Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate Pf6N2E2_1309 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1309 Length = 486 Score = 342 bits (878), Expect = 1e-98 Identities = 189/469 (40%), Positives = 286/469 (60%), Gaps = 17/469 (3%) Query: 35 ETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKA-VLNKLADL 93 + F +P T + ++A G + ++ +A++AA+ F + W+ ++PAK +A ++ KL +L Sbjct: 15 DVFVNYNPATGEAIGEVASGGAEEVAQAVAAAKEAFPK--WA-NTPAKERARLMRKLGEL 71 Query: 94 MEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMI 153 +E + +LA LETLDTG PI + IP A+ ++AE ++ G L Sbjct: 72 IEQNVPQLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGHTYPVDDQMLNYT 131 Query: 154 VREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLP 213 + +PVGV A + PWN P + WK P LA GN+ +LK SE SPL+A L LA EAG+P Sbjct: 132 LYQPVGVCALVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTANELGRLAVEAGIP 191 Query: 214 DGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSA 273 +GVLNV+ G+G AG AL RH D+ AI+FTG T TGK++++ AG +K+ +E GGKS Sbjct: 192 NGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG---LKKYSMELGGKSP 248 Query: 274 NIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGH 333 ++F D DL++A A IF G+ C AG+R+ ++ES+ +F+A +A+ G Sbjct: 249 VLIFEDA-DLERALDAALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFAARAKRLIVGD 307 Query: 334 PLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG---RNAGLAA------AIGPTIF 384 P DP T +G++I AH D V +I+ G +G LL G R A L A I PT+F Sbjct: 308 PQDPKTQVGSMITQAHYDKVTGYIKIGLEEGATLLAGGLERPANLPAHLSRGQFIQPTVF 367 Query: 385 VDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRL 444 DV+ +++EEIFGPV+ + F E +AL LAND++YGL + +WT+D+ +AHR++ + Sbjct: 368 ADVNNKMRIAQEEIFGPVVCLIPFKDEAEALHLANDTEYGLASYIWTQDIGKAHRLAHGI 427 Query: 445 KAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 +AG VF+N+ N D+ PFGG K SG GR+ ++ E F E+K + IS+ Sbjct: 428 EAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNVCISM 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: 533 Number of extensions: 18 Number of successful extensions: 4 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