Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 312 bits (799), Expect = 2e-89 Identities = 171/472 (36%), Positives = 266/472 (56%), Gaps = 17/472 (3%) Query: 15 EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVI 74 +GE V +P G V ++A A ++ A+ AA AF W +T+ R+ LLK+AD I Sbjct: 35 DGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPAWSRTSATERSNILLKIADRI 94 Query: 75 EENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI 134 E + A +E+ + GKP+ N ++ +VD FR+FAG R G A L+ HT + Sbjct: 95 ENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGSIAE--LDQHTVSV 152 Query: 135 R-RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFP 193 ++P+G+V I PWN+P++MA WK+APALAAG C ++KP+E TP + + L E+ D+ P Sbjct: 153 NVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIMILMEVIGDLLP 212 Query: 194 AGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPV 253 AGV+N++ G G G PL P++ V+ TG TG I+ + + ++ MELGGK+P Sbjct: 213 AGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYASENLNPVTMELGGKSPN 272 Query: 254 IVF------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATL 307 + F DD ++ +EG F N G+ CT RI + IYD +EK+ A + Sbjct: 273 VFFPSVMDADDEFLDKCLEGAVMFA-LNQGEVCTCPSRILVHEKIYDAFMEKVIARAEAI 331 Query: 308 KSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-----GNGYYYAP 362 + G P D++T +G +S E++ ++ K G +V+TGGE K NGYY P Sbjct: 332 QMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEG-AEVLTGGEVAKLNSGLENGYYVKP 390 Query: 363 TLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVS 422 TLL G + Q+E+FGPV SV F + E+ ++ +ND+ YGL + VWT+D A++V Sbjct: 391 TLLKGH-NKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVWTRDAHEAYQVP 449 Query: 423 ARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 ++ G WVN + + P GG K SG+G++ L L Y +++++ + Sbjct: 450 RAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNKNMLISY 501 Lambda K H 0.317 0.134 0.397 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: 599 Number of extensions: 32 Number of successful extensions: 5 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: 474 Length of database: 509 Length adjustment: 34 Effective length of query: 440 Effective length of database: 475 Effective search space: 209000 Effective search space used: 209000 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