Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase
Query= BRENDA::Q1XGK8 (486 letters) >NCBI__GCF_001484605.1:WP_058929223.1 Length = 508 Score = 338 bits (867), Expect = 3e-97 Identities = 186/480 (38%), Positives = 278/480 (57%), Gaps = 6/480 (1%) Query: 8 INGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAAL-KGPWGKLSVAER 66 I+GA+V S+SG TF ++P + G V A +VD AV+AAR A +G W + ++R Sbjct: 25 IDGAWVQSSSGETFACVDPYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWPQTLPSQR 84 Query: 67 AEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEAF 126 A +L R AD +T DE + + GK + + G V A L + + Sbjct: 85 AALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQMGQHAHYV-AGLAETIQGRTI 143 Query: 127 EMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPLT 186 E P+ A + R P GV+ +I+PWN PL+L++WK+ ALA GNTVV+KPSE TP + Sbjct: 144 ESNWPNTAA---FTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEATPTS 200 Query: 187 ATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAAAK 246 + E+ AG P GV NVV GFG G+ L +H VD FTG T G I + AA+ Sbjct: 201 TLRMAELAMEAGFPPGVINVVTGFG-QPTGSALVDHRGVDKIAFTGSTSAGRAINKQAAE 259 Query: 247 GVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDEFVA 306 +V+LELGGK+ I+F+D D+D A+ G + F GQ C+G RV V+ I+D+FV Sbjct: 260 RFARVTLELGGKSPNIIFSDADIDNAVHGAMAGIFGATGQTCMGGSRVLVQDSIYDDFVD 319 Query: 307 RLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMPAHL 366 R+ ++L +G P D + + GP+ + +KV+ Y +G V+ GG + L Sbjct: 320 RMARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGARCMTTSEL 379 Query: 367 AGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWTEN 426 + G + +PT++ +S++S + EEIFGP I F E+EA+++AN+ +GLA+ +WT + Sbjct: 380 SKGLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFGLAAGVWTND 439 Query: 427 GSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNICVKL 486 SRAHR+ ++ +G VWVN++ L + FGG KQSGIGRE G +L+ YTE+K+ + L Sbjct: 440 VSRAHRMIRRVRSGTVWVNTYRLTNYSVPFGGFKQSGIGRELGPDALDAYTEVKSAWIDL 499 Lambda K H 0.318 0.136 0.411 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: 662 Number of extensions: 29 Number of successful extensions: 5 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: 486 Length of database: 508 Length adjustment: 34 Effective length of query: 452 Effective length of database: 474 Effective search space: 214248 Effective search space used: 214248 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 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