Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Pf1N1B4_171 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_171 Length = 477 Score = 312 bits (799), Expect = 2e-89 Identities = 191/477 (40%), Positives = 259/477 (54%), Gaps = 14/477 (2%) Query: 16 VSVGSRSSSPLNNA----VIAKVHEAGRAEVDAAVAAAQAALK-GAWGRMSLAQRVEVLY 70 V G + PL+N V+ V A +VD AV AA+ A AW R +R +L+ Sbjct: 8 VEAGDGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRPRERQNLLW 67 Query: 71 AVADGINRRFDDFLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFE--MP 128 +AD + R + E + GK ++A+ +D+ + A + E MP Sbjct: 68 KLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLSIDFLRYMAGWATKIEGSSVEVSMP 127 Query: 129 TPDGVGAINYAVRRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAAL 188 ++ R VGVVG I WN PLLL WK+GPALA G TVV+KP++ETP TA Sbjct: 128 LMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADETPLTALK 187 Query: 189 LGEVMNTAGVPPGVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGAR 248 L E++ AG P GV+NVV G G + G LT +P V+ +TFTG T G+ I K A + Sbjct: 188 LAELVLEAGYPAGVFNVVTGTGITA-GSALTHNPLVDKLTFTGSTAVGKQIGKIAMESMT 246 Query: 249 PVSLELGGKNAAIVFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLK 308 V+LELGGK+ IV AD DL A G + F N GQVC R+YV+R FD V+ + Sbjct: 247 RVTLELGGKSPTIVMADADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDNVVADIA 306 Query: 309 KGAEGMQLGRPEDLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGG 368 A M+LG D + MGPLIS +E+V Y +K E+GAT+ GG E G Sbjct: 307 DIANAMKLGNGLDPSVEMGPLISARQQERVYGYIEKGRESGATIACGG------EQFGPG 360 Query: 369 AWVQPTIWTGLGDDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSR 428 +V+PT+ + + +EEIFGP + +PFD E + +R AND+ YGL IW+ +L+ Sbjct: 361 YFVKPTVIVDVDQQHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSNDLAA 420 Query: 429 AHRVAGAIEVGIAWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 HR+ I+ G WVN D FGG K SG+GRE G ++E YTELK+V IKL Sbjct: 421 VHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELKSVLIKL 477 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: 562 Number of extensions: 25 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: 485 Length of database: 477 Length adjustment: 34 Effective length of query: 451 Effective length of database: 443 Effective search space: 199793 Effective search space used: 199793 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: 51 (24.3 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