Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= BRENDA::C6KEM4 (506 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 342 bits (878), Expect = 1e-98 Identities = 207/503 (41%), Positives = 289/503 (57%), Gaps = 23/503 (4%) Query: 8 PRRGLFIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQ 67 P FIGG W G+ ++P I + +AEDVE+A+ AA A Sbjct: 17 PHYDNFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAARGA----- 71 Query: 68 WSRAPGAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEA-SGDMDDVAACFEYYADL 126 W R A R+ L IA +I+ + LA++ET+D+GKP+ E + D+ F Y+A Sbjct: 72 WGRTSPAERSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGC 131 Query: 127 AEALDGKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTIL 186 A +G IS + +Y EP+GVV I PWN+PLLMA WK+APALAAG IL Sbjct: 132 LRAQEGG----ISEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVIL 187 Query: 187 KPSELASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGK 246 KP+E +S + L + ++ LPPGVLN+I G G EAG PL+ + + KVAFTG T TG+ Sbjct: 188 KPAEQTPMSVMVLVDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGR 246 Query: 247 RIMTSAAQMVKPVSLELGGKSPLIVFDDIGD-----IDKAVEWTMFGIFA-NAGQVCSAT 300 IM A++ + PV+LELGGKSP I F D+ D DKA+E F +FA N G+VC+ Sbjct: 247 LIMQYASENIIPVTLELGGKSPNIFFADVADEDDDFFDKALEG--FSMFALNQGEVCTCP 304 Query: 301 SRLLLHEKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGA 360 SR L+ EKI +F++R VA K IK +PL+ +G+ S Q EKI ++ R EGA Sbjct: 305 SRALVQEKIYDRFMERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGA 364 Query: 361 TILYGGGRPQ---HLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELA 417 +L GGGR L GF+++PTI+ + M+I+QEE+FGPV+ V F+ D EA+E+A Sbjct: 365 KVLAGGGRADVGPELAGGFYVQPTIL-EGHNKMRIFQEEIFGPVLSVTSFKDDEEALEIA 423 Query: 418 NDTHYGLAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEW 477 NDT YGL V + + R R +A+ +G +W NC A +GG K+SG GRE + Sbjct: 424 NDTLYGLGAGVWTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKM 483 Query: 478 GLDNYLTVKQVTKYCSDEPWGWY 500 LD+Y K + S + G++ Sbjct: 484 MLDHYQKTKNMLVSYSPKALGFF 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: 671 Number of extensions: 31 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