Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Pf1N1B4_171 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_171 Length = 477 Score = 349 bits (895), Expect = e-100 Identities = 191/478 (39%), Positives = 282/478 (58%), Gaps = 11/478 (2%) Query: 5 LLINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPK 61 +LI G+ V +G+G+ P++NPATG+VL + A+ E VD AV AA AF + W +T P+ Sbjct: 1 MLIGGDWVEAGDGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRPR 60 Query: 62 VRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGL 121 R L KLAD+++ + ++ A+LE N GK A ++ +D R+ AG A + G Sbjct: 61 ERQNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLSIDFLRYMAGWATKIEGS 120 Query: 122 AAGEYL-----EGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEI 176 + + + S IRR+ +GVV +I WN+PL++A WKL PALA G VVLKP++ Sbjct: 121 SVEVSMPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADE 180 Query: 177 TPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISH 235 TPLTALKLAEL + +PAGV N++ G G T G LT +P V ++ TGS A G+ I Sbjct: 181 TPLTALKLAELVLEAGYPAGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGKI 240 Query: 236 TASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDT 295 S+ R +ELGGK+P IV DAD++ G + ++N GQ C A R+Y Q+ +D Sbjct: 241 AMESMTRVTLELGGKSPTIVMADADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDN 300 Query: 296 LVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG 355 +V + +K G D S E+GPL S ERV +E+ + +G I G ++ G Sbjct: 301 VVADIADIANAMKLGNGLDPSVEMGPLISARQQERVYGYIEKGRESG--ATIACGGEQFG 358 Query: 356 NGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDV 415 GY+ PT++ Q ++VQ+E+FGPV+ PFD+E + ANDS YGL +S+W+ D+ Sbjct: 359 PGYFVKPTVIVDVDQQHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSNDL 418 Query: 416 GRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 HR+ R++ G WVN H L +P GG K+SG G++M +E YT ++ V++K Sbjct: 419 AAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELKSVLIK 476 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: 593 Number of extensions: 27 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: 477 Length adjustment: 33 Effective length of query: 441 Effective length of database: 444 Effective search space: 195804 Effective search space used: 195804 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: 51 (24.3 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