Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF3484 PS417_17840 betaine-aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__WCS417:GFF3484 Length = 486 Score = 343 bits (880), Expect = 8e-99 Identities = 193/481 (40%), Positives = 291/481 (60%), Gaps = 19/481 (3%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 +ING + +TF +P T + ++A G + ++ A++AA+ F + W+ ++PAK Sbjct: 5 WINGREVES--KDTFINYNPATGEAIGEVASGGAEEVALAVAAAKEAFPK--WA-NTPAK 59 Query: 83 RKA-VLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE 141 +A ++ KL +L+E + LA LETLDTG PI + IP A+ ++AE ++ G Sbjct: 60 ERARLMRKLGELIEQNVPHLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGH 119 Query: 142 VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201 L + +PVGV + PWN P + WK P LA GN+ +LK SE SPL+A Sbjct: 120 SYPVDDQMLNYTLYQPVGVCGLVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTAN 179 Query: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261 L LA EAG+P+GVLNV+ G+G AG AL RH D+ AI+FTG T TGK++++ AG + Sbjct: 180 ELGRLAVEAGIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG---L 236 Query: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321 K+ +E GGKS ++F D DL++A + IF G+ C AG+R+ ++ES+ +F+A Sbjct: 237 KKYSMELGGKSPVLIFEDA-DLERALDSALFTIFSLNGERCTAGSRIFIQESVYPQFVAE 295 Query: 322 LKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG---RNAGLAA- 377 +A+ G P DP T +G++I AH D V +I+ G +G LL G R A L A Sbjct: 296 FAARAKRLIVGDPQDPKTQVGSMITQAHYDKVTGYIKIGIEEGATLLAGGLDRPANLPAH 355 Query: 378 -----AIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTR 432 I PT+F DV+ +++EEIFGPV+ + F E +ALQLAND++YGL + +WT+ Sbjct: 356 LSKGQFIQPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQ 415 Query: 433 DLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWIS 492 D+ +AHR++R ++AG VF+N+ N D+ PFGG K SG GR+ ++ E F E+K + IS Sbjct: 416 DIGKAHRLARGIEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNVCIS 475 Query: 493 L 493 + Sbjct: 476 M 476 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: 527 Number of extensions: 18 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: 495 Length of database: 486 Length adjustment: 34 Effective length of query: 461 Effective length of database: 452 Effective search space: 208372 Effective search space used: 208372 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