Align Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Query= SwissProt::D4GP41 (482 letters) >MicrobesOnline__882:208845 Length = 1006 Score = 267 bits (682), Expect = 1e-75 Identities = 162/458 (35%), Positives = 238/458 (51%), Gaps = 16/458 (3%) Query: 8 YVNGEWVTSETGETTEVTNPANPSEVVAAYQHSNENDAAAAVDAAVAAEDEWRNTPGPER 67 Y+ G VT T + TNPA P+EVVA+ + + A+ AA A WR+T +R Sbjct: 515 YIGGRDVT--TADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKAALTWRDTSPADR 572 Query: 68 GRILREAGTLLAQRKDELTEILTAEEGKARPEAAGEVQRAIDIFHYFSSKAADLGGTKKG 127 LR A + +R EL+ E GK +A +V ID Y++ + LG ++ Sbjct: 573 AAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRM 632 Query: 128 ASGPNTNLYTRQEPVGVAALITPWNYPIAIPAWKLAPALAAGNTVVLKPASIAPGVVIEI 187 P + + +P G+AA+I PWN+P AI + A+ GN V+ KP+SI+ + + Sbjct: 633 GRAPGEHNHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNL 692 Query: 188 ARALDEAGLPDGVLNVVTGPGSSVGSEFIGNEGTDLVSFTGSSQVGEMVYEQATDAG--- 244 A EAGLP+GV N G S +G + + L+ FTGS +VG + E+A Sbjct: 693 AEVFREAGLPEGVFNYCPGRSSIMGDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQ 752 Query: 245 ---KRVQTELGGKNPTLVADSANPAEAADIVANGGFGTTGQSCTACSRAIVHEDVYDDFV 301 KRV E+GGKN T++ D A+ EA V FG GQ C+ACSR IV + +YD F+ Sbjct: 753 RQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDRFI 812 Query: 302 AELVDRAESLDVGPGTD--HEMGPQVSESELSSTLEYIDIAEAEGATLVAGGGVPEGEAV 359 LV A S+ +GP D + MGP + + +YI IAE EG L+ +P Sbjct: 813 ERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVLLKRTDLP----- 867 Query: 360 ETGHFVEPTVFTDVDPDMRIAQEEVFGPVVAVIEVSDFDEGLAVANDVDYGLSASIVTDD 419 G +V T+ D+ P+ RIAQEE+FGPV+AV+ + FDE L++AN + L+ ++ + Sbjct: 868 AEGCYVPLTIVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRS 927 Query: 420 HTEANRFVDEVEAGVVKVNDKTTG-LELHVPFGGFKRS 456 ++ E G + +N +TG L PFGGF S Sbjct: 928 PEHLDKARREFRVGNLYLNKGSTGALVERQPFGGFAMS 965 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: 1063 Number of extensions: 49 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: 1006 Length adjustment: 39 Effective length of query: 443 Effective length of database: 967 Effective search space: 428381 Effective search space used: 428381 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: 54 (25.4 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