILGGNPSELGGTFFEPT 380 Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428 ++ Q+M +ETFGP+ P+ F+T +D I MAND+ +GL S Y ++L+ K + Sbjct: 381 IITGATQDMVFSQDETFGPMAPLFKFETEDDVIEMANDTIFGLASYFYAKDLSRVYKVAE 440 Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475 L++G +N G ++SG+G HG+ +YL+ + + Sbjct: 441 ALEYGIVGVNTGIISTELAPFGGVKQSGLGREGSHHGIEDYLEMKYI 487 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: 537 Number of extensions: 23 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