Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_013537247.1 THEAM_RS02515 aldehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000185805.1:WP_013537247.1 Length = 477 Score = 216 bits (549), Expect = 2e-60 Identities = 151/460 (32%), Positives = 225/460 (48%), Gaps = 19/460 (4%) Query: 40 LYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRS 99 + IGG+ V KE +V P S V GT + K + E A+E A K F+ K +R Sbjct: 6 MLIGGKKVFKKEEIVIDFPFDGSPV-GTVPRGKKEDVELAVETALKGFEKVKSMTAYERY 64 Query: 100 RLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEV 159 + L KAA ++ R RE L EVGK E+ +V A++ I A A R V Sbjct: 65 QALQKAARIIASRSREFAELLTLEVGKTIKESMGEVGRAVNTITLSAEEAKRVLGEEVRF 124 Query: 160 VPYPG-EDNESFY--VPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVG 216 PG + F+ VPLG I P+NFP+ + + +A GN V+ KP+E+ + Sbjct: 125 DAAPGIKGKVGFFRRVPLGVIGCITPFNFPLNLTCHKVAPALAAGNAVVIKPSENTSLTV 184 Query: 217 AKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276 K+ E+ EAGFPP VN + G GEE G LV R R I FTGS+ A G++ Sbjct: 185 IKLAEVLVEAGFPPEAVNVVTGYGEEAGDALVRDERVRMITFTGSV--------ATGKII 236 Query: 277 PGQTWFKRAYVETGGKDAIIV--DETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGA 334 + K+ +E G + V D+T AE + Y GQ C + R+ + + Sbjct: 237 MSRGGLKKYAMELGSNAGVYVDKDQTGRLKELAERIGRGGYALAGQVCISVQRVFVHESL 296 Query: 335 YEPVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRL 392 +E + + ++ L VG P E D+GPV+ +++ +IE ++ G Q++ GG+RL Sbjct: 297 FEEFTKELCSFSKSLKVGDPRLEETDVGPVIDRNAADRIMEWIEEARSMGAQVLCGGRRL 356 Query: 393 EGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR 452 I PTV VP +A++ ++E+FGPV+ V V A+E ND+PYGL G+++ Sbjct: 357 SET--LIEPTVVVNVPREAKLFRQEVFGPVIVVNPVDSLEAAIEAVNDSPYGLQAGIFTN 414 Query: 453 KREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSG 492 + E G + N +I V P+GG K SG Sbjct: 415 DLKAAFKFAEEVECGGIMVN-EIPTFRVDQMPYGGVKESG 453 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: 608 Number of extensions: 41 Number of successful extensions: 5 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: 477 Length adjustment: 34 Effective length of query: 482 Effective length of database: 443 Effective search space: 213526 Effective search space used: 213526 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 24 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