Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase
Query= BRENDA::P25526 (482 letters) >FitnessBrowser__azobra:AZOBR_RS09720 Length = 497 Score = 701 bits (1810), Expect = 0.0 Identities = 342/480 (71%), Positives = 403/480 (83%), Gaps = 1/480 (0%) Query: 3 LNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALP 62 L D+ L R Q ++G W+DA++G+ ++VTNPA+G LGSVP MGADETR AI+AA RA P Sbjct: 14 LKDAELLRFQGFVDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWP 73 Query: 63 AWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEE 122 AWRALTAKERA LR WF+LMM +Q+D+AR+MT EQGKPLAEA+GE++YAASFIEWFAEE Sbjct: 74 AWRALTAKERAKTLRTWFDLMMANQEDIARIMTAEQGKPLAEARGEVAYAASFIEWFAEE 133 Query: 123 GKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182 GKR+YGDTIP H +R++V K+PIGVTAAITPWNFPAAMITRKAGPALAAGC MV+KPA Sbjct: 134 GKRVYGDTIPQHLPGRRIVVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPA 193 Query: 183 SQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQLM 242 + TP +ALA+A LA RAG+PAG+ +VVTGSA A+G E+T NP VRKL+FTGSTEIG++LM Sbjct: 194 TATPLTALAMAVLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELM 253 Query: 243 EQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVY 302 QCA +KKVSLELGGNAPF+VF+DADLD+AV+GA+ASK+RN GQTCVCANRL VQ GVY Sbjct: 254 AQCAGTVKKVSLELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVY 313 Query: 303 DRFAEKLQQAVSKLHIGDGL-DNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH 361 D FA KL +AV L +G GL G GPLID AV KVE+HI DA EKGARVV GGK H Sbjct: 314 DAFAAKLAEAVKALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLGGKRH 373 Query: 362 ERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYAR 421 E GG+FF+PTIL DV KV++EETFGP+APLFRF+ E + + AN TEFGLAAYFY+R Sbjct: 374 ELGGSFFEPTILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFYSR 433 Query: 422 DLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481 D+ RV+RV EALEYGIVGIN GIIS EVAPFGG+K SG+GREGSKYGIEDYLEIKY+C+G Sbjct: 434 DIGRVWRVAEALEYGIVGINEGIISTEVAPFGGMKESGIGREGSKYGIEDYLEIKYLCMG 493 Lambda K H 0.318 0.135 0.395 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: 776 Number of extensions: 20 Number of successful extensions: 2 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: 482 Length of database: 497 Length adjustment: 34 Effective length of query: 448 Effective length of database: 463 Effective search space: 207424 Effective search space used: 207424 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 (21.7 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