Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF3171 PGA1_c32220 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase HpcC
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Phaeo:GFF3171 Length = 503 Score = 322 bits (825), Expect = 2e-92 Identities = 187/455 (41%), Positives = 267/455 (58%), Gaps = 7/455 (1%) Query: 37 FETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEA 96 F+T+ PV ++ + +A G + DID A AAR F +W +RK +L ++A+ +EA Sbjct: 39 FQTISPVDKSVICDVAHGTAADIDAAAQAARQAF--AEWRDLPAVQRKKILIRIAEGIEA 96 Query: 97 HAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVRE 156 AEE+AL E DTG+ + + + GA R++A+ + + S + + R Sbjct: 97 RAEEIALCECWDTGQAYKFMSKAALRGAEN-FRYFADQVVQARDGQHLQSPTLMNVTTRV 155 Query: 157 PVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGV 216 P+G + I PWN P +L+ WK+ PALAAG +V+ KP+E SPL+A L +A+EAGLP GV Sbjct: 156 PIGPVGVITPWNTPFMLSTWKIAPALAAGCTVVHKPAEASPLTARLLVEIAEEAGLPPGV 215 Query: 217 LNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIV 276 LN V GFG EAG+AL H I AIAF G +RTG + K D+ +KR LE GGK+ IV Sbjct: 216 LNTVNGFGDEAGKALCEHPAIRAIAFVGESRTGSLITKQGADT-LKRNHLELGGKNPVIV 274 Query: 277 FADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLD 336 F D DL++A A I+ G+ C + +RLL+++SI D+F A L ++ N + GHPLD Sbjct: 275 FEDA-DLERALDAVIFMIYSINGERCTSSSRLLIQDSIRDDFEARLIERINNIKVGHPLD 333 Query: 337 PATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRN--AGLAAAIGPTIFVDVDPNASLS 394 P T +G L+ H + V S+ +G + G I PT+F D + ++ Sbjct: 334 PTTEIGPLVSEEHFNKVTSYFDIATKEGATIAAGGEPVGEEGYFIRPTLFTDARNDMRIA 393 Query: 395 REEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNY 454 +EEIFGPVL FT+E +AL LAND+ YGL +WT DL+RA R + RL+AG ++VN+ Sbjct: 394 QEEIFGPVLTSIPFTTEAEALALANDTAYGLTGYLWTNDLTRALRFTDRLEAGMIWVNSE 453 Query: 455 NDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489 N + PFGG K SG GRD + E + E K I Sbjct: 454 NVRHLPTPFGGVKASGIGRDGGDWSFEFYMEQKHI 488 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: 560 Number of extensions: 24 Number of successful extensions: 6 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: 503 Length adjustment: 34 Effective length of query: 461 Effective length of database: 469 Effective search space: 216209 Effective search space used: 216209 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