Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate Echvi_2633 Echvi_2633 gamma-glutamyl phosphate reductase
Query= BRENDA::Q941T1 (735 letters) >FitnessBrowser__Cola:Echvi_2633 Length = 399 Score = 236 bits (601), Expect = 2e-66 Identities = 133/396 (33%), Positives = 230/396 (58%), Gaps = 10/396 (2%) Query: 331 LSSEERKKILLDIADALEANEDLITSENQADLDLAQDIGYDKSLVARMTIKPGKIKSLAG 390 LS++++ +L + ++ N + I + N+ADLD Q D++L R+ + KI + Sbjct: 4 LSTQKKNDVLASMIKIIDKNREKILTANKADLDAFQRD--DQALYDRLVVNDAKIDGMIQ 61 Query: 391 SIREIADMEDPISHTLKRTEVAKDLVFEKTYCPLGVLLIIFESRPDALVQIASLAIRSGN 450 +++E+ D +DP+ + + +A L P G ++II+ESRPD ++ A LA ++ + Sbjct: 62 AVQEVKDQDDPVGKEISKRTLANGLDITNKTAPFGTIMIIYESRPDVTIEAAVLAFKANS 121 Query: 451 GLLLKGGKEAMRSNTILHKVITGAIPDV-VGKKLIGLVK-NKDEIADLLKL-DDVIDLVI 507 +LLKGGKEA+ SN +L + A+ + + K I L N+++ LK + +DL++ Sbjct: 122 KILLKGGKEAVNSNKVLVECWHEALEENGLSKDWIELFTLNREQTQAFLKNPSEKLDLIV 181 Query: 508 PRGSNKLVSQIKAATKIPVLGHADGICHVYIDKSADMDMAKRIVLDAKVDYPAACNAMET 567 PRG +L++ +K + VL G Y+ + AD ++AK+++++AK + + CNA++ Sbjct: 182 PRGGERLIAFVKEHAQCAVLVSGRGNNFAYVAEDADWELAKKVIINAKTNKISGCNALDK 241 Query: 568 LLVHKDLNRTEG-LDDLLVELEKEGVVIYGG----PVAHDTLKLPKVDSFHHEYNSMACT 622 +LV + L E L DL L V + P ++P D+++ E+ ++ Sbjct: 242 ILVDEKLPDFESKLADLAKSLASYKVELVAEKELVPAIEGAKEVPSEDTWYEEFLALKAL 301 Query: 623 LEFVDDVQSAIDHINRYGSAHTDCIITTDGKAAETFLQQVDSAAVFHNASTRFCDGARFG 682 + V+ + AI IN+Y H+ I+TTD A TF++QVDSAAV+HNASTRF DG + G Sbjct: 302 IGKVNGLDEAIAKINKYSGGHSATILTTDKDKAATFMEQVDSAAVYHNASTRFTDGGQMG 361 Query: 683 LGAEVGISTGRIHARGPVGVDGLLTTRCILRGSGQV 718 +GAE+ IST ++H RGP+G++ L+T + + GSGQ+ Sbjct: 362 VGAELAISTDKLHHRGPLGLEQLVTNKYYVFGSGQI 397 Lambda K H 0.318 0.136 0.385 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: 603 Number of extensions: 24 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: 735 Length of database: 399 Length adjustment: 35 Effective length of query: 700 Effective length of database: 364 Effective search space: 254800 Effective search space used: 254800 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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