Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate PfGW456L13_3396 Fumarylacetoacetate hydrolase family protein
Query= metacyc::MONOMER-16233 (285 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3396 Length = 283 Score = 136 bits (343), Expect = 5e-37 Identities = 93/250 (37%), Positives = 131/250 (52%), Gaps = 19/250 (7%) Query: 37 ALAAAKGADVA-----SLPLVEGEPRYGVPVKGIGKIVAIGLNYEDHAIESNLPIPTEPM 91 A+AA +G SLPL + R P++ I ++V G NY H +E L P +P+ Sbjct: 38 AVAAGRGISSVRFAGPSLPL--SKVRLLPPIEPINRVVVAGANYAKHLVEFGLQAPAQPV 95 Query: 92 MFMKALSSLNGPNDEVVLPKNSTHGDWEVELGVVIGETCRFVSEDEALSKVAGYVLVNDV 151 F+KA +L G ND + P + D EVEL VIG + + L+ V GY + NDV Sbjct: 96 AFLKAYGALIGANDSIRFPPLTEELDHEVELVAVIG--TEEIDLENPLACVLGYTVGNDV 153 Query: 152 SERFNQKQR----GTQWSKGKGHDTFCPVGPWLVTPDEV--GDPQDLDMHLNVNGTRMQT 205 S R Q+ G K D +GPW+VT DE G P+ L + L VNG Q Sbjct: 154 SARDLQRSGPAGIGMDLFAAKSQDQTTGLGPWIVTKDEFPEGSPR-LRLTLKVNGEVRQD 212 Query: 206 GNTKTMIFNVAQLISYVSEYITLYPGDLMITGTPPGVGEGKKPQAIYLKAGDVMELGIEK 265 G+T M ++V QLI +V + + GD++ TG+P GVG G ++LK GDV+E +E Sbjct: 213 GSTGEMTWDVGQLIRFVQQRSSFASGDVLFTGSPAGVGMG---TGLFLKEGDVVEASVEG 269 Query: 266 LGTQRQQVSE 275 +GT R VS+ Sbjct: 270 IGTLRNVVSK 279 Lambda K H 0.316 0.137 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: 221 Number of extensions: 15 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: 285 Length of database: 283 Length adjustment: 26 Effective length of query: 259 Effective length of database: 257 Effective search space: 66563 Effective search space used: 66563 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: 42 (22.0 bits) S2: 47 (22.7 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