Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 15420 b1300 gamma-Glu-gamma-aminobutyraldehyde dehydrogenase, NAD(P)H-dependent (NCBI)
Query= BRENDA::Q83XU8 (485 letters) >lcl|FitnessBrowser__Keio:15420 b1300 gamma-Glu-gamma-aminobutyraldehyde dehydrogenase, NAD(P)H-dependent (NCBI) Length = 495 Score = 320 bits (821), Expect = 5e-92 Identities = 185/464 (39%), Positives = 269/464 (57%), Gaps = 15/464 (3%) Query: 25 PLNNAVIAKVHEAGRAEVDAAVAAAQAAL-KGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 P+ A +AK+ ++D A++AA+ +G W S A+R VL +AD + ++ Sbjct: 42 PVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEEL 101 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 E DTGKP+ + DIP A + +A+ + V E + + + VR P Sbjct: 102 ALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHE----LAMIVREP 157 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 VGV+ I PWN PLLL WK+GPALA GN+V++KPSE++P +A L + AG+P GV Sbjct: 158 VGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVL 217 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADG-ARPVSLELGGKNAAIV 262 NVV GFG + G+ L+ H D++AI FTG T TG+ ++K A D + V LE GGK+A IV Sbjct: 218 NVVTGFG-HEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIV 276 Query: 263 FADC-DLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPED 321 FADC DL +A T F N GQVC+ R+ +E I D F++ LK+ A+ Q G P D Sbjct: 277 FADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLD 336 Query: 322 LATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGD 381 AT MG LI H + V S+ ++ G ++ G A + PTI+ + Sbjct: 337 PATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGL-------AAAIGPTIFVDVDP 389 Query: 382 DSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIA 441 ++ ++REEIFGP +V F SEE+ ++ AND+ YGL +WT +LSRAHR++ ++ G Sbjct: 390 NASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSV 449 Query: 442 WVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 +VN++ D+ FGG KQSG GR+ +H+LE +TELK + I L Sbjct: 450 FVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 Lambda K H 0.318 0.135 0.406 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: 32 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: 485 Length of database: 495 Length adjustment: 34 Effective length of query: 451 Effective length of database: 461 Effective search space: 207911 Effective search space used: 207911 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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