Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_012708832.1 NGR_RS22740 aldehyde dehydrogenase family protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000018545.1:WP_012708832.1 Length = 502 Score = 306 bits (783), Expect = 1e-87 Identities = 177/484 (36%), Positives = 263/484 (54%), Gaps = 23/484 (4%) Query: 9 GELVSGEGEKQPVYN-------PATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPK 61 G + GE ++PV P TG L +IA + A ++ A+ AA AA +WG+T+ Sbjct: 16 GNFIGGEW-REPVAGRYFDNTTPVTGGSLCQIARSDAADIELALDAAHAAKEKWGRTSTT 74 Query: 62 VRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGL 121 R+ L+K+A +E+N ++ A E+ + GKP+ +IP +D FR+FA R G Sbjct: 75 ERSNILMKIAARMEDNLELLARAETWDNGKPIRETMAADIPLAIDHFRYFAACIRAQEG- 133 Query: 122 AAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTA 181 + GE + +PLGVV I PWN+P++MAAWK+APALAAGNCVVLKP+E TP + Sbjct: 134 SIGEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKVAPALAAGNCVVLKPAEQTPASI 193 Query: 182 LKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIK 241 L LAEL D+ P GV+NI+ G G G PL P++ ++ TG TG I+ + + ++ Sbjct: 194 LILAELIADLLPPGVLNIVNGFGLEAGKPLATSPRIAKIAFTGETTTGRLIMQYASQNLI 253 Query: 242 RTHMELGGKAPVIVF------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDT 295 +ELGGK+P I F DD + +EG F N G+ CT R Q+ IYD Sbjct: 254 PVTLELGGKSPNIFFADVLNEDDDYFDKALEGFAMFA-LNQGEVCTCPSRALVQESIYDR 312 Query: 296 LVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG----- 350 +E+ V ++ G P D +T +G +S LE++ ++ K G +V+ GG Sbjct: 313 FMERAVKRVEAIRQGNPLDSATMIGAQASGEQLEKILSYIDIGKQEG-AEVLAGGGRNVL 371 Query: 351 EKRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSV 410 E GYY PT+ G I Q+E+FGPVVSVT F E++ + AND+ YGL + V Sbjct: 372 EGDLAGGYYVKPTVFRGH-NKMRIFQEEIFGPVVSVTTFKTEDEALEIANDTLYGLGAGV 430 Query: 411 WTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 W++D R +R +Q G W N + + GG K SG G++ L+ Y +++ Sbjct: 431 WSRDANRCYRFGREIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNM 490 Query: 471 MVKH 474 +V + Sbjct: 491 LVSY 494 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: 603 Number of extensions: 27 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: 502 Length adjustment: 34 Effective length of query: 440 Effective length of database: 468 Effective search space: 205920 Effective search space used: 205920 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