Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Phaeo:GFF3174 Length = 494 Score = 471 bits (1213), Expect = e-137 Identities = 239/474 (50%), Positives = 318/474 (67%) Query: 24 INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83 I+G+ A G T + LSP+DGR L ++A + D RA+ +ARA F W+ PA R Sbjct: 21 IDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAFEDRRWAGQPPAAR 80 Query: 84 KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143 K L+++A+L+ + LA+L D G I + + AA I + AEA+DK+Y E+A Sbjct: 81 KKVLMKWAELIEADALNLAVLGVRDNGTEITMALKAEPGSAAATIRYYAEALDKIYGEIA 140 Query: 144 PTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRI 203 PT D LG+V +EPVGVVGAI+PWNFP+++ WKL PALA GNSVVLKPSE + L+ +R+ Sbjct: 141 PTSSDVLGMVHKEPVGVVGAIIPWNFPMMIGAWKLAPALAMGNSVVLKPSETASLSLMRM 200 Query: 204 AQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKR 263 +LA+EAG+P GVLN + G G VG+AL L MDVD LVFTGS + ++LM YA SN+KR Sbjct: 201 VELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGSGQTGRRLMEYAARSNLKR 260 Query: 264 IWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVV 323 ++LE GGKSPNIVFADAPDL AA+ A+ I N G+VC AGSRLLVE SI D F+ V Sbjct: 261 VYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAGSRLLVEASIHDAFVEEVA 320 Query: 324 EALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYV 383 +A + + G+PL T +GA+ Q+ L ++ +G +++ GG+R L ETGG+Y+ Sbjct: 321 KAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGGQIITGGQRLLSETGGSYM 380 Query: 384 EPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHK 443 PTI GVT +AQEE+FGPVL+V F+T EA+ IAN T YGLA +WTS +++AH+ Sbjct: 381 APTIVTGVTPDATLAQEEVFGPVLAVTPFETDAEALRIANATVYGLAGAVWTSGLTRAHR 440 Query: 444 TARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 + VR G + VN Y G D T P GG QSGNG DKSLHA++KY LK W+KL Sbjct: 441 MVQGVRTGVMHVNTYGGADGTVPLGGVGQSGNGADKSLHAIDKYINLKTAWMKL 494 Lambda K H 0.316 0.132 0.390 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: 666 Number of extensions: 32 Number of successful extensions: 2 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: 497 Length of database: 494 Length adjustment: 34 Effective length of query: 463 Effective length of database: 460 Effective search space: 212980 Effective search space used: 212980 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 (21.6 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