Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate WP_012169715.1 AZC_RS06095 betaine-aldehyde dehydrogenase
Query= SwissProt::D4GP41 (482 letters) >NCBI__GCF_000010525.1:WP_012169715.1 Length = 700 Score = 298 bits (762), Expect = 5e-85 Identities = 187/478 (39%), Positives = 254/478 (53%), Gaps = 11/478 (2%) Query: 6 KNYVNGEWVTSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDEWRNTPGP 65 +N + G V S T E NPA E++A + + + AV AA + +W G Sbjct: 220 RNQIGGGPVASRAATTFETRNPAT-GELLAEIEIAGPEEVDRAVAAARDGQRKWAAMTGA 278 Query: 66 ERGRILREAGTLLAQRKDELTEILTAEEGKARPEAAG-EVQRAIDIFHYFSSKAADLGGT 124 ERGRILR A LL R DEL + T + GK E + +V D YF+ A L G Sbjct: 279 ERGRILRRAADLLRARNDELARLETLDTGKPIQETSVVDVLSGADCLDYFAGVAPTLAGE 338 Query: 125 KKGASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVV 184 GP YTR+EP+GV A I WNYP+ I WK APALA GN ++ KPA + P Sbjct: 339 HVDL-GPEAFGYTRREPLGVVAGIGAWNYPLQIACWKAAPALACGNAMIFKPAELTPLTA 397 Query: 185 IEIARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAG 244 +++A EAGLPDGV NVV G + G + G VS TG + G V A + Sbjct: 398 VKLAEIFTEAGLPDGVFNVVQG-FADTGRLLTRHPGIAKVSLTGEAGTGRKVMADAAASL 456 Query: 245 KRVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFVAEL 304 K V ELGGK+P +V AN +A G F + G+ C+ +R VH + F+A+L Sbjct: 457 KHVTLELGGKSPLIVFPDANLEDAVSAAMLGNFYSGGEICSNGTRVFVHSSILKPFLAQL 516 Query: 305 VDRAESLDVGPGTDH--EMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAVETG 362 +R E + VG D +G +SE+ + L YI+ A+A GA LVAGG E A+ G Sbjct: 517 TERTERMVVGDPLDPATHVGALISEAHMKKVLGYIEAAKAAGARLVAGGHRVETGALARG 576 Query: 363 HFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDDHTE 422 +FV PT+F D DM +EE+FGPV++V+ D E +A AND +GL+A + T D Sbjct: 577 NFVAPTIFADCTDDMPNVREEIFGPVMSVLAFEDEAEVVARANDTAFGLAAGVFTADLAR 636 Query: 423 ANRFVDEVEAGVVKVND-KTTGLELHVPFGGFKRSSSETWREQGDAGLDFYTIEKTVY 479 A+R + ++EAG +N T +EL PFGG K+S RE A ++ YT K+VY Sbjct: 637 AHRVIAQLEAGTCWINQYNITPIEL--PFGGTKQSG--LGRENSRAAIEHYTQIKSVY 690 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: 766 Number of extensions: 32 Number of successful extensions: 4 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: 700 Length adjustment: 36 Effective length of query: 446 Effective length of database: 664 Effective search space: 296144 Effective search space used: 296144 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: 53 (25.0 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