Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 3608023 Dshi_1430 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Dino:3608023 Length = 487 Score = 312 bits (800), Expect = 1e-89 Identities = 190/463 (41%), Positives = 261/463 (56%), Gaps = 20/463 (4%) Query: 38 ETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAH 97 + +P T +A+I ++DRA++AAR FE G+WS + R +L+KL + + AH Sbjct: 29 DVTNPATGEKIAQIPACGPDEVDRAVTAARRAFEDGEWSRLTAVDRGRLLHKLGEAITAH 88 Query: 98 AEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREP 157 +ELA E DTGKP+ + R D+ AAR +Y A DKV+GE S + EP Sbjct: 89 GQELAEWEAKDTGKPLAQA-RADMVAAARYFEYYGAAADKVHGETIPFLSGYQVQTIFEP 147 Query: 158 VGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVL 217 GV I+PWN+P + PALA GN+V+LKP+E + L+ +R+A LA E G P G + Sbjct: 148 YGVTGHIIPWNYPAQMFGRSCAPALAMGNAVVLKPAEDACLTPLRIAELALEVGFPGGAI 207 Query: 218 NVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVF 277 NVVTG+G EAG AL+ H D+D ++FTGS G +++ A N LE GGKS IVF Sbjct: 208 NVVTGYGQEAGAALTTHRDVDFLSFTGSPEVG-VMIQTAAARNHIGCTLELGGKSPQIVF 266 Query: 278 ADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQ-----QAQNWQPG 332 AD DL A GI N GQ C AG+R L++ I D LA LK A WQ Sbjct: 267 ADA-DLDAAIPVLLNGIVQNGGQTCSAGSRALIQRDIFDAVLARLKAGFEALTAAPWQEN 325 Query: 333 HPLDPATTMGTLIDCAHADSVHSFIRE-GESKGQLLLDGRNAGLAAAIG----PTIFVDV 387 L P LI V FI E G + L+ GR A A+ G P +F V Sbjct: 326 GNLGP------LISHKQKRRVEGFIAEGGGADAPLVARGRIAASASEAGSFVAPALFGPV 379 Query: 388 DPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAG 447 L+REE+FGPVL FT E A+++AN + YGL A+VW+ D R R+++RL+ G Sbjct: 380 IEGHVLAREEVFGPVLSCIPFTDEADAIRIANATDYGLVASVWSADGGRQMRLAKRLRVG 439 Query: 448 SVFVNNYN-DGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489 VF+N Y G + +PFGG ++SG+GR+K AL +F+++KT+ Sbjct: 440 QVFLNCYGAGGGIELPFGGMRKSGHGREKGFAALHEFSQIKTV 482 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: 611 Number of extensions: 30 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: 495 Length of database: 487 Length adjustment: 34 Effective length of query: 461 Effective length of database: 453 Effective search space: 208833 Effective search space used: 208833 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