Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 303 bits (775), Expect = 1e-86 Identities = 187/477 (39%), Positives = 271/477 (56%), Gaps = 18/477 (3%) Query: 20 NRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSS 79 +R +I G++ A N + +P T+ +A++ G + D DRA AA F W+ S Sbjct: 5 SRFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPA--WAALS 62 Query: 80 PAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVY 139 A+R A L K+AD ++A +EL L + G P++ + R A I +A A ++ Sbjct: 63 GAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQ---AGNPIFTFA-ACARIA 118 Query: 140 GEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLS 199 E +++++ P G +A I PWNFPL K+G ALAAG +V+LKPSE +PL+ Sbjct: 119 AEGFAEERIGQSLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLN 178 Query: 200 AIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDS 259 A LA + + AGLP GV N+VTG+G G+AL+ H + A++FTGST GK++ A + Sbjct: 179 AFLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAA-A 237 Query: 260 NMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFL 319 +KRV LE GGKSA++V D DL A T AG F N GQ C A TRLL+ + E Sbjct: 238 TVKRVSLELGGKSASVVLPDA-DLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAA 296 Query: 320 ALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA---GLA 376 AL Q A + G PL + +G L+ V + I + + G LL G +A GL Sbjct: 297 ALAVQAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLP 356 Query: 377 AA--IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDL 434 + PT+F V P+A+L+REE+FGPVL + + E +A +AN + YGL AAVW+ + Sbjct: 357 TGYYVRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEE 416 Query: 435 SRAHRMSRRLKAGSVFVNN--YNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489 +RA +RRL+AG V +N +N + PFGG+KQSG GR+ H +E F E ++I Sbjct: 417 ARALAFARRLRAGQVDINGAFFN---LLAPFGGFKQSGYGRELGRHGVEDFLETQSI 470 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: 536 Number of extensions: 23 Number of successful extensions: 7 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: 476 Length adjustment: 34 Effective length of query: 461 Effective length of database: 442 Effective search space: 203762 Effective search space used: 203762 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 Apr 09 2024. 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