Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q8BH00 (487 letters) >NCBI__GCF_000745975.1:WP_035239838.1 Length = 484 Score = 300 bits (767), Expect = 1e-85 Identities = 163/458 (35%), Positives = 257/458 (56%), Gaps = 10/458 (2%) Query: 25 IDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQERSLVLNRLADVLEQSL 84 +D +P+TG++ VP G +E + A+ AA E+ AW S++ ERS +L + D+L ++ Sbjct: 29 VDVTNPATGQILGTVPFCGADETQRAINAANESLDAWRSKTAGERSAILRKWYDLLMENQ 88 Query: 85 EELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSECTQMSHLGCMHYTVRTP 144 E+LA + +QGK L +R +I + F +FA + + ++ P Sbjct: 89 EDLAVIMTAEQGKPLAESRG-EIAYAAAFFEWFAEEAKRVYGDVIPQTVASQRLVVIKQP 147 Query: 145 VGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFCKLLDKAGVPPGVI 204 VG+ I+PWN P ++T K A+AAG T++ KP+ T +A KL +AGVP GV Sbjct: 148 VGVVAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPFSALAIAKLGQQAGVPKGVF 207 Query: 205 NIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAIIFE 264 N+V G+ +G L ++P V ++FTGS +++ + A K+LS+ELGG P I+F+ Sbjct: 208 NVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCAGTMKRLSMELGGNAPFIVFD 267 Query: 265 DANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRFVEATRKWKVGVPSDPSA 324 DA+++ + + + N G+ C+C +R++VQ +Y EF ++ A ++ KVG D Sbjct: 268 DADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVYDEFCRKLTAAVQELKVGNGFDDGV 327 Query: 325 NMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRNQAG-YFMLPTVITDIKD 383 G LI A +E V S++ A +G ++L G R+ G F PT+I D+ D Sbjct: 328 QQGPLIDMAAVETVESHIKDAVDKGGKVLAG--------GTRHALGRTFFAPTIIADVTD 379 Query: 384 ESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKDVGRIHRVAKKLQSGLV 443 + R EE FGP+ V FD+EEEV+ +AN +GLAA +++D+ R R+ +KL+ GLV Sbjct: 380 DMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDMARSWRIGEKLEYGLV 439 Query: 444 WTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIK 481 N +I PFGG+K SG GREG+K D + EIK Sbjct: 440 GINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIK 477 Lambda K H 0.319 0.134 0.404 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: 529 Number of extensions: 23 Number of successful extensions: 3 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: 487 Length of database: 484 Length adjustment: 34 Effective length of query: 453 Effective length of database: 450 Effective search space: 203850 Effective search space used: 203850 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 (21.8 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