Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_012336432.1 M446_RS33000 aldehyde dehydrogenase family protein
Query= BRENDA::C6KEM4 (506 letters) >NCBI__GCF_000019365.1:WP_012336432.1 Length = 506 Score = 328 bits (840), Expect = 4e-94 Identities = 199/498 (39%), Positives = 282/498 (56%), Gaps = 23/498 (4%) Query: 13 FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72 FIGG W P GR +P T I ++ A+D+E A+ AA A +D W+R Sbjct: 22 FIGGQWVAPAAGRYFENTSPLTGRLICEVARSDAQDIERALDAAHAA--KDA---WARTA 76 Query: 73 GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEAS-GDMDDVAACFEYYADLAEALD 131 A RA L +A +++D LAL ET D+GKP+ E + D+ F Y+A A + Sbjct: 77 PAERARILTRMADRMEDNLDLLALAETWDNGKPIRETTHADIPLAIDHFRYFAGCVRAQE 136 Query: 132 GKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSEL 191 G +S + +Y EP+GVVG I PWN+P+LMA WK+APALAAG +LKP+E Sbjct: 137 GS----LSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQ 192 Query: 192 ASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTS 251 S L L I ++ LP GVLNI+ G G EAG PL+S + K+AFTG T TG+ IM Sbjct: 193 TPASVLVLAEIIGDL-LPAGVLNIVNGFGLEAGKPLASSPRIAKIAFTGETSTGRLIMQY 251 Query: 252 AAQMVKPVSLELGGKSPLIVFDDI-----GDIDKAVEWTMFGIFA-NAGQVCSATSRLLL 305 A+Q + PV+LELGGKSP I F+D+ +DKA+E F +FA N G+VC+ SR L+ Sbjct: 252 ASQNLIPVTLELGGKSPNIFFEDVMARDDAFLDKALEG--FAMFALNQGEVCTCPSRALV 309 Query: 306 HEKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYG 365 E I ++F+++ VA + I+ PL+ +G+ S Q KI +I R EGA +L G Sbjct: 310 QESIYERFIEKAVARVEAIRQGSPLDPATMIGAQASGEQLAKILSYIDIGRQEGAQLLTG 369 Query: 366 GGRPQ---HLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHY 422 G R GF+++PT+ M+I+QEE+FGPV+ V F+ ++EA+ +ANDT Y Sbjct: 370 GERAVLAGEFAEGFYVKPTVFRG-HNRMRIFQEEIFGPVLSVTTFKDEAEALAIANDTLY 428 Query: 423 GLAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNY 482 GL V + D R R + + +G +W NC A +GG K+SG GRE + LD+Y Sbjct: 429 GLGAGVWTRDGTRAYRFGREIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHY 488 Query: 483 LTVKQVTKYCSDEPWGWY 500 K + S + G++ Sbjct: 489 QQTKNLLVSYSPKALGFF 506 Lambda K H 0.318 0.136 0.418 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: 655 Number of extensions: 40 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: 506 Length of database: 506 Length adjustment: 34 Effective length of query: 472 Effective length of database: 472 Effective search space: 222784 Effective search space used: 222784 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