Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate PfGW456L13_3737 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3737 Length = 496 Score = 323 bits (827), Expect = 1e-92 Identities = 186/464 (40%), Positives = 255/464 (54%), Gaps = 11/464 (2%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALK-GAWGRMSLAQRVEVLYAVADGINRRFDD 82 +P + + +A V+ AV ++ A K G W + A R +L + ++ Sbjct: 38 NPATGQTLCETLDAPLELVERAVQSSHKAFKSGVWSSLRPADRERILLNFTRLVEEHAEE 97 Query: 83 FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEM--PTPDGVGAINYAV 140 E GK +++AR +D+ + + + + F++ P P G + Sbjct: 98 LAQLETLSQGKSINMARALDLNATVEFMRYMSGWATKIEGQTFDVSIPLPPGAKFTAFTK 157 Query: 141 RRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPP 200 R PVGVV I PWN PLL+ WK+ PALA G TV++KP+ ETP TA L E+ AG+P Sbjct: 158 REPVGVVVGIVPWNFPLLIAAWKLMPALATGCTVIIKPAMETPLTAMRLAELALEAGIPA 217 Query: 201 GVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAA 260 GV+NVV G G S G LT HP V+ ++FTG T G+++ A + SLELGGKN Sbjct: 218 GVFNVVTGGGA-SVGGVLTQHPLVSKVSFTGSTAVGKSVGVACMENMTRFSLELGGKNPM 276 Query: 261 IVFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPE 320 IV AD D++KA++G + N GQVC R YV R I D+FV L M +G Sbjct: 277 IVLADADIEKAVQGAILGGLLNNGQVCAAASRFYVHRSIHDQFVEALAAAVSSMPIGAGM 336 Query: 321 DLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKG-GAWVQPTIWTGL 379 + + PL+S++ ++ VL + + A + GA VVTGG E L+G G +VQPTI + Sbjct: 337 NCDAAINPLVSRKQQQSVLKHIELARQQGARVVTGG------ELLEGDGFFVQPTILADI 390 Query: 380 GDDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVG 439 VAREE+FGP VMPFD E+ VI ANDN YGLA +WT +L +A + IE G Sbjct: 391 DHSMAVAREEVFGPVLGVMPFDDEDAVIELANDNRYGLAASLWTNDLGKAMNLVPRIEAG 450 Query: 440 IAWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCI 483 WVN+ L D FGG KQSG+GRE G +E YTELK+VCI Sbjct: 451 TVWVNAHVLLDPAMPFGGVKQSGMGREFGRAVIEAYTELKSVCI 494 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: 569 Number of extensions: 24 Number of successful extensions: 3 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: 496 Length adjustment: 34 Effective length of query: 451 Effective length of database: 462 Effective search space: 208362 Effective search space used: 208362 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