Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_009488515.1 C683_RS01225 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000313915.1:WP_009488515.1 Length = 473 Score = 217 bits (552), Expect = 9e-61 Identities = 146/463 (31%), Positives = 230/463 (49%), Gaps = 20/463 (4%) Query: 36 RHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQ 95 + Y + GEW T + + P+ E+ GT + E E +++A +A K W+ Sbjct: 2 KSYLNLVNGEWKGTSQTITIKEPATGKEL-GTVPAMEEKEIEEVMQSARQAQKEWQALAV 60 Query: 96 EDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYP 155 +R+++L +AA L+++ E+ L E+ K+ + +V D I Y A R Sbjct: 61 VERAQILHQAAQLLKKEAVEIGTLLSKEIAKSRAASIQEVERTADLIAYTAEEGCRMEGQ 120 Query: 156 AVEVVPYPGED-NESFYV---PLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAED 211 +E + +D N+ +V +G + IAP+N+PV + I + GNTV+ K Sbjct: 121 ILEGGSFSKKDQNKIAFVHKEAMGVVLAIAPFNYPVNLAASKIAPALIGGNTVVFKTPTQ 180 Query: 212 AVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEA 271 + G ++ IFHEAG P GV+N + G G +G LV HP INFTGS E+G I E Sbjct: 181 GAISGLQLARIFHEAGVPAGVLNTVTGRGSVIGDALVTHPEVDAINFTGSTEIGTHIAEL 240 Query: 272 AGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILT 331 AG K +E GGKDA +V E AD + AA+ +V A+ + GQ+C+A R+ +T Sbjct: 241 AG--------MKPCIMELGGKDAALVLEDADLENAAKEIVAGAFQYSGQRCTAIKRVFVT 292 Query: 332 QGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQL--VLGG 389 + + ++ + K E LSVG EEN D+ P++ +R V +IE + L + Sbjct: 293 EKNADALVAAIQKEMETLSVGLPEENADITPLI----DRFVADHIEFLIEDALLKGAVAK 348 Query: 390 KRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGV 449 + + E I P + +V +A EE FGPVL ++RVKD E + +AN + YGL + Sbjct: 349 TKYQRERNLIWPMLLDQVTVDMDLAWEEPFGPVLPILRVKDVEEMIRLANASEYGLQSAI 408 Query: 450 YSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSG 492 ++ + VG ++ N + T PF G K SG Sbjct: 409 FTNNYPLAMEIGKALKVGTVHMNHR-TQRGADHFPFLGIKNSG 450 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: 492 Number of extensions: 23 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: 516 Length of database: 473 Length adjustment: 34 Effective length of query: 482 Effective length of database: 439 Effective search space: 211598 Effective search space used: 211598 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: 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