Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase
Query= BRENDA::Q9RW56 (523 letters) >FitnessBrowser__azobra:AZOBR_RS09720 Length = 497 Score = 212 bits (539), Expect = 3e-59 Identities = 147/475 (30%), Positives = 235/475 (49%), Gaps = 23/475 (4%) Query: 44 IDGQEVDTE-GK-IQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDARA 101 +DG+ +D + GK ++ NP D S V+G+ + A++ A +A+ +W+ RA Sbjct: 26 VDGRWIDADSGKTVEVTNPADGS-VLGSVPMMGADETRRAIEAAERAWPAWRALTAKERA 84 Query: 102 RILLKAAAILKRRRLEACALMSIEVGKNYAEADVEVAEAIDFLEYYARSAMKYAGFGSSE 161 + L ++ + + +M+ E GK AEA EVA A F+E++A + +G + Sbjct: 85 KTLRTWFDLMMANQEDIARIMTAEQGKPLAEARGEVAYAASFIEWFAEEGKRV--YGDTI 142 Query: 162 TTWFEGEENGLMSIPLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGF 221 G + P+GV +I+PWNFP A+ A + AG +V+KPA L A Sbjct: 143 PQHLPGRRIVVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPATATPLTALA 202 Query: 222 MVDILREAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPG 281 M + AG+PAG+L + G + +G +T + R +TFTGS +G + A Sbjct: 203 MAVLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELMAQCAGT--- 259 Query: 282 QKWIKRVIMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVYDEV 341 +K+V +ELGG +V AD++ A+ A + GQ C +RL+V VYD Sbjct: 260 ---VKKVSLELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVYDAF 316 Query: 342 VNGFVERAKALKMGTG--EENANVTAVVNQMSFNKIKGYLELAPSEG-KVLLGGEATGEA 398 E KALK+G G E A +++ + K++ ++ A +G +V+LG G+ Sbjct: 317 AAKLAEAVKALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLG----GKR 372 Query: 399 NGKQGYYIQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCS 458 + G + +PTI+ DV ++A+EE FGPV + R + ++A+ +AN+TE+GL S Sbjct: 373 HELGGSFFEPTILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFYS 432 Query: 459 NSRERLEQARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSG---TDSKAGGPDYL 510 R+ + E G + N I V PFGG SG SK G DYL Sbjct: 433 RDIGRVWRVAEALEYGIVGINEGIIS--TEVAPFGGMKESGIGREGSKYGIEDYL 485 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: 647 Number of extensions: 32 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: 497 Length adjustment: 34 Effective length of query: 489 Effective length of database: 463 Effective search space: 226407 Effective search space used: 226407 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 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