Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein
Query= BRENDA::Q1XGK8 (486 letters) >FitnessBrowser__Marino:GFF964 Length = 505 Score = 320 bits (820), Expect = 7e-92 Identities = 181/481 (37%), Positives = 271/481 (56%), Gaps = 11/481 (2%) Query: 3 EIKHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALK-GPWGKL 61 E + ++NG + +A+G F ++P +G+ + + +++ D AV AARAA + G W +L Sbjct: 26 EGRAYLNGTYQWAANGEAFTSVSPIDGRELASIASCDQSDADQAVMAARAAFEAGIWSQL 85 Query: 62 SVAERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNV 121 + A+R +L R A+ I A DE E LD GKP + AS++D+P A + A+ + V Sbjct: 86 APAKRKAVLLRFAELIEAHGDELALLETLDMGKPINHASNVDVPATARAIRWTAEAIDKV 145 Query: 122 ANEAFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSE 181 E P I R P GV+ I PWN P+++ WK+ PALA GN+V++KPSE Sbjct: 146 YGEL----APTPHNQIGMISREPMGVVAAIVPWNFPMIMAAWKIAPALATGNSVILKPSE 201 Query: 182 ETPLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIM 241 ++PL+A L + AGVPAGV+NV+ G+G + G L H DVD FTG T + +M Sbjct: 202 KSPLSAIRLAALAGEAGVPAGVFNVLPGYG-HTVGKALALHMDVDCLVFTGSTNVAKQLM 260 Query: 242 -RAAAKGVRQVSLELGGKNAGIVFADC-DMDKAIEGTLRSAFANCGQVCLGTERVYVERP 299 A +++V LE GGK+ IVFAD D+ KA + N G+VC R+ VE Sbjct: 261 IYAGQSNMKRVWLEAGGKSPNIVFADAPDLKKAAAEAASAIAFNQGEVCTAGSRLLVENS 320 Query: 300 IFDEFVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGV 359 I EFV + ++ G P D ++ G +V ++++ Y +G ++ GG Sbjct: 321 IRAEFVRLICEALKTWRPGHPLDPATTCGAIVDQAQLDRIIDYIGIGQSEGARLVEGG-- 378 Query: 360 PDMPAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLA 419 GG +VQPT++ G+++ + +EEIFGP + FDT +EA+ +AN YGLA Sbjct: 379 -QRILENTGGLFVQPTVFDGVNNQMRIASEEIFGPVLSVIGFDTADEAVAIANDSIYGLA 437 Query: 420 SAIWTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTEL 479 +A+WT N + AH+VA + AG VW+N + D+ FGG KQSG GR+ VH+ + YTEL Sbjct: 438 AAVWTSNINTAHKVAKALRAGSVWINHYDGGDMTAPFGGFKQSGNGRDKSVHAFDKYTEL 497 Query: 480 K 480 K Sbjct: 498 K 498 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: 651 Number of extensions: 45 Number of successful extensions: 7 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: 505 Length adjustment: 34 Effective length of query: 452 Effective length of database: 471 Effective search space: 212892 Effective search space used: 212892 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