Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_110207396.1 DNK54_RS13100 aldehyde dehydrogenase family protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_003194585.1:WP_110207396.1 Length = 507 Score = 315 bits (806), Expect = 3e-90 Identities = 183/463 (39%), Positives = 257/463 (55%), Gaps = 15/463 (3%) Query: 23 NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82 +P G EIA +AE ++AAV AA AA WG+T+ R+ LLK+AD +E + A Sbjct: 41 SPVNGKPFTEIARGTAEDIEAAVDAAWAAADAWGRTSTTDRSNILLKIADRMERHLDDLA 100 Query: 83 ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGVV 142 +E+ + GK + N ++P +D FR+FAGA R G E E + +PLGVV Sbjct: 101 VIETWDNGKAVRETLNADLPLAIDHFRYFAGALRGQEG-GISEIDENTVAYHFHEPLGVV 159 Query: 143 ASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILFG 202 I PWN+P++MA WKLAPALAAGNCVVLKP+E TP + LKL EL D+ PAGV+N++ G Sbjct: 160 GQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPWSILKLVELVGDLLPAGVLNVVNG 219 Query: 203 RGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVFD----- 257 G G PL P++R ++ TG TG I+ + + +I +ELGGK+P I FD Sbjct: 220 FGVEAGKPLASSPRIRKIAFTGETTTGRLIMQYASENIIPVTLELGGKSPNIFFDDVATS 279 Query: 258 -DADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDES 316 DA + +EG F N G+ CT R Q+ +Y V A V +K G P D S Sbjct: 280 RDAFYDKALEGFTMFA-LNQGEVCTCPSRALVQQSMYADFVPDAIARVEAIKQGNPLDVS 338 Query: 317 TELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKR-----KGNGYYYAPTLLAGALQD 371 T +G +S LE++ +E K G KV+TGGE+ GYY PT+ G Sbjct: 339 TMMGAQASNDQLEKILSYLEIGKQEG-AKVLTGGERNVLEGDLAEGYYVQPTVFEGN-NA 396 Query: 372 DAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTW 431 I Q+E+FGPVVS+T F +E + AND+ YGL + +WT+D RA R+ +Q G W Sbjct: 397 MRIFQEEIFGPVVSLTSFSDEADALQTANDTLYGLGAGLWTRDGSRAFRMGKGIQAGRVW 456 Query: 432 VNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 N + + GG K SG G++ L+ Y ++++V + Sbjct: 457 TNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNLLVSY 499 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: 612 Number of extensions: 32 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: 507 Length adjustment: 34 Effective length of query: 440 Effective length of database: 473 Effective search space: 208120 Effective search space used: 208120 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 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