Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF882 Psest_0905 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::A0A0E3T3B5 (503 letters) >FitnessBrowser__psRCH2:GFF882 Length = 499 Score = 370 bits (950), Expect = e-107 Identities = 210/491 (42%), Positives = 286/491 (58%), Gaps = 13/491 (2%) Query: 10 LFIDGEWREPVLKKRIPIINPATEQIIGDIPAATAEDVEIAVEAARKALARNKGRDWALA 69 LFID +W + + IINPA +I+ +IP ATA DV+ AV+AA++A W Sbjct: 19 LFIDNQWVSDEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAFMT-----WRTT 73 Query: 70 PGAVRAKYLRAIAAKIAERKSEIAKLEAIDCGKPLDEA-AWDIDDVSGCFEYYADLAEGL 128 A RA L IA + A LE +D GKP+ E+ + DI F Y+A G+ Sbjct: 74 SPAERANALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFA----GV 129 Query: 129 DAQQKTPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSE 188 Q + EQ S L EP+GVVG + PWN+PLLMA WK+APA+AAG ++KPSE Sbjct: 130 IRSQSDEAVMLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSE 189 Query: 189 LASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLASHPHVDKIAFTGSTMTGSKIMT 248 L VT LELA + +V LP GV+NI+TGLG G L HP + K+AFTGST G + Sbjct: 190 LTPVTILELAKIFAKV-LPAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVGELVAN 248 Query: 249 AAAQLVKPVSLELGGKSPIVVFDDVDIDKAAEWTAFGIFWTNGQICSATSRLIIHENIAA 308 AAA+ + P +LELGGKS +VF D + DKA E I W GQ+C + +RL +HE+I Sbjct: 249 AAAKKIIPATLELGGKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFVHESIYE 308 Query: 309 KFLDRLVQWCKNIKIADPLEEGCRLGPVVSGGQYEKILKFIATAKSEGARVLSGGAR--P 366 +FL L + +++ DPL +G VS Q E+IL ++ AK EGA VL GG R Sbjct: 309 RFLAELKHKFEAVRVGDPLNPDTMMGAQVSKSQMERILGYVDIAKQEGAEVLIGGGRLTG 368 Query: 367 EHLKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDSHYGLGAAVI 426 + GFFI+PTI+ V M++ EE+FGPVLCV F E E + +ANDS YGL AV Sbjct: 369 ANYDAGFFIQPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVW 428 Query: 427 SKDLERCERVSKALQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNYLTVKQVT 486 ++D+ R RV++A++ G +W+N AP+GG K+SG GRE K L+ Y K + Sbjct: 429 TQDINRALRVARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYSQKKNIY 488 Query: 487 EYVSDDPWGWY 497 +++ P G + Sbjct: 489 VSLNEAPLGLF 499 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: 604 Number of extensions: 25 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: 499 Length adjustment: 34 Effective length of query: 469 Effective length of database: 465 Effective search space: 218085 Effective search space used: 218085 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 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