Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF657 Psest_0671 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__psRCH2:GFF657 Length = 506 Score = 323 bits (828), Expect = 8e-93 Identities = 183/481 (38%), Positives = 276/481 (57%), Gaps = 18/481 (3%) Query: 7 INGELVSG-EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAE 65 INGE V G+ +P G + E + A ++ A+ AA AA WG+T+ + R+ Sbjct: 23 INGEFVEPVNGQYFTNLSPVNGQPIAEFPRSDAADIEKALDAAHAAADAWGKTSVQARSL 82 Query: 66 CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGE 125 LL++AD IE+N ++ A E+ + GK + N +IP D FR+FAG R G +A Sbjct: 83 ILLQIADRIEQNLEMLAVTETWDNGKAVRETLNADIPLAADHFRYFAGCIRAQEGTSAE- 141 Query: 126 YLEGHTSMIR-RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184 ++ HT+ +PLGVV I PWN+P++MAAWKLAPALAAGNCVVLKP+E TPL L Sbjct: 142 -IDEHTAAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQTPLGITVL 200 Query: 185 AELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244 E+ D+ P GV+N++ G G+ G+ L ++ ++ TGS G HI+ A +I + Sbjct: 201 MEVIGDLLPPGVLNVVQGYGREAGEALASSKRIAKIAFTGSTPVGSHIMKRAAEAIIPST 260 Query: 245 MELGGKAPVIVFDD------ADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 +ELGGK+P I F+D IE EG+ G++N G+ CT R Q+ IY +E Sbjct: 261 VELGGKSPNIYFEDIMQAEPTFIEKAAEGL-VLGFFNQGEVCTCPSRALVQESIYAPFME 319 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG--EKRKGN 356 + VA +K G P D T +G +S +++ +E AK G +V+TGG EK +G+ Sbjct: 320 AVMKKVAQIKRGDPLDTETMVGAQASQQQFDKIMSYLEIAKGEG-AEVLTGGAAEKLEGS 378 Query: 357 ---GYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTK 413 GYY PTLL G Q + Q+E+FGPV+ VT F +E + + AND++YGL + VWT+ Sbjct: 379 LATGYYIQPTLLKGTNQ-MRVFQEEIFGPVIGVTTFKDEAEALAIANDTEYGLGAGVWTR 437 Query: 414 DVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 D+ RA+R+ ++ G W N + + + GG K SG G++ L+ Y +++++ Sbjct: 438 DINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKRSGVGRETHKMILDSYQQTKNLLIS 497 Query: 474 H 474 + Sbjct: 498 Y 498 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: 557 Number of extensions: 24 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: 474 Length of database: 506 Length adjustment: 34 Effective length of query: 440 Effective length of database: 472 Effective search space: 207680 Effective search space used: 207680 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