Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Pedo557:CA265_RS24850 Length = 454 Score = 210 bits (534), Expect = 9e-59 Identities = 136/450 (30%), Positives = 219/450 (48%), Gaps = 12/450 (2%) Query: 21 VYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQV 80 + NPAT +++ + E + + A A +W T + R + +D++E + Sbjct: 3 IINPATAEIITSLEEDNLSTLQLKFDALQKAQPQWAGKTLQERIAVITHFSDLLEVEIEK 62 Query: 81 FAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLE---GHTSMIRRD 137 A + + GKPL + N+ A + A A + L A E + G +I+ + Sbjct: 63 LASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYL----ADEVMTDEPGIKEIIKYE 118 Query: 138 PLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPAGV 196 PLGVV +I+ WNYP ++ PAL +GN V+ KPSE LT +++ +L K P V Sbjct: 119 PLGVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDV 178 Query: 197 INILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVF 256 +I G K G L + TGS TG+ I A+ + +ELGGK P+ + Sbjct: 179 FHIAIG-AKETGSALL-NMDFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYIT 236 Query: 257 DDA-DIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDE 315 DD D+ A G +YN GQ C A RIY Q+ YD V + K+G P E Sbjct: 237 DDVTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAE 296 Query: 316 STELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDAIV 375 +G L+ + + V++A G K++TGG+ +G GYY+ PT+L D ++ Sbjct: 297 GVYIGALTRKEQISVLENQVKDALNKG-AKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVM 355 Query: 376 QKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTH 435 Q+E FGP++ + ++ + + D+ YGL +SV+T RA ++ A+L G + N Sbjct: 356 QEESFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCC 415 Query: 436 FMLVSEMPHGGQKLSGYGKDMSLYGLEDYT 465 + + +P G+K SG G +S G+ +T Sbjct: 416 DRVSAALPWSGRKYSGIGATLSHQGIRAFT 445 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: 476 Number of extensions: 24 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: 454 Length adjustment: 33 Effective length of query: 441 Effective length of database: 421 Effective search space: 185661 Effective search space used: 185661 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