Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate RR42_RS17940 RR42_RS17940 gamma-glutamyl kinase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__Cup4G11:RR42_RS17940 Length = 372 Score = 140 bits (353), Expect = 1e-37 Identities = 90/266 (33%), Positives = 141/266 (53%), Gaps = 19/266 (7%) Query: 15 KRIVVKVGTAVVTGKGGRLALGRLGALCEQLAELNSDGFEVILVSSGAVGLGRQRLRYRQ 74 KRIVVKVG+++VT G L + Q+A+L G EV+LVSSGA+ G QRL + Sbjct: 9 KRIVVKVGSSLVTNDGKGLDHEAIARWAAQIAKLRMAGKEVVLVSSGAIAEGMQRLGW-- 66 Query: 75 LVNSSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQLDVTAAQLLVNDSSFRDKDFR 134 +++P+ + +A A VGQ L YE+ F + + AQ+L+ + D++ Sbjct: 67 --------VRRPKEIHELQAAAAVGQMGLAQVYESQFGRYGIRTAQVLLTHADLADRERY 118 Query: 135 KQLNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDSLAALLALELKADLLIL 194 T+ ++L L V+PI NEND + T F DND+L AL+ ++ D L++ Sbjct: 119 LNARSTLLTLLSLGVVPIINENDTVVTDEIK-------FGDNDTLGALVTNLIEGDALVI 171 Query: 195 LSDVEGLYTGPP-SDPNSKLI-HTFVKEKHQDEITFGDKSRLGRGGMTAKVKAAVNAAYA 252 L+D GLYT P S+P ++ + + + G + +GRGGM K+ AA AA + Sbjct: 172 LTDQRGLYTADPRSNPQAEFVDEALAGAVELEAMAGGAGTSIGRGGMLTKILAAKRAAKS 231 Query: 253 GIPVIITSGYSAENIDKVLRGLRVGT 278 G +I SG A ++++ G +GT Sbjct: 232 GAHTVIASGREANVLERLAGGEGIGT 257 Lambda K H 0.318 0.135 0.378 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: 534 Number of extensions: 24 Number of successful extensions: 5 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: 717 Length of database: 372 Length adjustment: 35 Effective length of query: 682 Effective length of database: 337 Effective search space: 229834 Effective search space used: 229834 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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