Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 218 bits (555), Expect = 4e-61 Identities = 149/429 (34%), Positives = 222/429 (51%), Gaps = 25/429 (5%) Query: 76 EKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEA-DADT 134 E A+ +A EAF+TW + ER+ IL K A + +A + GK +E AD Sbjct: 54 ELAVDAAHEAFKTWSKTSSTERSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADL 113 Query: 135 AEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVA 194 +D Y+A +I G + + P+GV I PWNF L + + Sbjct: 114 PLGVDHFRYFAG-VIRAEEGSLSELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAP 172 Query: 195 PIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLI 254 + GN VVLKPA +TPV +E++ D LP GV+N V G G+E+G LV +PK S Sbjct: 173 ALAAGNCVVLKPAESTPVSIMVLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKA 231 Query: 255 TFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKD------TVVVDRDADLDLAAESI 308 FTGS G V++ ++ V +E+GGK +V+ + DA LD A E Sbjct: 232 AFTGSTPTG------RLVMQYATENIIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGA 285 Query: 309 LVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAF 368 ++ A G+ C+ SR +I +D+Y++ + K + K + +G P +R MG + F Sbjct: 286 VMFALN-QGEICTCPSRLLIQEDIYEKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQF 344 Query: 369 EKIMSYIEIGKKEG-RLMTGGE-----GDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVV 422 EKI +YI++GK+EG ++TGGE G+ G++I+PTI + + I QEEIFGPV+ Sbjct: 345 EKIAAYIKLGKEEGAEVLTGGEINELPGELGGGYYIKPTIFKGHN-KMRIFQEEIFGPVL 403 Query: 423 AFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYH 482 A + + A+EIAN+T YGL V TR+ + Q R G ++ N+ A Sbjct: 404 AVTTFKTVEEAIEIANDTLYGLGAGVWTRDAHELYQVPRAIQAGRVWVNQ--YHAYPAGA 461 Query: 483 PFGGFKMSG 491 PFGG+K SG Sbjct: 462 PFGGYKQSG 470 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: 592 Number of extensions: 36 Number of successful extensions: 6 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: 501 Length adjustment: 34 Effective length of query: 481 Effective length of database: 467 Effective search space: 224627 Effective search space used: 224627 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