Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate GFF3163 Psest_3223 Lactate dehydrogenase and related dehydrogenases
Query= BRENDA::F8A9V0 (325 letters) >FitnessBrowser__psRCH2:GFF3163 Length = 319 Score = 146 bits (368), Expect = 8e-40 Identities = 107/321 (33%), Positives = 163/321 (50%), Gaps = 32/321 (9%) Query: 2 KVIFFSMHPYEEEFLG--PILPSDWDVEMTPDFLDETTVEKAKGAQV-----VSLFVSDK 54 + +F + P E+ L P+ + ++ + VE+ +GAQV VSL Sbjct: 4 RAVFLDLSPLEQGDLDLDPLRNAFSELVCHEQSTTDQIVERLQGAQVAIVNKVSLTAETL 63 Query: 55 ADGPVLEALHSYGVGLLALRSAGYDHIDIETAKRLGIKVVNVPAYSPHAIADHTLAIMLA 114 A P L+ L+ + + G ++ID++ A+ GI V N AY +A HTL ++LA Sbjct: 64 AACPELK--------LILVSATGVNNIDLQAARERGIVVSNCQAYGTPTVAQHTLMLLLA 115 Query: 115 LIRRLHRAHDKVRLGDFDLDG---LMGF---DLNGKVAGVIGLGKIGRLVATRLKAFGCK 168 L RL V G + G L+ F +L GK G++G G++G VA +AFG + Sbjct: 116 LATRLPDYQAAVARGRWQESGQFCLLDFPIVELEGKTLGLLGHGELGSAVARLAEAFGMR 175 Query: 169 VLGYDPYIQPEIVENVDLDTLITQADIISIHCPLTRENFHMFNEETFKRMKPGAILVNTA 228 VL + +P+ E +DLD L+ Q D +++HCPLT + ++ + MKP A L+N A Sbjct: 176 VLVGNLPGRPKRPERLDLDELLPQVDALTLHCPLTEQTRNLIGARELQLMKPTAFLINAA 235 Query: 229 RGGLIDTKALLEALKSGKLGGAALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLANVVLT 288 RGGL+D +AL +AL+ G LGGAA DV E +P LA L +++T Sbjct: 236 RGGLVDEQALADALRRGHLGGAATDVLTSE---------PPRDDNPLLAP--DLPRLIIT 284 Query: 289 GHQAFLTREAVKNIEETTVEN 309 H A+ +REA + I EN Sbjct: 285 PHSAWGSREARQRIVAQLAEN 305 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: 197 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: 319 Length adjustment: 28 Effective length of query: 297 Effective length of database: 291 Effective search space: 86427 Effective search space used: 86427 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