Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Phaeo:GFF3174 Length = 494 Score = 441 bits (1134), Expect = e-128 Identities = 234/474 (49%), Positives = 313/474 (66%), Gaps = 4/474 (0%) Query: 24 INGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKR 83 I+G+ AA++ T + + P+ L +IARG D++RA+++AR FE W+ PA R Sbjct: 21 IDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAFEDRRWAGQPPAAR 80 Query: 84 KAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVA 143 K VL K A+L+EA A LA+L D G I +L+ + AA IR+YAEA+DK+YGE+A Sbjct: 81 KKVLMKWAELIEADALNLAVLGVRDNGTEITMALKAEPGSAAATIRYYAEALDKIYGEIA 140 Query: 144 TTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRL 203 TSS L M+ +EPVGV+ AI+PWNFP+++ WKL PALA GNSV+LKPSE + LS +R+ Sbjct: 141 PTSSDVLGMVHKEPVGVVGAIIPWNFPMMIGAWKLAPALAMGNSVVLKPSETASLSLMRM 200 Query: 204 AGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKR 263 LA EAGLP GVLN VTG G G+AL D+D + FTGS +TG++L++ A SN+KR Sbjct: 201 VELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGSGQTGRRLMEYAARSNLKR 260 Query: 264 VWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLK 323 V+LE GGKS NIVFAD PDL AA TAAGIF N GQVC+AG+RLL+E SI D F+ + Sbjct: 261 VYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAGSRLLVEASIHDAFVEEVA 320 Query: 324 QQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAAIG--- 380 + AQ + G PL T +G + A F+ E +G ++ G L+ G Sbjct: 321 KAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGGQIITGGQRLLSETGGSYM 380 Query: 381 -PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHR 439 PTI V P+A+L++EE+FGPVL VT F ++ +AL++AN + YGL AVWT L+RAHR Sbjct: 381 APTIVTGVTPDATLAQEEVFGPVLAVTPFETDAEALRIANATVYGLAGAVWTSGLTRAHR 440 Query: 440 MSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 M + ++ G + VN Y D TVP GG QSGNG DKSLHA++K+ LKT W+ L Sbjct: 441 MVQGVRTGVMHVNTYGGADGTVPLGGVGQSGNGADKSLHAIDKYINLKTAWMKL 494 Lambda K H 0.317 0.133 0.389 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: 550 Number of extensions: 27 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: 495 Length of database: 494 Length adjustment: 34 Effective length of query: 461 Effective length of database: 460 Effective search space: 212060 Effective search space used: 212060 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