Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 208541 DVU3027 glycolate oxidase, subunit GlcD
Query= BRENDA::A0A0G2K1W9 (482 letters) >MicrobesOnline__882:208541 Length = 461 Score = 241 bits (615), Expect = 4e-68 Identities = 147/462 (31%), Positives = 233/462 (50%), Gaps = 10/462 (2%) Query: 26 SQDFVEALKAVVGSPHVSTASAVRQHHGHDESMHRCRPPDAVVWPQNVDQVSRLASLCYN 85 S ++ +A++G +V T+ RQ + +D ++ P V+ P +Q+ +L LCY Sbjct: 3 SASLIKEFEAIIGKENVFTSEPDRQSYAYDSAVLDQVVPALVLRPTETEQLGKLVKLCYE 62 Query: 86 QGVPIIPFGTGTGVEGGVCA-VQGGVCISLTHMDQIMELNTEDFSVVVEPGVTRKALNTH 144 PI G GT + GG + G+ I +++I+E+N +D VVEPGV Sbjct: 63 NDHPITVRGAGTNLSGGTIPDKREGIVILTNSLNKIIEINEQDLYAVVEPGVVTAKFAAE 122 Query: 145 LRNSGLWFPVDPGADA--SLCGMAATGASGTNAVRYGTMRDNVINLEVVLPDGRLLHTAG 202 + GL++P DPG+ A +L G A A G ++YG +D V+ +E +G L+ T Sbjct: 123 VAKRGLFYPPDPGSQAVSTLGGNVAENAGGLRGLKYGVTKDYVMGIEFFDVNGGLVKTGS 182 Query: 203 RGRHYRKSAAGYNLTGLFVGSEGTLGIITSATLRLHPAPEATVAATCAFPSVQAAVDSTV 262 R K GYNL GL SEGTLG+ + TL+L P P+A+ A F V A ++ Sbjct: 183 RTV---KCVTGYNLAGLMAASEGTLGVFSQITLKLVPPPKASKAMMAVFDDVNKASEAVA 239 Query: 263 QILQAAVPVARIEFLDEVMMDACNRHSKLNCP--VAPTLFLEFHGSQQALAEQLQRTEAI 320 I+ A V +EF+D+ ++ +K P A L +E G + + Sbjct: 240 AIIAAHVVPCTLEFMDKSSINYVEDFTKAGLPREAAAILLIEVDGHPAQVEDDAATVVKA 299 Query: 321 TQDNGGSHFSWAKEAEKRNELWAARHNAWYAALALRPGSKAYSTDVCVPISRLPEILVET 380 +G + AK+A ++ +LW AR NA ALA R + D VP S++P ++ Sbjct: 300 LNASGATEVHVAKDAAEKFKLWEARRNA-LPALA-RARATTVLEDATVPRSQIPAMVKAI 357 Query: 381 KEELKASKLTGVIVGHVGDGNFHCILLVNPDDVEEQRRVKAFAENLGRRALALHGTCTGE 440 + K + GH GDGN H +L + D E RV++ + + AL+LHGT +GE Sbjct: 358 NDIAKKHNIAIGTFGHAGDGNLHPTILCDRRDKHEFERVESAVDEIFDVALSLHGTLSGE 417 Query: 441 HGIGLGKRQLLQEEVGPVGVETMRQLKDTLDPRGLMNPGKVL 482 HGIGL K + +++E +E R +K +DP+ ++NPGK++ Sbjct: 418 HGIGLAKSKWMEKETSKATIEYSRNMKRAIDPKYILNPGKII 459 Lambda K H 0.319 0.134 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: 495 Number of extensions: 25 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: 482 Length of database: 461 Length adjustment: 33 Effective length of query: 449 Effective length of database: 428 Effective search space: 192172 Effective search space used: 192172 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: 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