Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_085218595.1 B9N75_RS09590 aldehyde dehydrogenase family protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_900177405.1:WP_085218595.1 Length = 479 Score = 216 bits (550), Expect = 1e-60 Identities = 150/467 (32%), Positives = 234/467 (50%), Gaps = 19/467 (4%) Query: 18 KQP-----VYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLAD 72 KQP V + TG V +A+A A+ +DA + AA A + R L D Sbjct: 17 KQPNADLEVTDKYTGKVAFRVAQADAKTIDAGIAAAVKAAEPMARMASYERQAVLQHCVD 76 Query: 73 VIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG----LAAGEYLE 128 E A GKP++ A E+ ++D FR A + + G L + Sbjct: 77 RFTERFDELAYALCVEAGKPINDA-EGEVTRLIDTFRIAAEESVRMTGEVQPLDISKRAR 135 Query: 129 GHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAE-L 187 G+ + +R P+G + I+P+N+PL +AA K+APA+A G V+KP+ TPL A+ + E L Sbjct: 136 GYMGIWKRVPIGPCSFISPFNFPLNLAAHKIAPAIAVGCPFVMKPASRTPLGAIIMGEVL 195 Query: 188 AKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMEL 247 A+ P G +IL + D T +++++S TGS G + + K+ +EL Sbjct: 196 AETDLPKGAFSILPAH-REGADMFTEDERLKLLSFTGSPGVGWDLKAKAGK--KKVVLEL 252 Query: 248 GGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATL 307 GG A VIV DAD+E V + +Y +GQ C RI IYD L EKL A TL Sbjct: 253 GGNAAVIVDKDADLEDAVARIIFGAFYQSGQSCIGVQRIIIHADIYDALKEKLAAKTKTL 312 Query: 308 KSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAG 367 +G P D T +GP+ L R+ ++EA G K++ GG K +G TLL G Sbjct: 313 VAGDPHDRKTFVGPMIDLKEATRLDNWIQEA-VEGGAKLLVGG---KRDGAMLEATLLEG 368 Query: 368 ALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQY 427 + + ++E FGPV ++ FD+ ++ NDS++GL + ++T+D+ + RL Sbjct: 369 VDRSATVYREEAFGPVAILSKFDDFAAALDEVNDSKFGLQAGIFTRDIFQVLNAWDRLDV 428 Query: 428 GCTWVN-THFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 G +N V MP+GG K SG G++ + +ED T +R+++++ Sbjct: 429 GGVVINDVPSYRVDNMPYGGVKDSGLGREGIRFAMEDMTEIRNLVIR 475 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: 484 Number of extensions: 22 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: 474 Length of database: 479 Length adjustment: 33 Effective length of query: 441 Effective length of database: 446 Effective search space: 196686 Effective search space used: 196686 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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