Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate WP_108402515.1 B9Z44_RS11745 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25526 (482 letters) >NCBI__GCF_003063475.1:WP_108402515.1 Length = 492 Score = 596 bits (1536), Expect = e-175 Identities = 288/482 (59%), Positives = 364/482 (75%), Gaps = 7/482 (1%) Query: 3 LNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALP 62 LND L + ALING W+ DV +PA G KL V +G + AAIDAAN A P Sbjct: 11 LNDPTLLKTDALINGHWV--KGASRFDVHDPATGKKLADVANLGPADASAAIDAANAAWP 68 Query: 63 AWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEE 122 AWR T KER+ ILR WF+L+M HQ+DL R+MT EQGKP AEAKGE+ Y ASF+EWFAEE Sbjct: 69 AWRNKTGKERSIILRKWFDLLMAHQEDLGRIMTAEQGKPFAEAKGEVVYGASFVEWFAEE 128 Query: 123 GKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182 KR+ G+T+P ++RL+V+KQPIGV AAITPWNFP AMITRK PALAAGC +V+KPA Sbjct: 129 AKRVNGETLPQFDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKPA 188 Query: 183 SQTPFSALALAELAIRAGVPAGVFNVVTGSAG---AVGNELTSNPLVRKLSFTGSTEIGR 239 P +ALA AELAIRAG+P GV N++T + A+G S+ +VR +SFTGSTE+GR Sbjct: 189 ELPPLTALAAAELAIRAGIPDGVLNILTADSDNSIAIGKVFCSSDIVRHISFTGSTEVGR 248 Query: 240 QLMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQD 299 LM Q A IKK++LELGGNAPFIVFDDAD+D AVEGA+ASK+RNAGQTCVCANR+YVQD Sbjct: 249 ILMAQSAPSIKKLALELGGNAPFIVFDDADIDSAVEGAMASKYRNAGQTCVCANRIYVQD 308 Query: 300 GVYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGK 359 VYD F +K V L +G+G ++GVT GPLI++ AV KVE H+ DAL KG +++ GG Sbjct: 309 AVYDEFVQKFAAKVKALKVGNGFEDGVTQGPLIEDAAVDKVERHVQDALHKGGKLITGG- 367 Query: 360 AHERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFY 419 H+ G FF+PT++ D A+ ++EETFGP AP+FRF + + I AN+TEFGLA+YFY Sbjct: 368 -HKLTGQFFEPTVIADARADMLCAREETFGPFAPVFRFHKDQEAIDAANNTEFGLASYFY 426 Query: 420 ARDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMC 479 +RD+ R++RV EALEYG+VGIN GII++E PFGG+K SGLGREGS +G+++Y+E+KY+C Sbjct: 427 SRDIGRIYRVSEALEYGMVGINVGIIASEHVPFGGVKQSGLGREGSSHGMDEYVEMKYLC 486 Query: 480 IG 481 +G Sbjct: 487 LG 488 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: 715 Number of extensions: 23 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: 482 Length of database: 492 Length adjustment: 34 Effective length of query: 448 Effective length of database: 458 Effective search space: 205184 Effective search space used: 205184 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 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