Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_099617963.1 CLH62_RS09710 2-hydroxymuconic semialdehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >NCBI__GCF_002744735.1:WP_099617963.1 Length = 486 Score = 687 bits (1772), Expect = 0.0 Identities = 332/462 (71%), Positives = 377/462 (81%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 SP++N VIA + EAG+AEVD AV+AA+ AL G WG++S RV++LY VAD I RRFDDF Sbjct: 25 SPVDNQVIASIAEAGQAEVDQAVSAAKHALAGEWGQLSTNDRVDLLYGVADEITRRFDDF 84 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 +AAE+ DTG+P + H IPRGAANFK+FAD++KNVPTE F M TPDG GA+NY VR P Sbjct: 85 VAAEMADTGQPHHVMTHAFIPRGAANFKVFADIIKNVPTESFHMDTPDGRGALNYGVRVP 144 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 GV+GV+ PWN P LLMTWKVGPALACGNTVVVKPSEETP TA LLGEVMN GVP GVY Sbjct: 145 KGVIGVVAPWNAPFLLMTWKVGPALACGNTVVVKPSEETPLTATLLGEVMNKVGVPKGVY 204 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 NV++GFGP+S GEFLT H DV+AITFTGET TG IMKAA+DG R VS E+GGKNA IVF Sbjct: 205 NVINGFGPDSAGEFLTRHKDVDAITFTGETRTGSTIMKAASDGIRDVSFEMGGKNAGIVF 264 Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323 ADCDLD A++G RS F N GQVCLGTERVYVERPIFDRFV+ LK+ AEG+ GRP D Sbjct: 265 ADCDLDNAVDGIFRSSFLNTGQVCLGTERVYVERPIFDRFVTALKEKAEGVTFGRPTDAG 324 Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383 GPLISQEHREKVLSYY KA GAT+VTGGGVP+MP L G+WVQPTIWT L + S Sbjct: 325 VNYGPLISQEHREKVLSYYAKARADGATIVTGGGVPDMPADLAEGSWVQPTIWTDLPESS 384 Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443 V +EEIFGPC + PFDSEEEVI AN +DYGLA IWT NL+RAHRVAG ++VGI WV Sbjct: 385 AVIQEEIFGPCCHIRPFDSEEEVIELANASDYGLATTIWTENLTRAHRVAGKVDVGITWV 444 Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 NSWFLRDLRTAFGG+KQSGIGREGGVHSLEFYTE++NVCIK+ Sbjct: 445 NSWFLRDLRTAFGGAKQSGIGREGGVHSLEFYTEMRNVCIKM 486 Lambda K H 0.318 0.135 0.406 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: 737 Number of extensions: 16 Number of successful extensions: 1 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: 485 Length of database: 486 Length adjustment: 34 Effective length of query: 451 Effective length of database: 452 Effective search space: 203852 Effective search space used: 203852 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 (21.7 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