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) >FitnessBrowser__Keio:15420 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:
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