Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate HSERO_RS04810 HSERO_RS04810 aldehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__HerbieS:HSERO_RS04810 Length = 504 Score = 283 bits (725), Expect = 7e-81 Identities = 166/461 (36%), Positives = 248/461 (53%), Gaps = 12/461 (2%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P + G A V+AA AAQ A + W +S A R LYAV I + Sbjct: 43 NPATGRASLSYRDGGAAAVEAAAVAAQRAQR-QWWALSHAARGRALYAVGAVIRAEAEPL 101 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 E +GKP+ R ++ + A F+ +A E +P+ +NY R P Sbjct: 102 ARLEAISSGKPIRDCR-AEMQKVAEMFEYYAGWADKFYGEVIPVPSSH----LNYTRREP 156 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 G V + PWN P W++GPALA GN V++KPSE TP ++ + + AG+P G+ Sbjct: 157 YGTVLQMTPWNAPAFTCGWQLGPALATGNAVLLKPSELTPFSSLAIARLGEQAGLPAGLV 216 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 NV+ G G + + + V + F G TG I KAAA P LELGGK+A I+F Sbjct: 217 NVLAGLGQTMVPQAMATWT-VKKVIFVGSPATGALIAKAAAARVMPCVLELGGKSANIIF 275 Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323 D DL A G + F+ GQ C+ R+ V+R ++DRFV + GAE ++LG P D + Sbjct: 276 EDADLRLAAFGAQAAIFSGAGQSCVAGSRLLVQRKVYDRFVETVAAGAEKIRLGAPLDDS 335 Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383 T +GP+ +++ E + + +EAGAT+ G + G +V+PT+ + Sbjct: 336 TEVGPINNRKQYEHIQRMVARGLEAGATLAAGH-----TRYGEEGYFVRPTLLAHASNAM 390 Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443 VAR EIFGP A+ +PF+ EEE I AND+++GLA +WT +++RAHRVA ++ G WV Sbjct: 391 EVARSEIFGPVAVAIPFEDEEEAIAIANDSEFGLAGAVWTRDVARAHRVAASVNAGTFWV 450 Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIK 484 NS+ ++ + FGG +SG GR G+ +L YT+ K+V ++ Sbjct: 451 NSYKTINVASPFGGFNRSGYGRSSGMEALYDYTQTKSVWVE 491 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: 573 Number of extensions: 18 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: 504 Length adjustment: 34 Effective length of query: 451 Effective length of database: 470 Effective search space: 211970 Effective search space used: 211970 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