Align Putative D-lactate dehydrogenase C713.03, mitochondrial; EC 1.1.2.4 (characterized)
to candidate H281DRAFT_00697 H281DRAFT_00697 FAD/FMN-containing dehydrogenase
Query= SwissProt::Q9C1X2 (526 letters) >FitnessBrowser__Burk376:H281DRAFT_00697 Length = 469 Score = 300 bits (768), Expect = 8e-86 Identities = 170/445 (38%), Positives = 256/445 (57%), Gaps = 11/445 (2%) Query: 76 STDPADLDAFNIDWMNKYRGKTQLALKPKTTQQVSEILKYCNQKKLAVVPQGGNTGLVGG 135 S D + DA DW + R + ++ L P+T V+ L+ + + VV QGG TGL GG Sbjct: 23 SLDASVADAHAGDWSDAPRVRPRMTLFPRTPAHVARALRVLAKHRQPVVVQGGLTGLAGG 82 Query: 136 SVPVFDEIVLNLGLMNQIHTFDEISGVITLDSGVILENADNFLAEKGYMFPLDLGAKGSC 195 + P E+ L+L +N I +FD I G +T+ +GV LE F+ + + FPLDLGA+G+C Sbjct: 83 ATPQAGEVALSLARVNAIESFDRIGGTLTVQAGVPLEQLQTFVEAEEWFFPLDLGARGTC 142 Query: 196 QVGGCAATAAGGLRLLRYGSLHGSILGMEAVLPDGTILDNLVTLRKDNTGLDIKQLFIGS 255 Q+GG AAT AGG R++R+G++ ILG+E LPDGT+L + + K+ TG+D+KQLFIGS Sbjct: 143 QIGGNAATNAGGNRVIRFGTMRDRILGLEVALPDGTVLSMMNRVTKNTTGIDLKQLFIGS 202 Query: 256 EGYLGVITKLSVICPKRPSSTNVAFFGVPSYENVLKAFSETRSHLTEILSAFELMDNTSQ 315 EG LGVIT+L + +PS+ N A V S+E+ + R+ L LS+FELM Sbjct: 203 EGSLGVITRLVLKLEPKPSAANTALCAVASFEDATRLLKYLRARLAS-LSSFELMWQDFM 261 Query: 316 TLVDKYSGTQRPLEDEHPFYVLVETQGSNKEHDEQKITALVEDLLEKEIISDGVLAQDES 375 + + + P ++ P YVLVET G + + D + +E +LE+ ++ D ++AQ Sbjct: 262 SAAMDIAQLKAPFDERFPVYVLVETLGESYDDDRLALEQSLERMLEEGVVQDVIIAQTID 321 Query: 376 QLRVLWERREGITECLAKAGSGVYKYDVSLPLPVLYDLVNDTKKRLIEFNLLDDTPEHPV 435 + LW RE + E L+K +D+ +P+ + V+D + L E P Sbjct: 322 HAKQLWAYRETVGELLSKLKPHA-AFDIGIPMDRMERFVDDARSSLSE--------RFPQ 372 Query: 436 IDVVGFGHMGDGNLHLNIAVRQFDKRVEKCLEPWVYEWVSRHRGSISAEHGLGLLKKPFV 495 + FGH+GDGNLHL ++ D +E +Y VS G ISAEHG+G++K+PF+ Sbjct: 373 QTHLFFGHLGDGNLHL-LSGPYADASNLLEVEELIYAAVSEAEGCISAEHGIGVIKEPFL 431 Query: 496 GYSKSKEMIHLMKTLKNVFDPNGIM 520 YS+S+ I LM LK + DP G++ Sbjct: 432 HYSRSEPEIELMNKLKALLDPTGML 456 Lambda K H 0.319 0.138 0.405 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: 536 Number of extensions: 27 Number of successful extensions: 4 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: 526 Length of database: 469 Length adjustment: 34 Effective length of query: 492 Effective length of database: 435 Effective search space: 214020 Effective search space used: 214020 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: 52 (24.6 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