Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_004305670.1 C665_RS08800 aldehyde dehydrogenase
Query= BRENDA::A0A0E3T3B5 (503 letters) >NCBI__GCF_000310185.1:WP_004305670.1 Length = 506 Score = 330 bits (846), Expect = 7e-95 Identities = 201/497 (40%), Positives = 278/497 (55%), Gaps = 22/497 (4%) Query: 11 FIDGEWREPVLKKRIPIINPATEQIIGDIPAATAEDVEIAVEAARKALARNKGRDWALAP 70 FI G+W PV + ++ P T Q +TAED+E+A++AA A + W A Sbjct: 22 FIGGQWVAPVKGQYFDVVTPITGQKYTQAARSTAEDIELALDAAHAAFPK-----WGKAD 76 Query: 71 GAVRAKYLRAIAAKIAERKSEIAKLEAIDCGKPLDEAA-WDIDDVSGCFEYYADLAEGLD 129 R+ L IA ++ +A E +D GKP+ E DI F Y+A G Sbjct: 77 ATTRSNILLKIADRLEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFA----GCL 132 Query: 130 AQQKTPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSEL 189 Q+ IS E ++ + EP+GVVG I PWN+P+LMA WK+APAL AG +LKP+E Sbjct: 133 RSQEGGISEIDENTMAYHIHEPLGVVGQIIPWNFPILMAAWKLAPALGAGNCVVLKPAES 192 Query: 190 ASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLASHPHVDKIAFTGSTMTGSKIMTA 249 ++ L L ++ ++ LPPGVLNI+ G G EAG PLA+ + KIAFTGST TG I A Sbjct: 193 TPISILVLMELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTSTGRVIAQA 251 Query: 250 AAQLVKPVSLELGGKSPIVVF------DDVDIDKAAEWTAFGIFWTNGQICSATSRLIIH 303 AA + P +LELGGKSP + F DD +DKA E F G++C+ SR +I Sbjct: 252 AANNLIPATLELGGKSPNIFFADVMDMDDAFLDKAIEGLVLFAF-NQGEVCTCPSRALIQ 310 Query: 304 ENIAAKFLDRLVQWCKNIKIADPLEEGCRLGPVVSGGQYEKILKFIATAKSEGARVLSGG 363 E+I +F++R V+ IK PL+ +G S Q KI ++ K EGA+VL GG Sbjct: 311 ESIYDRFIERAVKRVAAIKQGSPLDTDTMMGAQASSEQMSKIQSYLQLGKDEGAQVLIGG 370 Query: 364 ARPE---HLKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDSHYG 420 AR + L G++I+PT+ M+I++EE+FGPVL V TF E EAL +AND+ YG Sbjct: 371 ARAQLDGDLADGYYIQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALAIANDTLYG 429 Query: 421 LGAAVISKDLERCERVSKALQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNYL 480 LGA V S++ R+ +A+QAG VW NC A +GG K SG GRE K LD+Y Sbjct: 430 LGAGVWSRNGNVAYRMGRAIQAGRVWTNCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQ 489 Query: 481 TVKQVTEYVSDDPWGWY 497 K + S++ G++ Sbjct: 490 QTKNLLVSYSENKLGFF 506 Lambda K H 0.319 0.136 0.419 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: 629 Number of extensions: 27 Number of successful extensions: 5 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: 506 Length adjustment: 34 Effective length of query: 469 Effective length of database: 472 Effective search space: 221368 Effective search space used: 221368 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