Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PP_3646 PP_3646 Aldehyde dehydrogenase family protein
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Putida:PP_3646 Length = 493 Score = 410 bits (1054), Expect = e-119 Identities = 219/478 (45%), Positives = 305/478 (63%), Gaps = 6/478 (1%) Query: 38 QIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMD 97 Q+ I+ +W DA S KTF ++NP+T + Q+ + D+ DV+ AV+AA+ AF WR + Sbjct: 7 QMCIDGQWRDAQSGKTFDSLNPATAQAWAQLPDADEADVELAVQAAQRAFD-SKAWRSIT 65 Query: 98 ASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYH 157 A+ RG+LL RL DLI ++ +LA LE+ DNGK + + + + Y AG ADK Sbjct: 66 ATARGKLLRRLGDLIAENKEHLAQLESRDNGK-LIRETRGQVGYLPEFFHYTAGLADKLE 124 Query: 158 GKTIPIDG-DFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPL 216 G T+P+D D F+YT HEP+GV IIPWN PL + A KL PALA GN +V+K +E Sbjct: 125 GGTLPLDKPDLFAYTVHEPIGVVAGIIPWNSPLYLTAIKLAPALAAGNTIVLKPSEHASA 184 Query: 217 TALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGS 276 T L +A L EAGFP GVVN+V G+GP+ GAA+ H V K+AFTG R + V + + Sbjct: 185 TILELARLALEAGFPAGVVNVVTGYGPSTGAALTRHPLVRKIAFTGGAATARHV-VRSSA 243 Query: 277 SNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFV 336 N +++LELGGKSPNII +DAD+D A+ A ++ GQ C AGSR VQ++I+DEFV Sbjct: 244 ENFAKLSLELGGKSPNIIFADADLDSAINGAVAGIYAASGQSCVAGSRLLVQDEIFDEFV 303 Query: 337 ERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIA--ADR 394 ER +ARAK +GNP D +E GP Q + G + K EGAKL GG A Sbjct: 304 ERLIARAKRIRIGNPQDDASEMGPMATAQQLAVVEGLVAAAKAEGAKLHMGGKRADVEGD 363 Query: 395 GYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLD 454 G+F +PT+F + MTI +EE+FGPV +++FKT EE + AN+S +GLAA ++T+DL Sbjct: 364 GWFYEPTLFECDSNAMTIMQEEVFGPVAAVIRFKTEEEALAMANDSQFGLAAGIWTRDLG 423 Query: 455 KANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512 +A+ L++ +++G +WVN Y A +P GG+K SG GRE G + AYTE+KTV + + Sbjct: 424 RAHRLARDVRSGIIWVNTYRAVSAMAPIGGFKNSGYGRESGIDSVLAYTELKTVWINL 481 Lambda K H 0.319 0.136 0.409 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: 616 Number of extensions: 33 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: 517 Length of database: 493 Length adjustment: 34 Effective length of query: 483 Effective length of database: 459 Effective search space: 221697 Effective search space used: 221697 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