Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 254 bits (648), Expect = 6e-72 Identities = 151/475 (31%), Positives = 254/475 (53%), Gaps = 15/475 (3%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 +I G+FV + DV++P V +++ G+A D A+DAA +A P W A ER+ Sbjct: 25 FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPAWSRTSATERS 84 Query: 70 SWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128 + L KI+ I + ++A+ + GK +++ ++A D+ Y A R EG I + Sbjct: 85 NILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGSIAE 144 Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188 D+ ++ + K +G+ I+PWNFP + KMAPAL G ++KP+E TP + + Sbjct: 145 LDQHTVSVNV-KEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIMIL 203 Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248 +++ ++ LP GV N+V G G G+ LA +P++ V+ TG + G IM A++N+ V Sbjct: 204 MEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYASENLNPV 262 Query: 249 CLELGGKAPAIVMD---DADLELAVKAIVDSRV--INSGQVCNCAERVYVQKGIYDQFVN 303 +ELGGK+P + DAD E K + + + +N G+VC C R+ V + IYD F+ Sbjct: 263 TMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQGEVCTCPSRILVHEKIYDAFME 322 Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVE---- 359 ++ +A+Q G+P ++ + MG + E++ + +EGA V GG+ + Sbjct: 323 KVIARAEAIQMGHPLDKTTM-MGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLNSG 381 Query: 360 -GKGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQ 418 GYY PTLL +M + EE FGPV V F +E+AIS++ND+ YGL + ++T+ Sbjct: 382 LENGYYVKPTLLKG-HNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVWTR 440 Query: 419 NLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473 + + A + + +K G ++N + G++KSG G L+ Y Q + Sbjct: 441 DAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNK 495 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: 34 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 479 Length of database: 509 Length adjustment: 34 Effective length of query: 445 Effective length of database: 475 Effective search space: 211375 Effective search space used: 211375 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