Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_068174307.1 HTA01S_RS19000 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >NCBI__GCF_001592305.1:WP_068174307.1 Length = 482 Score = 203 bits (517), Expect = 9e-57 Identities = 157/461 (34%), Positives = 231/461 (50%), Gaps = 12/461 (2%) Query: 5 INGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAV 64 + G W +G V NP +G V+ AA+ +A AA A+P W + ER AV Sbjct: 16 VGGQWFSGTAHIEVS-NPATGAVIATVPRLGAAETREAIEAANRAWPAWRARTAKERSAV 74 Query: 65 VERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIA-ISIKAYHVRTGEQRSEM 123 + ++ AL+ +N+ +L I+ E GKP EA E+ + I S +A V + + Sbjct: 75 LAQWYALIMANQDDLALIMTSEQGKPLAEARGEIAYAASFIQWFSEEAKRVYGDTIPAPV 134 Query: 124 PDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRL 183 + P GV A P+NFP + PAL AG T++ KP+ TP + A+ L Sbjct: 135 ASQRIVVIKEPIGVCAAITPWNFPAAMITRKAGPALAAGCTMVVKPASQTPLTALALAVL 194 Query: 184 WQQAGLPPGVLNLVQG-GRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILAL 242 ++AG+PPGV ++V G R+ G L+ + L FTGS G L + + +K+ ++ Sbjct: 195 AERAGVPPGVFSVVTGSARDVGDELADNPLVRKLSFTGSTEVGRSLMARTAATVKKV-SM 253 Query: 243 EMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARL-VAV 301 E+GGN P I+ E AD+DAAV I S + AGQ C CA RL + S +AF A+L VAV Sbjct: 254 ELGGNAPFIVFEDADLDAAVEGAIVSKYRNAGQTCVCANRLYVHSKVY-EAFAAKLAVAV 312 Query: 302 SQ-RLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360 SQ ++ G D IG LI ++A +V A G R L R G S P Sbjct: 313 SQLKVGEGTGADVR---IGPLIDDKAVLKVEQHIADAVAKGARVLSGGRRHALGQSFFEP 369 Query: 361 GII-EMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLL 419 I+ ++T V EE FGPL ++R++T DE + MAN+T FGL+ + + + ++ Sbjct: 370 TILGDVTQDMLVAREETFGPLAPLFRFETEDEVVAMANDTEFGLASYFYARDLGRVWRVA 429 Query: 420 LEARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAAD 460 G+V N L + APFGG+ SG R + D Sbjct: 430 ERLEYGMVGVNTGLI-SNEVAPFGGVKQSGIGREGSHLGMD 469 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: 553 Number of extensions: 22 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: 492 Length of database: 482 Length adjustment: 34 Effective length of query: 458 Effective length of database: 448 Effective search space: 205184 Effective search space used: 205184 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 Apr 09 2024. 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