Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate PP_0708 PP_0708 putative Betaine-aldehyde dehydrogenase
Query= CharProtDB::CH_122352 (572 letters) >FitnessBrowser__Putida:PP_0708 Length = 476 Score = 160 bits (406), Expect = 8e-44 Identities = 146/487 (29%), Positives = 221/487 (45%), Gaps = 35/487 (7%) Query: 76 EVKSSSSLTQSNPASHGPVATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAA 135 E + S ++ ++PA P A A+ V A+ +A A +W ST ++RA+ A Sbjct: 13 EGQGSDCISVNDPALGQPFAELMAASVSQVDQAVAAARSALPAWKSTCASERAAFLRGFA 72 Query: 136 DLISTKYRYDVMALTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHH---- 191 + + + R ++ + M GK +AEID + F Y +L Q P + Sbjct: 73 EQLGQR-REALVTVQMRNNGKPRHEAEIDLDDAIATF-----GYYAELAEQLPSKNRTVP 126 Query: 192 --APGVWNRVEYRPLEGFVYAISPFNFTAIGGNLAGAPALM-GNVVVWKPSPSAIASNWL 248 APG R P+ G V I P+NF + APAL G VV KPS Sbjct: 127 LAAPGFTARTRLEPV-GVVGLIVPWNFPLVTSAWKLAPALAAGCTVVLKPSEVTPLIEQA 185 Query: 249 VHQILLEAGLPKNVIQFVPGEAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAA 308 QI GLP V+ V G+AE + +H L FTGS +V G R A+ Sbjct: 186 YGQIADALGLPAGVLNIVNGKAE-TGAALSNHNGLDKLSFTGSNSV-----GSQVMRSAS 239 Query: 309 GKYRSYPRIVGETGGKNFHLIHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIAD 368 + R + E GGK+ ++ D+ A V G GQ CSATSR+ V IAD Sbjct: 240 AQCRP---VTLELGGKSAIVVFDDCDVDQAVEWIVAGISWNAGQMCSATSRLLVQDGIAD 296 Query: 369 SFLEQVASEAKSLKVGPPSDFTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDS 428 + L ++ + ++L+VG P GP+ +A + K+A A+ + L+ LAGG Sbjct: 297 ALLPRLQAALENLRVGNPLTEEVDMGPLTSQAQWLKVASYFATAREE-GLQCLAGGHALD 355 Query: 429 SKGWYIQPTVYRTTNPDHPLLTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTG 488 +GW++ PT+Y D L T E+FGP+L + +A IA+ D+ +GL Sbjct: 356 REGWFVSPTLYTDVPKDSRLWTEEIFGPVLCARRFATEEQA----IAEANDS--RFGLVA 409 Query: 489 SVFAQDREALAVANDVLRNAAGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSR 548 +V + D E D L G+ +IN S AV + +GG + SG + G LS Sbjct: 410 TVCSADLERAERVADALE--VGHVWIN--SVQAVFVETSWGGTKGSGIGRELGPWG-LSA 464 Query: 549 FVSLRSI 555 + S++ + Sbjct: 465 YQSIKHV 471 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: 571 Number of extensions: 23 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: 476 Length adjustment: 35 Effective length of query: 537 Effective length of database: 441 Effective search space: 236817 Effective search space used: 236817 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