Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Pf1N1B4_4424 D-2-hydroxyglutarate dehydrogenase
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4424 Length = 474 Score = 171 bits (433), Expect = 5e-47 Identities = 141/471 (29%), Positives = 221/471 (46%), Gaps = 24/471 (5%) Query: 19 REIVADLADLLPEGGLISDERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRY 78 R + L LL + S+E + TD Y +A V P +TE VAAV++ C Sbjct: 3 RPLFVALQQLLGARHVQSNEEAAA-YLTDKQGRYVGQVIAAVHPASTEEVAAVVRACVAC 61 Query: 79 GIPIVPRGAGTSLSGGAIPQED--AIVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDA 136 P+V +G T L GGA P A+++ L +M+R +D N T TV+AG I D Sbjct: 62 DTPVVVQGGNTGLMGGATPDASGRAVLLLLDRMNRVRAVDTDNDTLTVEAGCILQTIQDV 121 Query: 137 VSADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LG 195 G + ++ +CTIGGN+G N+GG L+YG T +LG+++V G + L Sbjct: 122 ARDAGRLFPLSLGAEGSCTIGGNLGTNAGGTAVLRYGNTRELILGLEVVTAQGEIWNGLR 181 Query: 196 GKALDAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGARPVLFGFASSESAGSCVADI- 254 G D GYDL L GSEG LGI+T AT++L P+ L F S A + ++ Sbjct: 182 GLRKDNTGYDLRDLFIGSEGTLGIITAATLKLFPLPKAQATALLAFDSLAQAVTFLSHAR 241 Query: 255 IGSGIIPVAIEFMDRPAIEIC-EAFAQAGYPL-----DVEALLIVEVEGSEAEMDATLAG 308 G G A E ++ + + E F + P ALL + SE+ Sbjct: 242 AGFGASLTAFELLNAECLALLREQFPEGPQPFLGARQPWFALLELSDNHSESHAREAFEQ 301 Query: 309 II-EIARRHGVMTIRESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQLSHVLR 367 ++ E + + ++S ++ +W R++ A R + D +VP+SQ+ + Sbjct: 302 VLGEAFEQRLLADALIAESLAQSQALWLLRENMSEAQKRAGRNMKHDISVPISQVVAFVA 361 Query: 368 RTGEIVAGY--GLRVANVFHAGDGNMHPLILYNINDPEEAARAE-----AAGNDILKLCV 420 T ++ + G+R H GDGN+H YN+ P+++ AA + ++ Sbjct: 362 DTDALLQCHFPGVRHYTFGHLGDGNLH----YNVAHPQDSTVEAHMVHYAALSQLVHDSA 417 Query: 421 EA-GGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKV 470 A GG ++ EHG+G KRD++ S +L + A DP+ L+NP KV Sbjct: 418 HAHGGSISAEHGIGQHKRDMLGRYKSPVELDLMRRIKQALDPKNLLNPGKV 468 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: 542 Number of extensions: 29 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: 474 Length adjustment: 33 Effective length of query: 446 Effective length of database: 441 Effective search space: 196686 Effective search space used: 196686 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