Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011427653.1 RHE_RS22980 carnitine dehydratase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000092045.1:WP_011427653.1 Length = 487 Score = 308 bits (790), Expect = 2e-88 Identities = 175/470 (37%), Positives = 267/470 (56%), Gaps = 6/470 (1%) Query: 7 INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPKVRA 64 I+GE GE P +PATG E+ EA VD AV AA+ A E W + T R Sbjct: 8 IDGEFSDGEAS-YPSIDPATGAAWAEMPEAREGDVDRAVNAAEKALYEGPWAKMTATQRG 66 Query: 65 ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124 + L KLAD++ N QV AELE+R+ GK + + +I + + +R++AG + + G Sbjct: 67 KLLYKLADLVAANAQVLAELETRDTGKIIRET-SAQIAYVAEYYRYYAGISDKIEGSYLP 125 Query: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184 +RR+P+GVVA + PWN L ++A K+ PALAAG +V+K SE P L+ Sbjct: 126 IDKPDMDVWLRREPIGVVAMVVPWNSQLFLSAVKIGPALAAGCTMVVKASEDGPAPLLEF 185 Query: 185 AELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRT 243 A L + FPAGV+NI+ G G + G L HPKV V+ TG T H++ ++A ++ T Sbjct: 186 ARLVHEAGFPAGVVNIITGFGPSCGAALGRHPKVAHVAFTGGPETARHVVRNSAENLAST 245 Query: 244 HMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAA 303 +ELGGK+P IVF DAD+E+ + GQ C A R+ ++ + D V L Sbjct: 246 SLELGGKSPFIVFADADLESAANAQVAGIFAATGQSCVAGSRLIVERSVKDRFVALLRQK 305 Query: 304 VATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPT 363 A ++ GAP D +TE+GPL++ + +G +E + +G +++TGG K G GYY+ PT Sbjct: 306 AAAIRIGAPLDMATEVGPLATKRQQDNIGVLIERSIESG-ARLVTGGRKIDGEGYYFPPT 364 Query: 364 LLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSA 423 +L + +E FGPV+SV F+ E + + AND++YGLAS ++T+++ RAHR+ Sbjct: 365 ILDCDDVASPSLIEEFFGPVLSVVSFETEAEALKLANDTRYGLASGIFTQNLTRAHRLMK 424 Query: 424 RLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 ++ G WVNT+ + P GG LSG+G++ + DYT + + ++ Sbjct: 425 AIRAGIVWVNTYRAVSPIAPFGGFGLSGHGREGGMAAALDYTRTKTIWLR 474 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: 580 Number of extensions: 25 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: 487 Length adjustment: 34 Effective length of query: 440 Effective length of database: 453 Effective search space: 199320 Effective search space used: 199320 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 24 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