Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_052367856.1 U743_RS09915 aldehyde dehydrogenase family protein
Query= BRENDA::Q9RW56 (523 letters) >NCBI__GCF_000733765.1:WP_052367856.1 Length = 539 Score = 176 bits (446), Expect = 2e-48 Identities = 143/474 (30%), Positives = 219/474 (46%), Gaps = 21/474 (4%) Query: 54 KIQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDARARILLKAAAILKR 113 +I NP T E +GT AT + + A++ A A + W + R +L + + Sbjct: 19 EIDCRNPA-TGETLGTLPAATPAEVQEAVERARAAQKQWAQSSFRQRRAVLRRMLQSILD 77 Query: 114 RRLEACALMSIEVGKNYAEADV-EVAEAIDFLEYYARSAMKYAGFGSSETTWFEGEENGL 172 E CA + + GK + A + EV + + + R K+ S + + ++ + Sbjct: 78 DVDELCAAVVADSGKTWENALLGEVMPVCNKIRWIIRYGEKHLRSESVPSGLLKHKKGRI 137 Query: 173 MSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREA--- 229 PLGV I PWN+P G AP++AGN VV+K +E + EA Sbjct: 138 EYRPLGVVACIVPWNYPFQNIFGSLVAPLMAGNAVVLKASEAVAWSTQRFRRVFEEALVA 197 Query: 230 -GLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRV 288 G PA +Q + G G E G L ++ + I F GS G I E +A+ + V Sbjct: 198 EGFPAETVQIINGYG-ETGAALV-RSRVQKILFIGSVGNGRKIIEGSAE------HLTPV 249 Query: 289 IMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVER 348 +MELGGKD +I+ + A +E A+ +A G F GQ C A RLIV ++D V Sbjct: 250 VMELGGKDPMIICDDAHLEQAVHSALSGCFINLGQNCIASERLIVQAGIFDRFVEEVTRI 309 Query: 349 AKALKMGTGEE--NANVTAVVNQMSFNKIKGYLELAPSEG-KVLLGGEATGEANGKQGYY 405 A ++ G E+ +V A+ + + A + G + L+GG G G + Sbjct: 310 AGDMRQGVPEQPGTLDVGAMTTPQQVRIVDELVRDALASGARALVGGRLP---EGASGSF 366 Query: 406 IQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLE 465 PT++ DV R+A+EE+FGPV+ ++RA D +A+ IAN+ ++GL V S R+R E Sbjct: 367 YPPTVLVDVTPEMRIAREEVFGPVMLIMRAADDAEAVRIANAIDFGLQSSVFSRDRKRAE 426 Query: 466 QARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTV 519 + AE E G N + PFGG SG + G D L + K V Sbjct: 427 RIAAELEAGATCINDFGLCYLNQDLPFGGVKYSGF-GRMNGRDGLRAYTNPKAV 479 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: 621 Number of extensions: 34 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: 523 Length of database: 539 Length adjustment: 35 Effective length of query: 488 Effective length of database: 504 Effective search space: 245952 Effective search space used: 245952 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 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