Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 197 bits (502), Expect = 5e-55 Identities = 137/457 (29%), Positives = 227/457 (49%), Gaps = 15/457 (3%) Query: 23 NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82 NP G+V E +A+ A+ A A E +TT R LL +A + +N + A Sbjct: 22 NPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDIA 81 Query: 83 ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG--LAAGEYLEGHT--SMIRRDP 138 + + GKP+ + E+ ++ A R ++G + + G S R P Sbjct: 82 KTITDEVGKPITYS-RIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSRVP 140 Query: 139 LGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAEL--AKDIFPAGV 196 GVV +I P+N+PL + A K+APAL AGN V+LKP+ PLTA K A+L + Sbjct: 141 CGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKDA 200 Query: 197 INILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVF 256 +++++G VG L R++S TGS+ GE I ++ IK+ +ELGG A + Sbjct: 201 LSVVYG-DADVGGTLVTSEIPRVISFTGSVGVGEIITK--SAGIKKVSLELGGNAATFID 257 Query: 257 DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDES 316 A+++ + + N+GQ C + RIY K IY K+ A L G+P +E Sbjct: 258 KSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYEED 317 Query: 317 TELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDAIVQ 376 T +GPL + +R + V+ A G ++ + + G + P ++A +D AIV Sbjct: 318 TFMGPLVNDEAAKRAMEWVQSAIKEGATPIL----EPRVEGRVFYPCVMADVKEDMAIVC 373 Query: 377 KEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTHF 436 +EVF P+VS+ + ++ + N+S YGL S++T D+ R L G +N Sbjct: 374 QEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDMP 433 Query: 437 MLVSEM-PHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 L ++ P+GG KLSG G++ + +E+ + ++ V++ Sbjct: 434 TLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470 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: 459 Number of extensions: 32 Number of successful extensions: 6 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: 471 Length adjustment: 33 Effective length of query: 441 Effective length of database: 438 Effective search space: 193158 Effective search space used: 193158 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 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