Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate HSERO_RS04810 HSERO_RS04810 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__HerbieS:HSERO_RS04810 Length = 504 Score = 316 bits (809), Expect = 1e-90 Identities = 176/469 (37%), Positives = 254/469 (54%), Gaps = 6/469 (1%) Query: 7 INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAEC 66 INGELV+G+GE +YNPATG L + A V+AA AA A +W + R Sbjct: 27 INGELVAGQGEIIQLYNPATGRASLSYRDGGAAAVEAAAVAAQRAQRQWWALSHAARGRA 86 Query: 67 LLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEY 126 L + VI + A LE+ + GKP+ E+ + ++F ++AG A G Sbjct: 87 LYAVGAVIRAEAEPLARLEAISSGKPIRDC-RAEMQKVAEMFEYYAGWADKFYGEVI-PV 144 Query: 127 LEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAE 186 H + RR+P G V + PWN P W+L PALA GN V+LKPSE+TP ++L +A Sbjct: 145 PSSHLNYTRREPYGTVLQMTPWNAPAFTCGWQLGPALATGNAVLLKPSELTPFSSLAIAR 204 Query: 187 LAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHM 245 L + PAG++N+L G G+T+ V+ V GS ATG I A+ + + Sbjct: 205 LGEQAGLPAGLVNVLAGLGQTMVPQAMATWTVKKVIFVGSPATGALIAKAAAARVMPCVL 264 Query: 246 ELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVA 305 ELGGK+ I+F+DAD+ G + + AGQ C A R+ Q+ +YD VE + A Sbjct: 265 ELGGKSANIIFEDADLRLAAFGAQAAIFSGAGQSCVAGSRLLVQRKVYDRFVETVAAGAE 324 Query: 306 TLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGN-GYYYAPTL 364 ++ GAP D+STE+GP+++ E + + V G + G R G GY+ PTL Sbjct: 325 KIRLGAPLDDSTEVGPINNRKQYEHIQRMVARGLEAG--ATLAAGHTRYGEEGYFVRPTL 382 Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424 LA A + + E+FGPV PF++EE+ + ANDS++GLA +VWT+DV RAHRV+A Sbjct: 383 LAHASNAMEVARSEIFGPVAVAIPFEDEEEAIAIANDSEFGLAGAVWTRDVARAHRVAAS 442 Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 + G WVN++ + P GG SGYG+ + L DYT + V V+ Sbjct: 443 VNAGTFWVNSYKTINVASPFGGFNRSGYGRSSGMEALYDYTQTKSVWVE 491 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: 632 Number of extensions: 26 Number of successful extensions: 4 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: 504 Length adjustment: 34 Effective length of query: 440 Effective length of database: 470 Effective search space: 206800 Effective search space used: 206800 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