Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein
Query= SwissProt::D4GP41 (482 letters) >NCBI__GCF_000504245.1:WP_034273599.1 Length = 496 Score = 332 bits (851), Expect = 2e-95 Identities = 192/479 (40%), Positives = 269/479 (56%), Gaps = 9/479 (1%) Query: 8 YVNGEWV-TSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDE--WRNTPG 64 +++G WV T+ T V NPAN +E+ + ++E D AAV AA A D+ WR T Sbjct: 5 FIDGRWVDTTGTAPARVVLNPANAAELATVCE-ADEKDVDAAVAAARRAFDDSPWRATTA 63 Query: 65 PERGRILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGT 124 ERG +LRE LL + K+ L + + GK E +V +F Y+++ A + G Sbjct: 64 RERGELLREIARLLQRDKEHLARTESLDTGKTMAEGRVDVDDVTSVFRYYANLADNEAGR 123 Query: 125 KKGASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVV 184 + EPVGV +LI PWNYP+ +WKLAPALAAGNTVV+KP+ + P Sbjct: 124 VVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTPLTT 183 Query: 185 IEIARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAG 244 IE+ R ++EAG+P GV+N+V G G++VG+ + + DLVSFTG + G+ + A + Sbjct: 184 IELMRLVEEAGVPAGVVNLVLGGGANVGAPMVSHPDVDLVSFTGGLETGKKIMAMAAEGV 243 Query: 245 KRVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFVAEL 304 KRV ELGGKNP +V A+ A D F +GQ C+A SR IV D++D+FVAEL Sbjct: 244 KRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEFVAEL 303 Query: 305 VDRAESLDVGPGTD--HEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETG 362 RA+++ +G G D E GP S +I+ A+ EGA LV GG P + G Sbjct: 304 ARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPELADG 363 Query: 363 HFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTE 422 +F+ PTVF D D +MRI Q+EVFGPVV V DE + +AND +YGL+ ++ T D + Sbjct: 364 YFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTSDASR 423 Query: 423 ANRFVDEVEAGVVKVNDKTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTVYDS 481 A R + G V +ND L +GGF +S RE G +GL+ Y K +Y + Sbjct: 424 AQRVAGALRHGTVWINDFHPYLP-QAEWGGFGKSG--IGRELGPSGLEEYRETKHIYQN 479 Lambda K H 0.310 0.130 0.370 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: 612 Number of extensions: 31 Number of successful extensions: 3 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: 482 Length of database: 496 Length adjustment: 34 Effective length of query: 448 Effective length of database: 462 Effective search space: 206976 Effective search space used: 206976 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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