Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate PfGW456L13_1617 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= BRENDA::F8A9V0 (325 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1617 Length = 321 Score = 137 bits (345), Expect = 4e-37 Identities = 100/303 (33%), Positives = 149/303 (49%), Gaps = 22/303 (7%) Query: 16 LGPILPSDWDVEMTPDFLDETTVEKAKGAQVVSLFVSDKADGPVLEALHSYGVGLLALRS 75 L P+ D+++ L + +E KGA V +S+K S + L+ + + Sbjct: 22 LDPLRSCFGDLQLFAQTLPDQVIEHLKGATVA---ISNKILIDAAAMAASPDLKLILITA 78 Query: 76 AGYDHIDIETAKRLGIKVVNVPAYSPHAIADHTLAIMLALIRRLHRAHDKVRLG------ 129 G +++D+ A+ GI V N Y ++A HT+ ++L L RL V G Sbjct: 79 TGTNNVDLAAARAHGITVCNCQGYGTPSVAQHTIMLLLNLATRLADYQKAVGEGRWQQAK 138 Query: 130 DFDLDGLMGFDLNGKVAGVIGLGKIGRLVATRLKAFGCKV-LGYDPYIQPEIVENVDLDT 188 F L +L GK G++G G++G VA +AFG +V LG P +P + + LD Sbjct: 139 QFCLLDYPIVELEGKTLGLLGHGELGGAVARLAEAFGMRVVLGQIPG-RPARPDRLPLDE 197 Query: 189 LITQADIISIHCPLTRENFHMFNEETFKRMKPGAILVNTARGGLIDTKALLEALKSGKLG 248 L+ Q D +++HCPL H MKPGA +VNTARGGLID +AL AL++G LG Sbjct: 198 LLPQVDALTLHCPLNEHTRHFIGARELAAMKPGAFVVNTARGGLIDEQALANALRNGHLG 257 Query: 249 GAALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLANVVLTGHQAFLTREAVKNIEETTVE 308 GAA DV E + +P LA + +++T H A+ +REA + I E Sbjct: 258 GAATDVLSVEPPV---------NGNPLLAH--DIPRLIVTPHNAWGSREARQRIVGQVTE 306 Query: 309 NIL 311 N L Sbjct: 307 NAL 309 Lambda K H 0.321 0.140 0.407 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: 210 Number of extensions: 10 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: 325 Length of database: 321 Length adjustment: 28 Effective length of query: 297 Effective length of database: 293 Effective search space: 87021 Effective search space used: 87021 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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