Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate PP_3646 PP_3646 Aldehyde dehydrogenase family protein
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__Putida:PP_3646 Length = 493 Score = 244 bits (623), Expect = 5e-69 Identities = 151/473 (31%), Positives = 252/473 (53%), Gaps = 8/473 (1%) Query: 11 IDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFP--AWSEQSSLRR 68 IDG+ + + + + + NPAT A++ A+ + V+ AV +A AF AW ++ R Sbjct: 10 IDGQWRDAQSGKTFDSLNPATAQAWAQLPDADEADVELAVQAAQRAFDSKAWRSITATAR 69 Query: 69 SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSD 128 +++ + +L+ + + LAQ+ SR++GK++ + G+V E Y G + L+ Sbjct: 70 GKLLRRLGDLIAENKEHLAQLESRDNGKLIRETRGQVGYLPEFFHYTAGLADKLEGGTLP 129 Query: 129 NIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLM 188 + + + +P+GV AG+ P+N P+ + + AL AGN +LKPSE + L + Sbjct: 130 LDKPDLFAYTVHEPIGVVAGIIPWNSPLYLTAIKLAPALAAGNTIVLKPSEHASATILEL 189 Query: 189 ARLLTEAGLPDGVFNVVQGDKVAVDALL-QHPDIEAISFVGSTPIAEYIHQQGTAQGKRV 247 ARL EAG P GV NVV G + A L +HP + I+F G A ++ + ++ Sbjct: 190 ARLALEAGFPAGVVNVVTGYGPSTGAALTRHPLVRKIAFTGGAATARHVVRSSAENFAKL 249 Query: 248 QALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPR 307 G K+ I+ DADLD A + + Y ++G+ C+A S + ++ DE + +L+ R Sbjct: 250 SLELGGKSPNIIFADADLDSAINGAVAGIYAASGQSCVAGSRLLVQDEIFDEFVERLIAR 309 Query: 308 IDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFFV 367 +++IGN Q ++MGP+ TA+ A VEG + A AEGA+L + G+ V G G+F Sbjct: 310 AKRIRIGNPQDDASEMGPMATAQQLAVVEGLVAAAKAEGAKLHMGGKRADVEG--DGWFY 367 Query: 368 GATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARA 427 TLF+ + M+I Q+E+FGPV ++R A+A+ N +FG +TRD G A Sbjct: 368 EPTLFECDSNAMTIMQEEVFGPVAAVIRFKTEEEALAMANDSQFGLAAGIWTRDLGRAHR 427 Query: 428 FARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSV 480 AR ++ G++ +N V A GG+K S +G G + + Y+ K+V Sbjct: 428 LARDVRSGIIWVNTYRAV-SAMAPIGGFKNSGYG--RESGIDSVLAYTELKTV 477 Lambda K H 0.320 0.137 0.412 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: 547 Number of extensions: 30 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: 500 Length of database: 493 Length adjustment: 34 Effective length of query: 466 Effective length of database: 459 Effective search space: 213894 Effective search space used: 213894 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 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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