Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF964 HP15_943 aldehyde dehydrogenase family protein
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Marino:GFF964 Length = 505 Score = 302 bits (774), Expect = 2e-86 Identities = 176/462 (38%), Positives = 262/462 (56%), Gaps = 13/462 (2%) Query: 22 SSSPLNNAVIAKVHEAGRAEVDAAVAAAQAALK-GAWGRMSLAQRVEVLYAVADGINRRF 80 S SP++ +A + +++ D AV AA+AA + G W +++ A+R VL A+ I Sbjct: 46 SVSPIDGRELASIASCDQSDADQAVMAARAAFEAGIWSQLAPAKRKAVLLRFAELIEAHG 105 Query: 81 DDFLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDG-VGAINYA 139 D+ E D GKP++ A +VD+P A + A+ + V E PTP +G I+ Sbjct: 106 DELALLETLDMGKPINHASNVDVPATARAIRWTAEAIDKVYGEL--APTPHNQIGMIS-- 161 Query: 140 VRRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVP 199 R P+GVV I PWN P+++ WK+ PALA GN+V++KPSE++P +A L + AGVP Sbjct: 162 -REPMGVVAAIVPWNFPMIMAAWKIAPALATGNSVILKPSEKSPLSAIRLAALAGEAGVP 220 Query: 200 PGVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIM-KAAADGARPVSLELGGKN 258 GV+NV+ G+G ++ G+ L H DV+ + FTG T + +M A + V LE GGK+ Sbjct: 221 AGVFNVLPGYG-HTVGKALALHMDVDCLVFTGSTNVAKQLMIYAGQSNMKRVWLEAGGKS 279 Query: 259 AAIVFADC-DLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLG 317 IVFAD DL KA + N G+VC R+ VE I FV + + + + G Sbjct: 280 PNIVFADAPDLKKAAAEAASAIAFNQGEVCTAGSRLLVENSIRAEFVRLICEALKTWRPG 339 Query: 318 RPEDLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWT 377 P D AT G ++ Q ++++ Y GA +V GG + GG +VQPT++ Sbjct: 340 HPLDPATTCGAIVDQAQLDRIIDYIGIGQSEGARLVEGG---QRILENTGGLFVQPTVFD 396 Query: 378 GLGDDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIE 437 G+ + +A EEIFGP V+ FD+ +E + AND+ YGLA +WT+N++ AH+VA A+ Sbjct: 397 GVNNQMRIASEEIFGPVLSVIGFDTADEAVAIANDSIYGLAAAVWTSNINTAHKVAKALR 456 Query: 438 VGIAWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELK 479 G W+N + D+ FGG KQSG GR+ VH+ + YTELK Sbjct: 457 AGSVWINHYDGGDMTAPFGGFKQSGNGRDKSVHAFDKYTELK 498 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: 588 Number of extensions: 35 Number of successful extensions: 6 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: 505 Length adjustment: 34 Effective length of query: 451 Effective length of database: 471 Effective search space: 212421 Effective search space used: 212421 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 17 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