Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_012991282.1 THAL_RS01185 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::O04226 (716 letters) >NCBI__GCF_000025605.1:WP_012991282.1 Length = 441 Score = 271 bits (694), Expect = 4e-77 Identities = 153/415 (36%), Positives = 244/415 (58%), Gaps = 21/415 (5%) Query: 302 ARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLTI 361 AR R L +L +E + + LL A + +D I+ NE D+ AQ AG L+ RL + Sbjct: 15 ARSTLRTLMSLPTEVKNRTLLRAAQLMLERKDFIKEANEKDIQYAQEAGLSPALIDRLLL 74 Query: 362 KPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALVQ 421 +I +AK +R +A++ DP+ +I + + + L + + PLGV+ IV+E+RP+ V+ Sbjct: 75 NDKRIEGMAKVLRDVASLPDPVGEITRMWTLPNGLRVGRMRVPLGVVFIVYEARPNVTVE 134 Query: 422 IASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVG--EKLIGLVTTRDE--IADL 477 ASL ++S N ++L+GGKEAI SN L +++ +A R G E I + D + + Sbjct: 135 AASLCMKSSNAIVLRGGKEAINSNRALVEILKEAC-REEGFPEDAIQFIDIPDREIVWHI 193 Query: 478 LKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVMDAKI 537 L+++ ID+ IPRG L+ + ++PV+ H G+C++Y+D AD++ A HIV +AK+ Sbjct: 194 LQMEGKIDVAIPRGGESLIRAVAERARVPVIKHYKGVCNIYVDDEADLEKAYHIVYNAKV 253 Query: 538 DYPAACNAMETLLVHKDLMKS--PGLDDIL------VALKTEGVNIYGGPIAHKALGFPK 589 P+ CNA+E L++++ ++ P + IL + E + + + L F K Sbjct: 254 QRPSVCNAVENLIINRKILHKFFPKMAYILGKAGVELRCDEESLEVIN---SDPRLSFVK 310 Query: 590 AV-----SFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVD 644 A ++ E+ + V+ V+D+ AI I +YGS H+D IVT + A F+R VD Sbjct: 311 AKPAVEEDYYEEFLDLILAVKVVEDIDEAIAFIEKYGSKHSDAIVTENYSKALKFIREVD 370 Query: 645 SAAVFHNASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699 SAAV+ NASTRF+DG FGLGAE+GIST +IHARGP+G+E L ++++ G GQV Sbjct: 371 SAAVYVNASTRFTDGNEFGLGAEMGISTDKIHARGPMGLEELTIQKFVILGEGQV 425 Lambda K H 0.317 0.134 0.377 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: 629 Number of extensions: 19 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: 716 Length of database: 441 Length adjustment: 36 Effective length of query: 680 Effective length of database: 405 Effective search space: 275400 Effective search space used: 275400 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: 53 (25.0 bits)
This GapMind analysis is from Apr 10 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