Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >FitnessBrowser__Dyella79:N515DRAFT_4232 Length = 1074 Score = 159 bits (403), Expect = 4e-43 Identities = 142/435 (32%), Positives = 200/435 (45%), Gaps = 32/435 (7%) Query: 56 VDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEALGEV 115 V++A+ A A W PA R A+++ E L + + L EAGK +A+ E+ Sbjct: 619 VEKALANAVAAQHGWDRLPAASRAAILEHAAEQLEARRGEFIALCVREAGKGLPDAIAEI 678 Query: 116 QEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPL---GVVGVISAFNFPVAVWAWN 172 +E D + ++R+ +G+ P + PG L GV IS +NFP+A++ Sbjct: 679 REAADFLRYYATMARRYFGQ--PEQLPGPTGESNQLFLNGRGVFVCISPWNFPLAIFLGQ 736 Query: 173 AAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVG-AADVGERLVD 231 A AL G++V+ KP+E T L A LL +AG P + Q + G A VG L Sbjct: 737 VAAALAAGNSVIAKPAEQTSLIGHAAVQLLH----EAGVPADVLQYLPGDGATVGAALTR 792 Query: 232 SPRVPLVSATGSTRMGRAVGPRVAAR---FGRTILELGGNNAAVVTPSADLDLTVNAAVF 288 PRV V+ TGST A+ +AAR I E GG NA + SA + V AV Sbjct: 793 DPRVAGVAFTGSTETAWAINRALAARNAPIAALIAETGGQNAMIADSSALPEQIVKDAVS 852 Query: 289 AAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAAFGR 348 +A +AGQRC+ R L V EDIAD V L A L +GDP Q +T VGP+++E A Sbjct: 853 SAFQSAGQRCSAARVLYVQEDIADKVCAMLAGAMAELKVGDPAQLSTDVGPVIDEDARKI 912 Query: 349 MREAVERATAEGGTLCAGGERQFPDAAPG-AYYVRPALVRMPAQTAVVREETFAPILYVL 407 + + R E + GE A G + P +P + R E F P+L+V+ Sbjct: 913 LVDHAARMDQEAKKI---GEVALDPATTGNGTFFAPRAYEIPGLATLTR-EIFGPVLHVI 968 Query: 408 TYR--DLDEAIRLNNEVPQACRQG--SRTDG------APADDPRCRARRRAGGANCPAVP 457 ++ +LD+ + N G SR D + A C R GA P Sbjct: 969 RWKGSELDKVVDEINATGYGLTLGIHSRIDDTVEFIQSRARVGNCYVNRNQIGAVVGVQP 1028 Query: 458 ----GRSGTGAGAGG 468 G SGTG AGG Sbjct: 1029 FGGEGLSGTGPKAGG 1043 Lambda K H 0.320 0.135 0.406 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: 971 Number of extensions: 36 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: 496 Length of database: 1074 Length adjustment: 40 Effective length of query: 456 Effective length of database: 1034 Effective search space: 471504 Effective search space used: 471504 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 (21.8 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 17 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