Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC
Query= CharProtDB::CH_122352 (572 letters) >FitnessBrowser__Phaeo:GFF3174 Length = 494 Score = 159 bits (402), Expect = 2e-43 Identities = 158/500 (31%), Positives = 240/500 (48%), Gaps = 46/500 (9%) Query: 71 VIAGKEVKSSSSLTQS--NPASHGPVATYSNATAKDVQAAIESALEA--RKSWASTPFAD 126 +I G++V +S T +P + + T +D++ AI SA A + WA P A Sbjct: 20 LIDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAFEDRRWAGQPPAA 79 Query: 127 RASVFLKAADLISTKYRYDVMALTMHGQGKN------AWQAEIDSAAELCDFFRFGVKYA 180 R V +K A+LI D + L + G N A +AE SAA R+ + Sbjct: 80 RKKVLMKWAELIEA----DALNLAVLGVRDNGTEITMALKAEPGSAAAT---IRYYAEAL 132 Query: 181 EDLYAQQPVHHAPGVWNRVEYRPLEGFVYAISPFNFTAIGGNLAGAPAL-MGNVVVWKPS 239 + +Y + + V V P+ G V AI P+NF + G APAL MGN VV KPS Sbjct: 133 DKIYGEI-APTSSDVLGMVHKEPV-GVVGAIIPWNFPMMIGAWKLAPALAMGNSVVLKPS 190 Query: 240 PSAIASNWLVHQILLEAGLPKNVIQFVPGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLY 299 +A S + ++ LEAGLP V+ V GE V + + D L FTGS Sbjct: 191 ETASLSLMRMVELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGS-------- 242 Query: 300 GQISTRVAAGKYRS-YPRIVGETGGKNFHLIHKSA-DIRNAAVQTVRGAFEYQGQKCSAT 357 GQ R+ RS R+ E GGK+ +++ A D+ +AA T G F GQ C A Sbjct: 243 GQTGRRLMEYAARSNLKRVYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAG 302 Query: 358 SRVYVASSIADSFLEQVASEAKSLKVGPPSDFTNFCGPVIHEASFTKLAKVIDEAKNDPE 417 SR+ V +SI D+F+E+VA A+ ++VG P G + EA + + + A+ + Sbjct: 303 SRLLVEASIHDAFVEEVAKAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGG 362 Query: 418 LELLAGGS--YDSSKGWYIQPTVYRTTNPDHPLLTRELFGPILVVYAYPDATEADFARIA 475 +++ GG + G Y+ PT+ PD L E+FGP+L V P T+A+ RIA Sbjct: 363 -QIITGGQRLLSETGGSYMAPTIVTGVTPDATLAQEEVFGPVLAV--TPFETDAEALRIA 419 Query: 476 QKIDATGEYGLTGSVFAQDREALAVANDVLRNA-AGNFYINCKSTGAVVGQQPFGGARAS 534 +AT YGL G+V+ L A+ +++ G ++N + G G P GG S Sbjct: 420 ---NAT-VYGLAGAVWT---SGLTRAHRMVQGVRTGVMHVN--TYGGADGTVPLGGVGQS 470 Query: 535 GTNDKAGSGNLLSRFVSLRS 554 G N S + + ++++L++ Sbjct: 471 G-NGADKSLHAIDKYINLKT 489 Lambda K H 0.316 0.130 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: 577 Number of extensions: 27 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: 572 Length of database: 494 Length adjustment: 35 Effective length of query: 537 Effective length of database: 459 Effective search space: 246483 Effective search space used: 246483 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 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