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) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3604 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:
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