Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_015447966.1 R2APBS1_RS10710 aldehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >NCBI__GCF_000230695.2:WP_015447966.1 Length = 476 Score = 213 bits (543), Expect = 9e-60 Identities = 149/455 (32%), Positives = 228/455 (50%), Gaps = 19/455 (4%) Query: 42 NGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQARFEEFVAA 101 +G+L + V DAK V +A+ AA NA K P + R ++ A R +E A Sbjct: 28 SGRLATRVAVPDAKAVEKAIAAAVNAAK-PMREFKPWARQTVLQYCAARFAERRDELAEA 86 Query: 102 EVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDG-SGALNYTVRKPLG 160 + G+P+ A ++ R I FR A+ A + + + + G YT R PLG Sbjct: 87 LCIEAGKPIKDAAG-EVTRLIETFRIAAEEAVRINGETINLELASRLDGYHGYTRRVPLG 145 Query: 161 VIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGVPPGVFNL 220 + I+P+N PL L KVAPA+A G V KPSE++P A ++ EV+ + +P G F++ Sbjct: 146 PVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPSEKTPIGALIIGEVLAETDLPKGAFSI 205 Query: 221 IHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKNAAVVFAD 280 + G +A L + P L+FTG + +A G K+V+ ELGG A +V AD Sbjct: 206 LTLDGAHAAP--LVEDPRFKLLSFTGGQVGWALKARA---GHKKVTLELGGNAACIVDAD 260 Query: 281 AD--LDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGYPDQDG 338 D LD ++ ++ +F SGQ C+ +R+Y H I+D L ++L G P Sbjct: 261 QDGKLDHVVQRLVFGAFYQSGQSCIGVQRIYAHADIYDALKRKLVAATKKLKAGDPKDRS 320 Query: 339 VNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTIWTGLSDKA 398 V +GP+I +++ + A G ++ GG + G + T+ + A Sbjct: 321 VFLGPMIDEAAAERLHGWILEAKQAGGRILCGG--------KRHGNMLDATLMENVPADA 372 Query: 399 RCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHVGLVWV 458 + E FGP ++PF DE I VNDS+YGL I+T +L+ A R ++ G V V Sbjct: 373 KANRMEAFGPFALLAPFRRFDEAIAMVNDSDYGLQAGIFTDSLAHAMRAWNELEQGGVIV 432 Query: 459 NTW-YLRDLRTPFGGVKLSGLGREGGRFSMDFYSD 492 N R P+GGVKLSGLGREG R++++ S+ Sbjct: 433 NDIPSFRVDNMPYGGVKLSGLGREGVRYAIEDMSE 467 Lambda K H 0.318 0.135 0.405 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: 528 Number of extensions: 14 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: 500 Length of database: 476 Length adjustment: 34 Effective length of query: 466 Effective length of database: 442 Effective search space: 205972 Effective search space used: 205972 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