Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate PP_5063 PP_5063 betaine aldehyde dehydrogenase, NAD-dependent
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__Putida:PP_5063 Length = 490 Score = 243 bits (620), Expect = 1e-68 Identities = 151/484 (31%), Positives = 248/484 (51%), Gaps = 24/484 (4%) Query: 39 LIINGERVT--TEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEE 96 L I+G V ++ ++ NPA +++ V +A + EKA++SA+ + W + + Sbjct: 9 LYIDGAYVDAGSDATFEAINPAT-GEVLAHVQRATEADVEKAVESAERGQKVWAAMTAMQ 67 Query: 97 RANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEAD-ADTAEAIDFLEYYARQMIELNRGK 155 R+ IL +A I+R R E + + GK + E D D LEYYA ++ G+ Sbjct: 68 RSRILRRAVDILRERNDELAMLETLDTGKSYSETRYVDIVTGADVLEYYAG-LVPAIEGE 126 Query: 156 EILSRPGEQNRYFYT---PMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPV 212 +I P ++ + YT P+GVTV I WN+ + I + + + GN ++ KP+ T + Sbjct: 127 QI---PLRESSFVYTRREPLGVTVGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSL 183 Query: 213 VAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAV 272 K E+ +AGLP GV N + GSG EVG +L +HP+ ++FTG G ++ A+ Sbjct: 184 TTLKLAEIYTEAGLPNGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTTTGKKVMASAS- 242 Query: 273 VRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDV 332 + LK V +E+GGK +++ DADLD AA+ +++ F SGQ C+ G+R I ++ Sbjct: 243 ----SSSLKEVTMELGGKSPLIICADADLDKAADIAMMANFYSSGQVCTNGTRVFIPAEM 298 Query: 333 YDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGE-- 389 K + VG+P + + GP++ + E ++ YI GK+EG R++ GGE Sbjct: 299 KAAFEAKIAERVARIRVGNPEDENTNFGPLVSFQHMESVLGYIAKGKEEGARVLCGGERL 358 Query: 390 --GDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGA 447 GD + G F+ PT+ D + I++EEIFGPV++ + + AN+T+YGL Sbjct: 359 TAGDFAKGAFVAPTVFTDCTDDMTIVKEEIFGPVMSILTYETEEEVIRRANDTDYGLAAG 418 Query: 448 VITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQ 507 V T + + + G + N G P GG+K SG + G LA + + Sbjct: 419 VCTNDITRAHRIIHKLEAGICWI--NAWGESPAEMPVGGYKQSGV-GRENGVSSLAQYTR 475 Query: 508 AKTV 511 K+V Sbjct: 476 IKSV 479 Lambda K H 0.316 0.134 0.388 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: 588 Number of extensions: 31 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: 515 Length of database: 490 Length adjustment: 34 Effective length of query: 481 Effective length of database: 456 Effective search space: 219336 Effective search space used: 219336 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