Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate WP_012385772.1 BIND_RS14385 aldehyde dehydrogenase family protein
Query= SwissProt::A1B4L2 (508 letters) >NCBI__GCF_000019845.1:WP_012385772.1 Length = 506 Score = 787 bits (2033), Expect = 0.0 Identities = 373/488 (76%), Positives = 427/488 (87%) Query: 21 YDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWGATSPA 80 YDNFIGG+W V G+ F N +PI G IARS A D+ELALDAAHAA+EKW TSP Sbjct: 19 YDNFIGGKWTPSVKGQKFDNVSPIDGRVFCTIARSTAEDVELALDAAHAAREKWAQTSPL 78 Query: 81 ERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLRAQEGS 140 ER+ ++L++ADRME L+ LA ET DNGKP+RET AAD+PLAIDHFRYFAG LRAQEGS Sbjct: 79 ERSRVLLRLADRMESKLDTLAMVETIDNGKPLRETKAADVPLAIDHFRYFAGCLRAQEGS 138 Query: 141 ISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQTPAGIM 200 IS+ID DTVAYHFHEPLGVV QIIPWNFPLLMA WK+APA+AAGNC+VLKPAEQTP +M Sbjct: 139 ISEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKIAPALAAGNCIVLKPAEQTPMSVM 198 Query: 201 VWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYASENLIP 260 V ++IGDLLPPGVLN++NGFG+E GKPLA S RIAK+AFTGETTTGRLIMQYASEN+IP Sbjct: 199 VLMDIIGDLLPPGVLNVINGFGVECGKPLAQSKRIAKVAFTGETTTGRLIMQYASENIIP 258 Query: 261 VTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESIYDKFM 320 VTLELGGKSPNIFFADVA EDDDFFDKALEGF+MFALNQGEVCTCPSR L+ E IYD+F+ Sbjct: 259 VTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVHEKIYDRFI 318 Query: 321 ERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAADLGGE 380 ERA+ RV+AI+QG+P + TMIGAQAS++Q EKILSY+DIGK+EGA +LTGG A++G + Sbjct: 319 ERAIARVKAIRQGNPLDMATMIGAQASNDQLEKILSYIDIGKQEGASLLTGGGRAEVGAD 378 Query: 381 LSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAGVWSRD 440 +GG+Y++PT+F+G+NKMRIFQEEIFGPV+SVTTFKD EAL+IANDTLYGLGAGVW+R+ Sbjct: 379 FAGGFYVQPTVFQGHNKMRIFQEEIFGPVLSVTTFKDDEEALQIANDTLYGLGAGVWTRN 438 Query: 441 ANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNMLVSY 500 YR GR I+AGRVWTNCYH YPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNMLVSY Sbjct: 439 GTRAYRFGRAIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNMLVSY 498 Query: 501 SPKKLGFF 508 SPK LGFF Sbjct: 499 SPKALGFF 506 Lambda K H 0.319 0.136 0.411 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: 870 Number of extensions: 33 Number of successful extensions: 1 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: 508 Length of database: 506 Length adjustment: 34 Effective length of query: 474 Effective length of database: 472 Effective search space: 223728 Effective search space used: 223728 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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