Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase
Query= BRENDA::Q8BH00 (487 letters) >FitnessBrowser__azobra:AZOBR_RS09720 Length = 497 Score = 298 bits (764), Expect = 2e-85 Identities = 163/479 (34%), Positives = 263/479 (54%), Gaps = 11/479 (2%) Query: 6 ELLMLENFIGGKFLPCNS--YIDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSS 63 ELL + F+ G+++ +S ++ +P+ G V VP G +E A+EAA A+PAW + Sbjct: 18 ELLRFQGFVDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWPAWRA 77 Query: 64 RSPQERSLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLH 123 + +ER+ L D++ + E++A+ + +QGK L AR ++ + +FA Sbjct: 78 LTAKERAKTLRTWFDLMMANQEDIARIMTAEQGKPLAEARG-EVAYAASFIEWFAEEGKR 136 Query: 124 HVSECTQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMT 183 + G + P+G+ I+PWN P ++T K PA+AAG ++ KP+ T Sbjct: 137 VYGDTIPQHLPGRRIVVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPATAT 196 Query: 184 SVTAWMFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLS 243 +TA L ++AG+P G++++V G+ +G + +P V ++FTGS + + Sbjct: 197 PLTALAMAVLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELMAQC 256 Query: 244 APHCKKLSLELGGKNPAIIFEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEF 303 A KK+SLELGG P ++F DA+L+E + + S + N G+ C+C +R+ VQ +Y F Sbjct: 257 AGTVKKVSLELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVYDAF 316 Query: 304 LKRFVEATRKWKVGVP-SDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLS 362 + EA + KVG + A G LI A +EKV ++ A +GAR++ G +L Sbjct: 317 AAKLAEAVKALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLGGKRHEL- 375 Query: 363 LPLRNQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAAT 422 G F PT++ D+ + EE FGPV + F++EEE + AN+ +GLAA Sbjct: 376 ------GGSFFEPTILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAY 429 Query: 423 VWSKDVGRIHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIK 481 +S+D+GR+ RVA+ L+ G+V N +I PFGGMK SGIGREG+K + + EIK Sbjct: 430 FYSRDIGRVWRVAEALEYGIVGINEGIISTEVAPFGGMKESGIGREGSKYGIEDYLEIK 488 Lambda K H 0.319 0.134 0.404 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: 552 Number of extensions: 20 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: 487 Length of database: 497 Length adjustment: 34 Effective length of query: 453 Effective length of database: 463 Effective search space: 209739 Effective search space used: 209739 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 (21.8 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