Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_082908505.1 BJL86_RS03515 aldehyde dehydrogenase
Query= BRENDA::Q9RW56 (523 letters) >NCBI__GCF_001659785.1:WP_082908505.1 Length = 507 Score = 201 bits (510), Expect = 7e-56 Identities = 159/515 (30%), Positives = 251/515 (48%), Gaps = 38/515 (7%) Query: 19 ENVQAYQAALAKVRKELLGKHYPLIIDGQEVDTEG--KIQSINPCDTSEVVGTTAKATIG 76 E V +AL+ + + +H L I GQ + G KI ++P ++ E +G+ A Sbjct: 15 EEVPTLSSALSD---QAVTEHSTLFIGGQWREPNGREKITVVSP-NSGEEIGSVPLANRA 70 Query: 77 DAENALQGAWKAFES---WKKWDMDARARILLKAAAILKRRRLEACALMSIEVGKNYAEA 133 D + A+ A +AF+ W + RA L + A L+ R + +L+S + G A Sbjct: 71 DIDAAVATARQAFDDPSVWSGLEPAERAAHLRRFADELEARGEKIASLVSSQNGMPVTIA 130 Query: 134 -DVEVAEAIDFLEYYARSAMKYAGFGSSETTWFEGEENGLMSI---PLGVGVSISPWNFP 189 +E L YY+ K EG G++ + P+GV +I PWN+P Sbjct: 131 GQMEAVYPATLLRYYSDLIEKQT------PDLREGMMGGVVEVQRQPIGVVGAIVPWNYP 184 Query: 190 CAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREAGLPAGVLQFLPGVGKEVGEY 249 ++ A + AG +V+KP+ + L + + + AGLPAGV+ +PG G++ G Y Sbjct: 185 QSLAAFKYAPALAAGCTMVIKPSPETVLDSVVLAEAAEAAGLPAGVVNIVPG-GRDEGAY 243 Query: 250 LTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRVIMELGGKDGLIV--DETADIE 307 L HA + FTGS A G I EV ++ ++ V +ELGGK IV D D+E Sbjct: 244 LVEHADIDKVAFTGSTAAGKKIAEVCGRL------LRPVTLELGGKSASIVLDDAELDLE 297 Query: 308 NAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEVVNGFVERAKALKMGTGEENAN-VTAV 366 NGQ C +R++ S Y EVV+ A ++ +G + A + + Sbjct: 298 TIGNDLFVSTLVNNGQTCFLGTRVLAPKSRYGEVVDALTAFAGSMAVGDSLDPATQIGPM 357 Query: 367 VNQMSFNKIKGYLELAPSEG-KVLLGGEATGEANGKQG-YYIQPTIVGDVDRNSRLAQEE 424 Q +++GY+E SEG ++ GG G G+ G +++ PT+ DV+ + +A+EE Sbjct: 358 ATQTHLGRVEGYIEKGRSEGGRITTGG---GRPEGRDGGWFVSPTVFADVNNSDTIAREE 414 Query: 425 IFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLEQARAEFEVGNLYFNRKITG 484 IFGPV++V++ D DA+ IAN +EYGL G V S+ ER + G + NR I Sbjct: 415 IFGPVLSVIQYDDDADAVRIANESEYGLGGTVWSSDPERARSVASRVNTGTIGINRYIPD 474 Query: 485 AIVGVQPFGGYNMSGTDSKAGGPDYLSNFMQLKTV 519 V PFGG SG + GP+ L+ + LK++ Sbjct: 475 P---VAPFGGVKHSGMGREL-GPEGLAAYQNLKSI 505 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: 562 Number of extensions: 24 Number of successful extensions: 7 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: 507 Length adjustment: 35 Effective length of query: 488 Effective length of database: 472 Effective search space: 230336 Effective search space used: 230336 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