Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_086508153.1 BZY95_RS01060 succinylglutamate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >NCBI__GCF_002151265.1:WP_086508153.1 Length = 489 Score = 566 bits (1459), Expect = e-166 Identities = 283/482 (58%), Positives = 355/482 (73%), Gaps = 1/482 (0%) Query: 3 LWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62 L I G W G+ KR+PV+GE LWQG A +QV A AAR AFP WARL FAER Sbjct: 7 LMIGGRWQPGEAMQFTKRDPVAGETLWQGAAASDSQVAAAVEAARGAFPGWARLGFAERL 66 Query: 63 AVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSE 122 +VVERF LLE+++ +L IA ETGKP WEA TEV AMI K+AIS +AY RTGE+ + Sbjct: 67 SVVERFRDLLETHREDLAHAIAGETGKPLWEARTEVGAMIGKVAISARAYQERTGERSRD 126 Query: 123 MPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMR 182 + D A LRHRPHGV+AVFGPYNFPGHLPNGH+VPALLAGNT++FKPSE TP + + ++ Sbjct: 127 LGDTTAVLRHRPHGVMAVFGPYNFPGHLPNGHMVPALLAGNTVVFKPSEQTPLTADLTLQ 186 Query: 183 LWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILAL 242 WQ+AGLP GV+NLVQG GQALS+ +DGLLFTGSA G L+RQ + Q EKILAL Sbjct: 187 CWQEAGLPAGVINLVQGAAPVGQALSSHPGIDGLLFTGSARVGGLLNRQFADQLEKILAL 246 Query: 243 EMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVS 302 E+GGNNPL++ +V D DA V +QSAF++ GQRCTCARRL++ G GD L LV Sbjct: 247 ELGGNNPLVVKDVHDQDATVLTILQSAFLSGGQRCTCARRLIVPEGQVGDHLLDALVDAI 306 Query: 303 QRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGI 362 RL +EP PF GGL+S++AA+ ++ A +LEA+GG L LQ GTSLL+P + Sbjct: 307 ARLRVAGQFEEPAPFYGGLVSQEAAEGLLKAQDELEALGGVVLARMACLQEGTSLLSPAL 366 Query: 363 IEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEA 422 I++TG+ VPDEE FGPLL+V+RY +DEA+R+AN+TR+GL+ GL+ ER +D LL Sbjct: 367 IDVTGL-DVPDEEHFGPLLKVYRYRDWDEALRLANDTRYGLAAGLIGGERADWDDFLLRI 425 Query: 423 RAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLNP 482 RAGIVNWN+ TGA+ APFGG+G SGNHRPSA+YAADYCA+P+AS+E+++LTLP L P Sbjct: 426 RAGIVNWNRQTTGASGDAPFGGVGISGNHRPSAYYAADYCAYPVASMEAETLTLPDNLPP 485 Query: 483 GL 484 G+ Sbjct: 486 GV 487 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: 824 Number of extensions: 36 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: 492 Length of database: 489 Length adjustment: 34 Effective length of query: 458 Effective length of database: 455 Effective search space: 208390 Effective search space used: 208390 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 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