Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate CA265_RS09620 CA265_RS09620 FAD-binding oxidoreductase
Query= BRENDA::O29853 (443 letters) >FitnessBrowser__Pedo557:CA265_RS09620 Length = 467 Score = 260 bits (665), Expect = 6e-74 Identities = 168/448 (37%), Positives = 245/448 (54%), Gaps = 23/448 (5%) Query: 12 EVFPPSDA---YRFDETPPLVAPRAAENFVVVKPSNSEEVSAILKFANEKSIPVFMRGGG 68 +VF +D+ Y DET L + VVVKP+ EEVSA+LK N +PV RGGG Sbjct: 22 KVFTDADSLENYSHDETEDL----RYQPEVVVKPTTPEEVSALLKICNAHHVPVTPRGGG 77 Query: 69 TGLSGGAVPTEEGIVLSTEKMTE-LEVDADNRVAICGAGVTLKQLDDAAFRHGLSFPPHP 127 TGLSG A+P GI LS EK L++D +N A GV ++ +A GL +P P Sbjct: 78 TGLSGAALPIYGGISLSMEKFKAILDIDTENLQATVEPGVITEEFINAVAEKGLLYPVDP 137 Query: 128 GAE-TATVGGMIATNAGGVRALKYGTMRNYVLSLEAVLADGRIINVGGKTIKNSSGYSLL 186 ++ + +GG +A +GG R +KYGT+R Y+L+LE VL +G II G T+K +SGY+L Sbjct: 138 SSKGSCFIGGNVAHGSGGPRVVKYGTIREYILNLEVVLPNGDIIWTGANTLKYASGYNLT 197 Query: 187 HLLVGSEGTLAVITKATIRLFPQMRDMTVLAIPFPTMEDAMNCVVEVARK-MLPMALEFM 245 L++GSEGTLAV+TK +L P+ ++ F T EDA V + R + P ALEFM Sbjct: 198 QLMIGSEGTLAVVTKIVTKLLPKPSQSVLMMGSFSTNEDACAAVSAIFRAGVTPSALEFM 257 Query: 246 EKRAVEIGEKVSGERWVSREGEAHLLMVFESFDEAEEAAK-------IAQSLGAIDVYAA 298 E++ VE K ++ ++ A LLM+ D+ ++ K + + +V A Sbjct: 258 ERKGVEWVIKFDDIKFDLKDDVAALLMIEFDGDDLDDIFKNCEKTNIVLEEHNCTEVLFA 317 Query: 299 TTKKDQDRLLKVRGMIYEGLR-KEVIEVLDACVPPAKIAEYWRRSNELAEEYGIELITYG 357 T ++ L ++R + E ++ V + D VP A + + E+ +YG E + YG Sbjct: 318 DTAAQKEELWRMRRTMAESVKSNSVYKEEDTVVPRAALPKLVNGIKEIGAKYGFESVCYG 377 Query: 358 HAGDGNVH----QHPLVYEGWEKSYFEFRKSLLSLAVSLGGVISGEHGIGAVKLSELEEL 413 HAGDGN+H + + E W+ + L +LGG +SGEHGIG V+ + Sbjct: 378 HAGDGNLHVNIIKAGMSDEDWKNKLKFGIAEIFELTTALGGTLSGEHGIGLVQKEFMPIK 437 Query: 414 FPE-QFELMRQIKLLFDPKNILNPGKVV 440 + E LMR IK +FDPK ILNPGK++ Sbjct: 438 YSEIHLNLMRGIKNIFDPKGILNPGKIM 465 Lambda K H 0.317 0.136 0.388 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: 502 Number of extensions: 25 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: 443 Length of database: 467 Length adjustment: 33 Effective length of query: 410 Effective length of database: 434 Effective search space: 177940 Effective search space used: 177940 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: 51 (24.3 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