Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 304 bits (779), Expect = 4e-87 Identities = 172/463 (37%), Positives = 261/463 (56%), Gaps = 15/463 (3%) Query: 23 NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82 +P G V+ +A +SAE V+ A+ AA AA WG+T+P R+ LL++AD IE+ + A Sbjct: 40 SPIDGRVICTVARSSAEDVELALDAAHAARGAWGRTSPAERSLALLRIADRIEQKLDMLA 99 Query: 83 ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGVV 142 +E+ + GKP+ ++P VD FR+FAG R G E + +PLGVV Sbjct: 100 MVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEG-GISEIDHDTVAYHFHEPLGVV 158 Query: 143 ASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILFG 202 A I PWN+PL+MA WKLAPALAAGNCV+LKP+E TP++ + L ++ D+ P GV+N++ G Sbjct: 159 AQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMSVMVLVDMIGDLLPPGVLNVING 218 Query: 203 RGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVF------ 256 G G PL + ++ V+ TG TG I+ + + +I +ELGGK+P I F Sbjct: 219 FGVEAGKPLAQNKRIAKVAFTGETTTGRLIMQYASENIIPVTLELGGKSPNIFFADVADE 278 Query: 257 DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDES 316 DD + +EG F N G+ CT R Q+ IYD +E+ A V +K G P D + Sbjct: 279 DDDFFDKALEGFSMFA-LNQGEVCTCPSRALVQEKIYDRFMERAVARVKKIKQGNPLDPA 337 Query: 317 TELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEK-----RKGNGYYYAPTLLAGALQD 371 T +G +S LE++ ++ + G KV+ GG + G+Y PT+L G Sbjct: 338 TMIGAQASNDQLEKILSYLDIGRQEG-AKVLAGGGRADVGPELAGGFYVQPTILEGH-NK 395 Query: 372 DAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTW 431 I Q+E+FGPV+SVT F ++E+ + AND+ YGL + VWT++ RA+R ++ G W Sbjct: 396 MRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGLGAGVWTRNGTRAYRFGRAIEAGRVW 455 Query: 432 VNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 N + + + GG K SG G++ L+ Y ++++V + Sbjct: 456 TNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQKTKNMLVSY 498 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: 578 Number of extensions: 25 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: 506 Length adjustment: 34 Effective length of query: 440 Effective length of database: 472 Effective search space: 207680 Effective search space used: 207680 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