Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 6937470 Sama_1626 succinylglutamic semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P76217 (492 letters) >FitnessBrowser__SB2B:6937470 Length = 495 Score = 554 bits (1427), Expect = e-162 Identities = 272/481 (56%), Positives = 351/481 (72%) Query: 4 WINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHA 63 +I G W G G NP +GEV+W GN A+A QV+ A +AAR+AF W+ + AER A Sbjct: 13 FIGGQWQPGHGKGFESINPANGEVIWCGNGANAEQVDTAVKAARSAFYNWSAMPLAERLA 72 Query: 64 VVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEM 123 ++E F A L + + +IA ETGK WE+ TEV AM KIAISI+A+ RTG + M Sbjct: 73 IIEAFGAQLGEHSEAMARLIAEETGKALWESRTEVAAMTGKIAISIRAHSERTGTVENPM 132 Query: 124 PDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRL 183 P A +RH+PHGV+AVFGPYNFPGHLPNGHIVPAL+AGNT++FKPSELTP + + L Sbjct: 133 PGARAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAQFTVEL 192 Query: 184 WQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALE 243 WQ+AGLP GV+NL+QG ETG+AL+ +DGL FTGS+NTG+ LH+Q +GQP KILALE Sbjct: 193 WQKAGLPAGVINLLQGEVETGKALAGHPGIDGLFFTGSSNTGHLLHQQYAGQPGKILALE 252 Query: 244 MGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQ 303 MGGNNPLI+ +VA+++AAVH IQSAF+++GQRCTCARRL +K A GDA LA+L+ S+ Sbjct: 253 MGGNNPLIVKDVANVNAAVHDIIQSAFISSGQRCTCARRLFIKKDANGDAILAKLIEASR 312 Query: 304 RLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGII 363 ++ E QPF G +IS +AA +V A ++++GG LL + +TPGII Sbjct: 313 QIRVDEPFAENQPFYGAMISAKAAAAMVKAQTDIQSLGGISLLELKQPDLALGFVTPGII 372 Query: 364 EMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEAR 423 ++T V +PDEE FGPLL+V+RYD FD AI ANNT FGLS GL++ +D R Sbjct: 373 DVTHVKALPDEEHFGPLLKVYRYDDFDAAIDEANNTAFGLSAGLLADNEADYDHFFRRIR 432 Query: 424 AGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLNPG 483 AGIVNWNKP+TGA+S APFGGIGASGNHR SA+YAADYCA+P++S+E+ S++LPA+L+PG Sbjct: 433 AGIVNWNKPITGASSAAPFGGIGASGNHRASAFYAADYCAYPVSSVEASSVSLPASLSPG 492 Query: 484 L 484 L Sbjct: 493 L 493 Lambda K H 0.318 0.134 0.412 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: 810 Number of extensions: 33 Number of successful extensions: 1 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: 492 Length of database: 495 Length adjustment: 34 Effective length of query: 458 Effective length of database: 461 Effective search space: 211138 Effective search space used: 211138 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 (21.7 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