Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 277 bits (709), Expect = 5e-79 Identities = 158/443 (35%), Positives = 250/443 (56%), Gaps = 6/443 (1%) Query: 1 MSVPVQHPMYIDGQFVTWRGDAWIDVVNPATEA-VISRIPDGQAEDARKAIDAAERAQPE 59 M P+ YI+GQ++ + ++ NPA ++ +++ P QA+D +A+ AA +A Sbjct: 1 MKTPLNCQNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGS 60 Query: 60 WEALPAIERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWA 119 W +PA RA ++ ++ + + E++ LI E GK A +V D Y A Sbjct: 61 WRKVPAPARAEYIFRVGELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEG 120 Query: 120 RRYEGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSE 179 RR G+ S+ P + + + +GV I PWNFP + K PAL+ GNT+++KP+E Sbjct: 121 RRLFGQTTPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAE 180 Query: 180 FTPNNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMA 239 TP A +I GLP GV NLV G GE G+ L +P + +VS TGS + G + Sbjct: 181 DTPACATKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGE 240 Query: 240 TAAKNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYD 299 T + +VCLE+GGK +VM+DADLELA+ + +GQ C R+ + + I + Sbjct: 241 TCGRTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKE 300 Query: 300 QFVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV- 358 +F L E ++ G E + +GP+IN L+RV + + A EEGA++ GG+ V Sbjct: 301 KFTTMLRERTSQLRLGAGTE-PETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVT 359 Query: 359 EG---KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSI 415 EG +GY++ PT+L +V +M + EE FGPV+ ++ T E+AI++ ND+ YGL+SS+ Sbjct: 360 EGQLKQGYFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSV 419 Query: 416 YTQNLNVAMKAIKGLKFGETYIN 438 YT+++N A A++ ++ G TYIN Sbjct: 420 YTRDINRAFVAMRDIEVGITYIN 442 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: 587 Number of extensions: 23 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: 498 Length adjustment: 34 Effective length of query: 445 Effective length of database: 464 Effective search space: 206480 Effective search space used: 206480 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 Apr 09 2024. 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