Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_085770964.1 B1812_RS07050 aldehyde dehydrogenase
Query= BRENDA::Q93YB2 (503 letters) >NCBI__GCF_002117405.1:WP_085770964.1 Length = 505 Score = 326 bits (836), Expect = 1e-93 Identities = 197/498 (39%), Positives = 281/498 (56%), Gaps = 24/498 (4%) Query: 11 FINGDWKAPVLNKRIPVINPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATAS 70 FI G+W AP + + P ++ ++P + + D+++A+ AA A W S Sbjct: 21 FIGGEWLAPRAGRYFENVTPVNGRMLCEVPRSDEIDIELALDAAHAAKEA-----WGRTS 75 Query: 71 GAVRARYLRAIAAKVTEKKPELAKLESIDCGKPLDEA-AWDIDDVAGCFEYYADLAEKLD 129 A R+R L A+A ++ + LA+ ES D GKP+ E A DI F Y+A + + Sbjct: 76 VAARSRLLNAVADRMEQNLAALAEAESWDNGKPIRETTAADIPLAIDHFRYFASV---IR 132 Query: 130 ARQKAPVSLPMDTFKSHVLREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSEL 189 A++ L DT H EP+GVVG I PWN+P+LMA WK+APALAAG +LKP+E Sbjct: 133 AQEGGVSELDHDTVAYH-FHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCVVLKPAEP 191 Query: 190 ASLTCLELGEICKEVGLPPGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMTA 249 + L E+ ++ LPPGV+NI+ G G EAG PLA+ + K+AFTG + TG I Sbjct: 192 TPASILVWAELVGDL-LPPGVVNIVNGFGLEAGKPLASSSRIAKIAFTGDTGTGRLIGEY 250 Query: 250 AAQLVKPVSLELGGKSPLVVFEDVD------LDKAAEWAIFGCFWTN-GQICSATSRLIL 302 AA+ + P +LELGGKSP + F DV LDKA E F F N G++C+ SR ++ Sbjct: 251 AARNLIPATLELGGKSPNIFFADVMADDDAFLDKALEG--FAMFALNQGEVCTCPSRALV 308 Query: 303 HESIATEFLNRIVKWIKNIKISDPLEEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTG 362 H SI F+ R +K + I DPL++ +G S Q EKIL ++ + EGA IL G Sbjct: 309 HRSIYDRFMERALKRVGAIVQGDPLDKRTMVGAQASREQMEKILAYIDIGRKEGAEILIG 368 Query: 363 GSRPE---HLKKGFFIEPTIITDVTTNMQIWREEVFGPVLCVKTFSTEEEAIDLANDTVY 419 G R + L G+++ PT++ M++++EE+FGPVL V F T+EEA +ANDTV+ Sbjct: 369 GGRADLGADLSGGYYVRPTVLLG-NNKMRVFQEEIFGPVLSVTVFDTDEEAAAIANDTVF 427 Query: 420 GLGAAVISNDLERCERVTKAFKAGIVWVNCSQPCFTQAPWGGVKRSGFGRELGEWGLDNY 479 GLGA V + D+ R R+ +A +AG VW NC A +GG K+SG GRE LD+Y Sbjct: 428 GLGAGVWTRDINRAYRMGRAIQAGRVWTNCYHAYPAHAAFGGYKQSGVGRENHRMMLDHY 487 Query: 480 LSVKQVTQYISEEPWGWY 497 K + S + G + Sbjct: 488 QQTKNLLVSYSPDKLGLF 505 Lambda K H 0.318 0.135 0.416 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: 634 Number of extensions: 24 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: 503 Length of database: 505 Length adjustment: 34 Effective length of query: 469 Effective length of database: 471 Effective search space: 220899 Effective search space used: 220899 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