Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate BWI76_RS12820 BWI76_RS12820 NAD-dependent phenylacetaldehyde dehydrogenase
Query= BRENDA::Q9RW56 (523 letters) >FitnessBrowser__Koxy:BWI76_RS12820 Length = 499 Score = 238 bits (608), Expect = 3e-67 Identities = 169/516 (32%), Positives = 262/516 (50%), Gaps = 38/516 (7%) Query: 25 QAALAKVRKELLGKHYPLIIDG--QEVDTEGKIQSINPCDTSEVVGTTAKATIGDAENAL 82 Q AL ++ L + + L +DG Q ++E ++ NP T + + +TA A D + A+ Sbjct: 5 QVALLASVQQFLDRQHGLYLDGTQQAAESEQRLTVWNPA-TGQAIASTADANAADVDRAV 63 Query: 83 QGAWKAF--ESWKKWDMDARARILLKAAAILKRRRLEACALMSIEVGK--NYAEADVEVA 138 AW+AF SW R RILL+ A ++++ E L ++E GK N + A EV Sbjct: 64 MSAWRAFVSRSWAGRTPADRERILLRFADLVEQHGEELAQLETLEQGKSINISRA-FEVG 122 Query: 139 EAIDFLEYYARSAMKYAG----------FGSSETTWFEGEENGLMSIPLGVGVSISPWNF 188 ++++ Y A K +G G W + E P+GV I PWNF Sbjct: 123 CTLNWMRYTAGLTTKISGRTLDVSIPFPAGGRYQAWTKKE-------PVGVVAGIVPWNF 175 Query: 189 PCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREAGLPAGVLQFLPGVGKEVGE 248 P I + + AG +V+KP+E L + ++ EAG+P GV + G G G Sbjct: 176 PLMIGMWKVMPALAAGCSIVIKPSETTPLTLLRVAELATEAGVPDGVFNVVTGSGAGCGA 235 Query: 249 YLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRVIMELGGKDGLIVDETADIEN 308 LT+H ++FTGS A G I VAA + RV +ELGGK+ IV + AD + Sbjct: 236 ALTSHPLVAKVSFTGSTATGKQIARVAA------DRLTRVTLELGGKNPAIVLKDADPQW 289 Query: 309 AITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVERAKALKMGTGE-ENANVTAVV 367 I G+F GQ C+A SR+ + ++D +V+GF + K+L++G G E++ + VV Sbjct: 290 VIEGLMTGSFLNQGQVCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMLESSQINPVV 349 Query: 368 NQMSFNKIKGYLELAPSEGKVLLGGEATGEANGKQGYYIQPTIVGDVDRNSRLAQEEIFG 427 +Q K+ YL+ A + L+ G A +A QGYYI PT+V + D RL +EE+FG Sbjct: 350 SQAHCAKVAAYLDEARQQKAELISGHAGPDA---QGYYIAPTLVINPDAGLRLCREEVFG 406 Query: 428 PVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLEQARAEFEVGNLYFNRKITGAIV 487 PVV ++R D ++AL +AN +++GLT V + + + G ++ N I Sbjct: 407 PVVNLVRVADGEEALLLANDSDFGLTASVWTRDLTQALSYTDRLQAGTVWVNSHT--LID 464 Query: 488 GVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTVTERW 523 PFGG SGT + GPD+L ++ + K+V R+ Sbjct: 465 ANLPFGGMKQSGT-GRDFGPDWLDDWCETKSVCVRY 499 Lambda K H 0.317 0.134 0.391 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: 595 Number of extensions: 21 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: 523 Length of database: 499 Length adjustment: 35 Effective length of query: 488 Effective length of database: 464 Effective search space: 226432 Effective search space used: 226432 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 Apr 09 2024. 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