Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_092344789.1 BLU87_RS03510 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_900107645.1:WP_092344789.1 Length = 452 Score = 216 bits (550), Expect = 1e-60 Identities = 134/452 (29%), Positives = 216/452 (47%), Gaps = 5/452 (1%) Query: 40 TVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHAD 99 +++P+T E + E E + +EA A+ + W T+ R +L K A ++ + D Sbjct: 5 SLNPATGEVLETFDEWSDEQVATTIEAVHGAYQN-WRTTSFAERKSLLLKAAVILRQRKD 63 Query: 100 TLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGV 159 A + AL+ GK ++ + ++ A A +++ D +Y P G+ Sbjct: 64 EFATMMALEMGKPVVEGRAEIEKCALVCNYYAENAEQMLAPEPIASDASRSYVAFRPQGI 123 Query: 160 CGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVV 219 ++PWNFP P L G VLK A + P AL + + EAG P V + Sbjct: 124 VLAVMPWNFPFWQVFRFAAPALMAGNVGVLKHASNVPRCALAIEQVFVEAGYPADVFRTL 183 Query: 220 SGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDA 279 G A + HP + TGS GR + + + + LKK +ELGG P IV +DA Sbjct: 184 M-IGSGKVAQVIEHPYVVATTLTGSDIAGRKVAEKSG-AMLKKSVMELGGSDPFIVLNDA 241 Query: 280 DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFM 339 D+ VT N+G+ C A R V++GIY+ + +FK +LK+GDP E T + Sbjct: 242 DLDLAASVAVTARCINSGQSCIAAKRFIVEDGIYETFLEKFKANMAALKMGDPCDETTQV 301 Query: 340 GAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRDEIF 399 G Q + + ++ + ++ +GA VI GG + F PTI V + +E F Sbjct: 302 GPQAREDLMRELHRQVEGSVAKGAKVILGG--MPGEAAFYPPTILTQVSKGMPAYNEEFF 359 Query: 400 GPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHP 459 GPV + + K EE + +AND+E+GL V T ++ ++ +I SG ++VN+ P Sbjct: 360 GPVAIVIRVKDAEEALFVANDTEFGLGGSVWTRDIIKGEKIAGEIRSGAVFVNSMTKSDP 419 Query: 460 MVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491 +PFGG SG GRE+ + + ++ V I Sbjct: 420 RLPFGGVGISGFGRELSHYGIKEFVNIQTVWI 451 Lambda K H 0.316 0.133 0.389 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: 510 Number of extensions: 26 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: 495 Length of database: 452 Length adjustment: 33 Effective length of query: 462 Effective length of database: 419 Effective search space: 193578 Effective search space used: 193578 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 (21.6 bits) S2: 51 (24.3 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