Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate PfGW456L13_3737 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::Q1XGK8 (486 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3737 Length = 496 Score = 337 bits (863), Expect = 7e-97 Identities = 193/481 (40%), Positives = 270/481 (56%), Gaps = 10/481 (2%) Query: 7 FINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALK-GPWGKLSVAE 65 FI+G +V A G + +NP+ GQ + +A V+ AV+++ A K G W L A+ Sbjct: 21 FIDGQWV-LAEGDSIAVVNPATGQTLCETLDAPLELVERAVQSSHKAFKSGVWSSLRPAD 79 Query: 66 RAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEA 125 R IL + +E + E L GK ++A +D+ + + + + Sbjct: 80 RERILLNFTRLVEEHAEELAQLETLSQGKSINMARALDLNATVEFMRYMSGWATKIEGQT 139 Query: 126 FEMATP--DGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEET 183 F+++ P GA + R P GV+ I PWN PLL+ WK+ PALA G TV++KP+ ET Sbjct: 140 FDVSIPLPPGAKFTAFTKREPVGVVVGIVPWNFPLLIAAWKLMPALATGCTVIIKPAMET 199 Query: 184 PLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRA 243 PLTA L E+ AG+PAGV+NVV G GG S G LT+HP V +FTG T G+ + A Sbjct: 200 PLTAMRLAELALEAGIPAGVFNVVTG-GGASVGGVLTQHPLVSKVSFTGSTAVGKSVGVA 258 Query: 244 AAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDE 303 + + + SLELGGKN IV AD D++KA++G + N GQVC R YV R I D+ Sbjct: 259 CMENMTRFSLELGGKNPMIVLADADIEKAVQGAILGGLLNNGQVCAAASRFYVHRSIHDQ 318 Query: 304 FVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMP 363 FV L A S+ IG + + PLVS K ++ VL + + A G V+TGG + + Sbjct: 319 FVEALAAAVSSMPIGAGMNCDAAINPLVSRKQQQSVLKHIELARQQGARVVTGGELLE-- 376 Query: 364 AHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIW 423 G +VQPTI + AV EE+FGP + PFD E+ IELAN YGLA+++W Sbjct: 377 ---GDGFFVQPTILADIDHSMAVAREEVFGPVLGVMPFDDEDAVIELANDNRYGLAASLW 433 Query: 424 TENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNIC 483 T + +A + +IEAG VWVN+ L D FGG KQSG+GRE G +E YTELK++C Sbjct: 434 TNDLGKAMNLVPRIEAGTVWVNAHVLLDPAMPFGGVKQSGMGREFGRAVIEAYTELKSVC 493 Query: 484 V 484 + Sbjct: 494 I 494 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: 639 Number of extensions: 37 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: 496 Length adjustment: 34 Effective length of query: 452 Effective length of database: 462 Effective search space: 208824 Effective search space used: 208824 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