Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= BRENDA::P25526 (482 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 261 bits (667), Expect = 4e-74 Identities = 169/467 (36%), Positives = 245/467 (52%), Gaps = 32/467 (6%) Query: 28 IDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWRALTAKERATILRNWFNLMMEHQ 87 +DV + +G V A T AI AA +A R ER +L++ E + Sbjct: 21 MDVLDKYSGKVATRVAVPDAKATEQAIAAAVKAAEPMRQFKPWERQAVLQHCVQRFTERR 80 Query: 88 DDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTIPGHQADKRL-----IV 142 D+LA + +E GKP+ ++ GE++ AEE R G+TI + KRL Sbjct: 81 DELAYALCVEAGKPIKDSAGEVTRLIETFGIAAEEAVRTNGETI-NLEIAKRLNGYHGYT 139 Query: 143 IKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSALALAELAIRAGVP 202 + P+G + ITP+NFP ++ K PA+AAGC VLKPA +TP AL + E+ +P Sbjct: 140 RRVPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLP 199 Query: 203 AGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQLMEQCAKDIKKVSLELGGNAPF 262 G F+++ G + L +P + LSFTGS +IG L + KKV+LELGGNA Sbjct: 200 KGAFSIL-NLDGKHASPLVEDPRFKLLSFTGS-QIGWDLKTRAGH--KKVTLELGGNAAC 255 Query: 263 IVFDDAD----LDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDRFAEKLQQAVSKLHI 318 IV DAD LD +E + F +GQ+C+ R+Y + +YD ++L AV L Sbjct: 256 IV--DADQLPRLDHVIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKA 313 Query: 319 GDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHERGGNFFQPTILVDVPA 378 GD +GP+IDE A ++ I +A + G +V+CGGK R G + T++ +V Sbjct: 314 GDPKKKETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGK---RKGPMLEATLMENVRG 370 Query: 379 NAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLSRVFRVGEALEYGIV 438 +AKV+++E FGP A L FK + IA ND+++GL A + L+ R LE G Sbjct: 371 DAKVNRQEVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQG-- 428 Query: 439 GINTGIISNEV-------APFGGIKASGLGREGSKYGIEDYLEIKYM 478 G+I N+V P+GG+K SG GREG +Y IED EI+ M Sbjct: 429 ----GVIVNDVPSFRVDNMPYGGVKLSGAGREGVRYAIEDMTEIRLM 471 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: 572 Number of extensions: 29 Number of successful extensions: 6 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: 476 Length adjustment: 34 Effective length of query: 448 Effective length of database: 442 Effective search space: 198016 Effective search space used: 198016 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: 51 (24.3 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