Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_022949182.1 H035_RS0111795 aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_000421465.1:WP_022949182.1 Length = 506 Score = 190 bits (483), Expect = 9e-53 Identities = 145/476 (30%), Positives = 225/476 (47%), Gaps = 34/476 (7%) Query: 30 SEYLGKDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEW 89 + Y+G + +NG+ E + + V++++ E E+A+ AA A + W Sbjct: 20 NNYIGGHWIAPVNGQYFENITPVTGTPFCE-------VARSTAEDIEKALDAAHAAKDAW 72 Query: 90 RYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEYYARQM 148 TSP RA +L + A ++ ++ + + GKP E AD A D Y+A Sbjct: 73 GKTSPAGRADLLLKIADRMEQQLEMLAVAETWDNGKPIRETLAADIPLAADHFRYFA-SA 131 Query: 149 IELAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAP-IVTGNTVVLKPA 207 I + + + P GV I PWNF +MA +AP + GN VVLKPA Sbjct: 132 IRTQESSVCEIDADTIAYHFHEPLGVVGQIIPWNFPL-LMASWKLAPALAAGNCVVLKPA 190 Query: 208 SATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIF 267 TP +E++ + +P GVVN V G G E G L + + + FTG G I Sbjct: 191 EQTPASILVLMELIGDL-IPPGVVNVVNGFGVEAGKPLARSSRIAKVAFTGETTTGRLIM 249 Query: 268 ERAAKVQPGQQHLKRVIAEMGGK------DTVVVDEDADIELAAQSIFTSAFGFAGQKCS 321 + A+ Q+L V E+GGK + V +D ++ A + + A G+ C+ Sbjct: 250 QYAS------QNLIPVTLELGGKSPNLFFEDVTAKQDTFVDKALEGFASFALN-QGEVCT 302 Query: 322 AGSRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQE 381 SRA++ +YD + R +E ++ P + +G +KI+SYI+I +QE Sbjct: 303 CPSRALLQASIYDDFIHRALERVKAIRQGNPLDTETMIGAQASAEQMEKILSYIDIARQE 362 Query: 382 GR--LVSGGT----GDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALE 435 G L+ G G+ + GY+I+PTIF + + R+ QEEIFGPV+A D +EALE Sbjct: 363 GTECLIGGERAQLQGELAGGYYIQPTIFKGHN-QMRVFQEEIFGPVLAVTTFRDEEEALE 421 Query: 436 VANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491 +AN+T YGL V T + R + G ++ NC + FGG+K SG Sbjct: 422 IANDTLYGLGAGVWTRDMNTAYRMGRGIQAGRVW--TNCYHLYPAHAAFGGYKQSG 475 Lambda K H 0.316 0.133 0.379 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: 608 Number of extensions: 43 Number of successful extensions: 7 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: 515 Length of database: 506 Length adjustment: 35 Effective length of query: 480 Effective length of database: 471 Effective search space: 226080 Effective search space used: 226080 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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