Align L-lactate dehydrogenase; EC 1.1.1.27 (characterized)
to candidate CA265_RS03080 CA265_RS03080 malate dehydrogenase
Query= CharProtDB::CH_024078 (330 letters) >FitnessBrowser__Pedo557:CA265_RS03080 Length = 312 Score = 221 bits (564), Expect = 1e-62 Identities = 124/316 (39%), Positives = 180/316 (56%), Gaps = 14/316 (4%) Query: 17 KISLIGSGNIGGVMAYLAQLKELG-DVVLFDIAPKLGAAKALDIMHANAIYDTSQNVIGT 75 K++++G+G +G A KEL ++VL DI KA+D+M + + G Sbjct: 2 KVTVVGAGAVGATCADNIARKELANELVLLDIKEGFAEGKAIDMMQTATLLGFDTKITGV 61 Query: 76 TS-YEDIAGSDVCIITAGLAKLPNKSDDEWSRDDLVAPNSKIMFTIGENIKKYAPNAFVI 134 T Y AGSDV +IT+GL + P + R++L+ N+ I+ + ENI K++P A I Sbjct: 62 TGDYSKTAGSDVVVITSGLPRKPGMT-----REELIGINAGIVKGVAENILKFSPEAIFI 116 Query: 135 CITNPLDVMVKMLLKSTGFPKNKVVGMGGLLDSSRMCHYIADKLRVNPRYVHGSCIGGHG 194 I+NP+D M + LKS G PKN+++GMGG LDSSR Y++ L NP + G IGGHG Sbjct: 117 VISNPMDTMTYLALKSLGLPKNRIIGMGGTLDSSRFKFYLSQALNCNPNDLQGFVIGGHG 176 Query: 195 D-SMIPLTNHVTVNGIPIQRFIERGEITQAELDKIAERTIGSGMELVQLYGNGSAFFAPA 253 D +MIPLT T +P+ +++ A LDK+A T+ G L L G SA++AP Sbjct: 177 DTTMIPLTRLATYQSLPVSNLLDK-----ATLDKVAADTMVGGATLTGLIGT-SAWYAPG 230 Query: 254 TAAIEMASAYLSDKRSVIVCSCYLEGEYGHNDVYLGTPAIIGANGIEKIITLKLSAEEQA 313 A + A L D++ + C LEGEYG D+ LG P IIG NG EKII KL+ +EQA Sbjct: 231 AAGAALVEAILRDEKKLFTCCVSLEGEYGQEDICLGVPVIIGRNGWEKIIDFKLTDDEQA 290 Query: 314 KLDASVKEIRRLEALV 329 + S +R + +++ Sbjct: 291 AFNKSADAVRNMNSVL 306 Lambda K H 0.319 0.136 0.390 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: 280 Number of extensions: 10 Number of successful extensions: 6 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: 330 Length of database: 312 Length adjustment: 28 Effective length of query: 302 Effective length of database: 284 Effective search space: 85768 Effective search space used: 85768 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 (21.7 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