Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein
Query= BRENDA::C6KEM4 (506 letters) >NCBI__GCF_002117405.1:WP_085772038.1 Length = 506 Score = 342 bits (878), Expect = 1e-98 Identities = 200/498 (40%), Positives = 287/498 (57%), Gaps = 23/498 (4%) Query: 13 FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72 FIGG W P G ++P T I + G A DVE+A+ AA A +D W + P Sbjct: 22 FIGGQWVAPLGGEYFDNISPITGHPICQVARGRAADVELALDAAHKA--KDA---WGKTP 76 Query: 73 GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEASG-DMDDVAACFEYYADLAEALD 131 A RAN L IA ++ D S LAL+ET+D+GKP+ E + D+ F Y+A A + Sbjct: 77 AAERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQE 136 Query: 132 GKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSEL 191 G +S + +Y EP+GVVG I PWN+P+LMA WK++PALAAG +LKP+E Sbjct: 137 GS----LSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQ 192 Query: 192 ASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTS 251 +S L + + ++ LPPGVLNI+ G G EAG PL+S+ + K+AFTG T TG+ IM Sbjct: 193 TPMSILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQY 251 Query: 252 AAQMVKPVSLELGGKSPLIVFDDI-----GDIDKAVEWTMFGIFA-NAGQVCSATSRLLL 305 AA+ + PV+LELGGKSP I F D+ +DKA+E F FA N G+VC+ SR L+ Sbjct: 252 AAENLIPVTLELGGKSPNIFFADVMAEDDAFLDKALEG--FASFALNQGEVCTCPSRALV 309 Query: 306 HEKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYG 365 I KF+++ +A I+ PL+ +G+ S Q EKI ++ R EGA +L G Sbjct: 310 QRSIYDKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIG 369 Query: 366 GGRPQ---HLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHY 422 G R L+ G++++PT + + M+++QEE+FGPV+ V F T+ EA+++ANDT Y Sbjct: 370 GERSVLEGELKEGYYMQPTAL-EGHNRMRVFQEEIFGPVVSVTTFETEEEALQIANDTLY 428 Query: 423 GLAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNY 482 GL + + D R R +A+ +G +W NC A +GG K+SG GRE + LD+Y Sbjct: 429 GLGAGLWTRDGSRAYRCGRAIRAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHY 488 Query: 483 LTVKQVTKYCSDEPWGWY 500 K + S + G + Sbjct: 489 QQTKNLLVSYSPKALGLF 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: 30 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 Apr 09 2024. 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