Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Phaeo:GFF2135 Length = 485 Score = 309 bits (791), Expect = 2e-88 Identities = 180/471 (38%), Positives = 263/471 (55%), Gaps = 10/471 (2%) Query: 7 INGELVSGE-GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAE 65 INGE V G PV ATG+ + + A+ V+ A+ A AA W + T R Sbjct: 13 INGEYVEDTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQKAWARMTGTERGR 72 Query: 66 CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG--LAA 123 L + AD++ E + LE+ + GKPL + + D +F G A L G + Sbjct: 73 ILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTGEHIPL 132 Query: 124 GEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALK 183 GE +R+ LG+ I WNYP +A WK APALA GN +V KPSE TPL ALK Sbjct: 133 GE----DWVYTKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCALK 188 Query: 184 LAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKR 242 +AE+ + PAGV N++ G G+ VG L P+V VSLTGS+ TG+ + + A +K Sbjct: 189 VAEILIEAGAPAGVFNVVQGMGE-VGGALVTDPRVDKVSLTGSVPTGKKVYAAAAEGMKH 247 Query: 243 THMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGA 302 MELGGK+P+I+FDDADI+ V G +Y++GQ C+ R++ QKGI + + +L Sbjct: 248 VTMELGGKSPLIIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARLAE 307 Query: 303 AVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAP 362 G P DE+T GP+ + + V +E+ K G ++I GG + +GY+ P Sbjct: 308 RTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEG-ARLICGGRRADMDGYFIEP 366 Query: 363 TLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVS 422 T+ A D I ++E+FGPV+SV FD EE+VV AND+++GL++ V+TKD RAHRV Sbjct: 367 TVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTRAHRVI 426 Query: 423 ARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 L+ G ++N++ E P GG K SG G++ S ++ ++ V+ V V+ Sbjct: 427 GNLEAGSCFINSYNDAPVEAPFGGVKASGVGRENSKEAIKHFSQVKSVYVR 477 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: 585 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: 485 Length adjustment: 34 Effective length of query: 440 Effective length of database: 451 Effective search space: 198440 Effective search space used: 198440 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