Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate PP_2487 PP_2487 putative aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Putida:PP_2487 Length = 503 Score = 351 bits (900), Expect = e-101 Identities = 193/474 (40%), Positives = 284/474 (59%), Gaps = 9/474 (1%) Query: 5 LLINGELVSGE-GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVR 63 L I+ + V+ E GE + NPA G +L I A+A VD AV+AA AF W T+P R Sbjct: 23 LFIDNQWVTAEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAFVTWRTTSPAER 82 Query: 64 AECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAA 123 A LLK+AD++E + FA LE+ + GKP+ + + +IP +D FR+FAG R + A Sbjct: 83 ANALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGVIRSQSDEAV 142 Query: 124 GEYLEGHT-SMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTAL 182 L+ T S+ +PLGVV + PWN+PL+MAAWK+APA+AAGN VV+KPSE+TP+T L Sbjct: 143 --MLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTPVTIL 200 Query: 183 KLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKR 242 +LA++ + PAGV+NI+ G G TVG L HP +R ++ TGS GE + + A I Sbjct: 201 ELAKIFAKVLPAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVGELVANAAAKKIIP 260 Query: 243 THMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGA 302 +ELGGK+ IVF DA+ + VEG +N GQ C + R++ + IY+ + +L Sbjct: 261 ATLELGGKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFLAELKH 320 Query: 303 AVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG----NGY 358 ++ G P + T +G S +ER+ V+ AK G +V+ GG + G G+ Sbjct: 321 KFEAVRVGDPLNPDTMMGAQVSKTQMERILGYVDIAKEEG-AEVLIGGGRLTGADYDAGF 379 Query: 359 YYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRA 418 + PT+L G D + +E+FGPV+ V PF +E +V+ ANDS+YGLA +VWT+D+ RA Sbjct: 380 FIQPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQDINRA 439 Query: 419 HRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 RV+ ++ G WVNT+ + + P GG K SG G++ LE Y+ +++ V Sbjct: 440 LRVARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYSQKKNIYV 493 Lambda K H 0.317 0.134 0.397 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: 532 Number of extensions: 19 Number of successful extensions: 3 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: 474 Length of database: 503 Length adjustment: 34 Effective length of query: 440 Effective length of database: 469 Effective search space: 206360 Effective search space used: 206360 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 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