Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate SMa0244 SMa0244 Dehydrogenase, FAD-dependent
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__Smeli:SMa0244 Length = 481 Score = 172 bits (436), Expect = 2e-47 Identities = 150/476 (31%), Positives = 233/476 (48%), Gaps = 43/476 (9%) Query: 20 EIVADLADLLPEGGLISDERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYG 79 E+ L +L E ++S+ + F D +AV+ P +T+ VAA +K C G Sbjct: 15 ELRLALRQMLGEDIVLSETEEMLRFCRDWHGDVTTGTVAVIRPRSTQQVAAAVKACRELG 74 Query: 80 IPIVPRGAGTSLSGGAIPQ--EDAIVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAV 137 + IVP+G T L GAIP E +V+ LS+M+R ID + +A V++G + DA+ Sbjct: 75 LSIVPQGGNTGLVLGAIPDAPERQVVLSLSRMNRIRKIDPADFSAVVESGCILSELKDAI 134 Query: 138 SADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LGG 196 + G F+ +Q +C IGGN+ N+GG + L+YG+T +LG+++VL DG+++E L Sbjct: 135 AKMGMFFPLALGAQGSCQIGGNVSTNAGGVNVLRYGMTRELVLGLEVVLPDGSILEGLST 194 Query: 197 KALDAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGARPVLFGFASSESA--------G 248 D G DL L G+EG LGI+T ++ L P+ L G AS E A Sbjct: 195 LRKDNRGIDLKQLFIGAEGTLGIITAVSITLTPYPDHVATALLGLASLEDAIRLYRRARR 254 Query: 249 SCVADIIGSGIIPVAIEFMDRPAIEIC-EAFAQAGYPLDVE--ALLIVEVEGSE-AEMDA 304 C D++ A EFM A + EA P+ E A +++E+ GS ++D Sbjct: 255 DC-CDLMS------AFEFMPPLAFTLAQEAMPDLPIPISAEYPAYVLMEISGSGLVDVDD 307 Query: 305 TLAGIIEIARRHGVM---TIRESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQ 361 + +E A G++ TI SQ+ +A +W R+ + ++ D +VPLSQ Sbjct: 308 LMQRFLEGAMEEGLVLDGTIAASQT--QARNLWLIREGMNEGQAKRGTHMRTDISVPLSQ 365 Query: 362 LSHVLRRTGEIV--AGYGLRVANVFHAGDGNMHPLILYNI-NDPEEAA----RAEAAGND 414 L+ + + V A G + H GDGN+H +L + PEE +A+ N+ Sbjct: 366 LASFVEEAEKAVSEALPGAVSVSYGHVGDGNVHLNVLPPAGSTPEERIQLIYKAKTVVNE 425 Query: 415 ILKLCVEAGGCLTGEHGVGIEKR---DLMLHQYSRADLGQQMAARAAFDPQWLMNP 467 +L G ++ EHG+G KR D L R L A + A DP+ +MNP Sbjct: 426 VLD---RYTGSISAEHGIGRLKRPDFDARLPATRRKLL---TALKHAVDPEMIMNP 475 Lambda K H 0.320 0.138 0.404 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: 560 Number of extensions: 26 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: 479 Length of database: 481 Length adjustment: 34 Effective length of query: 445 Effective length of database: 447 Effective search space: 198915 Effective search space used: 198915 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