Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate Dsui_0166 Dsui_0166 glutamate 5-kinase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__PS:Dsui_0166 Length = 377 Score = 146 bits (368), Expect = 2e-39 Identities = 96/270 (35%), Positives = 144/270 (53%), Gaps = 19/270 (7%) Query: 16 RIVVKVGTAVVTGKGGRLALGRLGALCEQLAELNSDGFEVILVSSGAVGLGRQRLRYRQL 75 R+VVKVG+A+VT G L L + Q+AEL +G +V+LVSSGA+ G QRL ++ Sbjct: 13 RLVVKVGSALVTNNGAGLDLAAIHEWARQIAELRHNGKQVVLVSSGAIACGMQRLGWQ-- 70 Query: 76 VNSSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQLDVTAAQLLVNDSSFRDKDFRK 135 ++P+ + +A A VGQ L YE+ F + AQ+L+ D+ Sbjct: 71 --------KRPKAVHELQAAAAVGQMGLAQVYESAFSAHGLHTAQILLTHDDLADRKRYL 122 Query: 136 QLNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDSLAALLALELKADLLILL 195 T+ ++L+L V+PI NEND + T F DND+L AL+A ++AD LI+L Sbjct: 123 NARATLTTLLELGVVPIINENDTVVTDEIK-------FGDNDTLGALVANLVEADCLIIL 175 Query: 196 SDVEGLYTGPP-SDPNSKLIHTF-VKEKHQDEITFGDKSRLGRGGMTAKVKAAVNAAYAG 253 +D GL+T P DP++ LI + + + + G +++G GGM KV AA AA +G Sbjct: 176 TDQPGLFTADPRKDPSATLITSARAGDPSLEAMAGGAGTQIGTGGMITKVLAAKRAARSG 235 Query: 254 IPVIITSGYSAENIDKVLRGLRVGTLFHQD 283 +I SG + ++ G VGTL D Sbjct: 236 ADTVIASGREKSPLTRLATGESVGTLLVAD 265 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: 22 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: 717 Length of database: 377 Length adjustment: 35 Effective length of query: 682 Effective length of database: 342 Effective search space: 233244 Effective search space used: 233244 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