Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__Phaeo:GFF2135 Length = 485 Score = 235 bits (600), Expect = 2e-66 Identities = 164/479 (34%), Positives = 236/479 (49%), Gaps = 17/479 (3%) Query: 41 YIGGEWV-DTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRS 99 +I GE+V DT + + +A E + T A A E AL A A K W +R Sbjct: 12 FINGEYVEDTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQKAWARMTGTERG 71 Query: 100 RLLLKAAALMRRRKRELEATLVYEVGKNWVEAS-ADVAEAIDFIEYYARAALRYRYPAVE 158 R+L +AA +MR R +L Y+ GK E AD D +EY+ A E Sbjct: 72 RILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASL---TGE 128 Query: 159 VVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAK 218 +P + + LG V I WN+P I +A GN+++ KP+E + K Sbjct: 129 HIPLGEDWVYTKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCALK 188 Query: 219 VFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPG 278 V EI EAG P GV N + G+GE VG LV PR ++ TGS+ G K+Y AA Sbjct: 189 VAEILIEAGAPAGVFNVVQGMGE-VGGALVTDPRVDKVSLTGSVPTGKKVYAAAAE---- 243 Query: 279 QTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPV 338 K +E GGK +I+ + AD D A G + + GQ CS +R+ + +G E Sbjct: 244 --GMKHVTMELGGKSPLIIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKF 301 Query: 339 LERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLEGEG 396 L R+ +R +G P +E GP+V+ Q VL YIE GK EG +L+ GG+R + +G Sbjct: 302 LARLAERTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGRRADMDG 361 Query: 397 YFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREH 456 YFI PTVF +V IA+EEIFGPV+SV+ E + ANDT +GL+ GV+++ Sbjct: 362 YFIEPTVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTR 421 Query: 457 LEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAER 515 G+ + N + PFGG K SG + + + ++ F ++K+V R Sbjct: 422 AHRVIGNLEAGSCFINSYNDAPVEA--PFGGVKASGV-GRENSKEAIKHFSQVKSVYVR 477 Lambda K H 0.319 0.137 0.403 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: 586 Number of extensions: 39 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: 516 Length of database: 485 Length adjustment: 34 Effective length of query: 482 Effective length of database: 451 Effective search space: 217382 Effective search space used: 217382 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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