Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_019866236.1 METMI_RS25445 MFS transporter
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000384075.1:WP_019866236.1 Length = 935 Score = 139 bits (350), Expect = 5e-37 Identities = 99/322 (30%), Positives = 158/322 (49%), Gaps = 17/322 (5%) Query: 172 VPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPG 231 VP G +V+ PWN+P+ + ++ +A GNTV+ KP+E A + I F PG Sbjct: 583 VPFGTVLVLVPWNYPLQLALMPLVAALAAGNTVVIKPSELAPASAVLLQAIARL--FEPG 640 Query: 232 VVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKI-YEAAGRLAPGQTWFKRAYVETG 290 +V+ + G G + L+E P F FTG E+G ++ +AA + P +E G Sbjct: 641 LVSVVNG-GADTARSLLEQPFDFFF-FTGGAEIGRQVALKAAAKGIP-------CVLELG 691 Query: 291 GKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLS 350 GK+ IVDE+A LAA +V + GQ C A + + + YE +L + K Sbjct: 692 GKNPCIVDESAPLALAARRIVWGKFFNAGQTCLAPDHVYVHRDVYEALLLEMAKVVGDFY 751 Query: 351 VGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPK 410 G +PDL +V+ ++L Y+E EG++ GG R + + I PT+ ++ P Sbjct: 752 GGQPWLSPDLAQIVNVRHFARLLGYLE----EGRVAHGG-RYDTDARRIGPTLLVDIVPN 806 Query: 411 ARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLY 470 A + +EEIFGP+L V+ D + L+ P L +++R+R+ + G++ Sbjct: 807 AAVMREEIFGPILPVLPYDDLSVLLDTLQSQPVPLAMYLHTRRRDTEALVLQRTRSGSVC 866 Query: 471 FNRKITGALVGVQPFGGFKLSG 492 N + A V PFGG SG Sbjct: 867 VNDHLMQAGVPALPFGGMAHSG 888 Lambda K H 0.319 0.137 0.403 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: 987 Number of extensions: 49 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: 516 Length of database: 935 Length adjustment: 39 Effective length of query: 477 Effective length of database: 896 Effective search space: 427392 Effective search space used: 427392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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