Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__Marino:GFF3684 Length = 489 Score = 251 bits (640), Expect = 6e-71 Identities = 151/466 (32%), Positives = 243/466 (52%), Gaps = 26/466 (5%) Query: 56 NPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEF 115 NPA Q++ V A++ + + AI+SA F W + ER+ IL++A AI+R R E Sbjct: 29 NPAT-GQVIYEVEVADESVQQAAIESARAGFAEWSAMTAIERSRILLRAVAILRERNDEL 87 Query: 116 SAWLVHEAGKPWKEADA-DTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYT---P 171 +A V + GKPW+EA+A D D +E++A + ++ L ++YT P Sbjct: 88 AAAEVRDTGKPWQEAEAVDVVTGADAVEFFAGLAPSIEGNQQDLG-----GDFYYTRREP 142 Query: 172 MGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVI 231 +G+ I WN+ + I + + GN ++ KP+ TP+ A K E+ +AG+P GV Sbjct: 143 LGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPSEETPMGAVKLAEIFTEAGVPAGVF 202 Query: 232 NYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKD 291 N V G+ AEVG +L HP+ + ++FTG G + V+ + LK V +E+GGK Sbjct: 203 NVVQGA-AEVGQWLTHHPEIAKVSFTGEVATGKK------VMAAASSTLKDVTMELGGKS 255 Query: 292 TVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAK-NLTVG 350 +++ DADL+ A + +V F G+ C+ G+R +H+D+Y +E+ + + N+ G Sbjct: 256 PLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFIERLLERTRNNIKPG 315 Query: 351 DPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTGG-----EGDSSTGFFIQPTIIAD 405 DP N D G +I K + ++ YI G EG ++ G DS G+F++PTI D Sbjct: 316 DPMNPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDSKGGYFVEPTIFTD 375 Query: 406 LDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHV 465 + I++EEIFGPV++ D D + ANNT+ GL V T + + + Sbjct: 376 CTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAGVFTNDIRRAHRVIHQIQA 435 Query: 466 GNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTV 511 G + N GA P GG+K+SG + G + +A + Q K+V Sbjct: 436 GICWI--NSYGASPAEMPVGGYKLSGI-GRENGRETIAHYTQIKSV 478 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: 619 Number of extensions: 33 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: 489 Length adjustment: 34 Effective length of query: 481 Effective length of database: 455 Effective search space: 218855 Effective search space used: 218855 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