Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate SMa2213 SMa2213 aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__Smeli:SMa2213 Length = 494 Score = 251 bits (640), Expect = 6e-71 Identities = 154/439 (35%), Positives = 229/439 (52%), Gaps = 18/439 (4%) Query: 67 VSKANQDLAEKAIQSADEAFQT--WRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAG 124 V + N + A++A+++A AF W ++P ER I+ + AA+I + V + G Sbjct: 38 VPRGNAEDADRAVRAAHRAFSQGPWGKMHPTERGRIIQRFAALIEEHADALADIEVRDNG 97 Query: 125 KPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNFA 184 + E + YYA ++ +P + P+GV V I PWN Sbjct: 98 RLLAEMTHQIRYIPRWYHYYAGFADKIEGTLHPCDKPALSFSR-HEPLGVCVGIVPWNAP 156 Query: 185 LAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDY 244 L + A + GNT+V+KPA T A K +E++E AG P GVIN V G G EVG+ Sbjct: 157 LLLFSLKAAPALAAGNTLVMKPAEFTSATALKLMELVEKAGFPTGVINVVTGYGPEVGEP 216 Query: 245 LVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLA 304 LV HP T + FTGS G LY AA +KRV +E+GGK +V DADLD A Sbjct: 217 LVTHPLTRHVGFTGSTKTGAHLYSLAA------KDVKRVSLELGGKSPNIVFGDADLDNA 270 Query: 305 AESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVID 364 ++ FG GQ C AGSR ++H+ ++DE LEK K +GDP + +GP+ + Sbjct: 271 VRGVVGGIFGAVGQTCIAGSRLLVHRSIHDEFLEKLAVFTKTARIGDPRKVETQIGPIAN 330 Query: 365 EKAFEKIMSYIEIGKKEGR--LMTGGEGD---SSTGFFIQPTIIADLDPEAVIMQEEIFG 419 FEK++ YI+I ++EG ++ GG D TG+FI+PTI A + + I +EE+FG Sbjct: 331 SMQFEKVLGYIDIARREGAELILGGGRPDLEECGTGYFIEPTIFAGVSNDMRIAREEVFG 390 Query: 420 PVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIV 479 PV++ ++ + AL IAN++E+GL V T + + G+++ N T + Sbjct: 391 PVLSAIVFDEPEEALAIANDSEFGLGAGVWTSDMRLALKMSERLEAGSVWVN---TYRDI 447 Query: 480 GY-HPFGGFKMSGTDSKAG 497 Y PFGG+K SG + G Sbjct: 448 SYTTPFGGYKKSGIGRENG 466 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: 29 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: 494 Length adjustment: 34 Effective length of query: 481 Effective length of database: 460 Effective search space: 221260 Effective search space used: 221260 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