Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate PfGW456L13_3604 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::A0A0E3T3B5 (503 letters) >lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3604 Aldehyde dehydrogenase (EC 1.2.1.3) Length = 490 Score = 570 bits (1470), Expect = e-167 Identities = 276/489 (56%), Positives = 348/489 (71%), Gaps = 4/489 (0%) Query: 9 QLFIDGEWREPVLKKRIPIINPATEQIIGDIPAATAEDVEIAVEAARKALARNKGRDWAL 68 QL+I+GEW P L + +I+PATEQ + A T EDV+ AV AAR+A W Sbjct: 4 QLYINGEWVSPDLGGYLDVIDPATEQAFHRVAAGTEEDVDHAVRAARRAFDNG----WGQ 59 Query: 69 APGAVRAKYLRAIAAKIAERKSEIAKLEAIDCGKPLDEAAWDIDDVSGCFEYYADLAEGL 128 GA R ++L A+A ++ + +A+LE D GKPL EA WDI D CF YYA LA L Sbjct: 60 TSGAERGQWLEALADELESGQQALAELEVRDNGKPLPEAQWDIGDAIACFRYYAGLAREL 119 Query: 129 DAQQKTPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSE 188 D QQ P++LP +F + EPIGV G I PWNYPLLMA WKVAPALAAG +LKPSE Sbjct: 120 DQQQDQPLALPDARFCCRIRHEPIGVAGQIIPWNYPLLMAAWKVAPALAAGATVVLKPSE 179 Query: 189 LASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLASHPHVDKIAFTGSTMTGSKIMT 248 L +T LELA +GLP GVLN++TGLG +AG+PL HP VDK+AFTGS TG+KIM+ Sbjct: 180 LTPLTALELAAAADRIGLPAGVLNLVTGLGADAGSPLTEHPGVDKLAFTGSVPTGAKIMS 239 Query: 249 AAAQLVKPVSLELGGKSPIVVFDDVDIDKAAEWTAFGIFWTNGQICSATSRLIIHENIAA 308 AAA+ +K +SLELGGKS +VFDD D++ A EW FGIFW GQ+CSATSRL++ E IAA Sbjct: 240 AAARDIKNISLELGGKSAFIVFDDADVEAAVEWILFGIFWNQGQVCSATSRLLVQETIAA 299 Query: 309 KFLDRLVQWCKNIKIADPLEEGCRLGPVVSGGQYEKILKFIATAKSEGARVLSGGARPEH 368 + ++RLV+ + I I ++ G LGP+VS GQY+K+L FI + GAR+L+GG RP H Sbjct: 300 RLIERLVEETRKISIGPGMQPGVLLGPLVSQGQYDKVLGFIDQGLASGARLLTGGRRPAH 359 Query: 369 LKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDSHYGLGAAVISK 428 L++G+F+EP I + S +WREEVFGPVLC+K F +E++AL++AN S +GL AAV+S Sbjct: 360 LREGYFVEPAIFDEPGHSSILWREEVFGPVLCIKRFKTEEQALQMANASRFGLAAAVMSA 419 Query: 429 DLERCERVSKALQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNYLTVKQVTEY 488 DL+R RV+ L+AGIVW+NCSQP F +APWGG K SG GRELG+WGL NYL VKQVTEY Sbjct: 420 DLQRTARVANQLRAGIVWVNCSQPTFVEAPWGGMKHSGIGRELGQWGLHNYLEVKQVTEY 479 Query: 489 VSDDPWGWY 497 VSD PWGWY Sbjct: 480 VSDQPWGWY 488 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: 754 Number of extensions: 23 Number of successful extensions: 2 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: 490 Length adjustment: 34 Effective length of query: 469 Effective length of database: 456 Effective search space: 213864 Effective search space used: 213864 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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