Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate CA265_RS19585 CA265_RS19585 pyruvate dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_479 (423 letters) >FitnessBrowser__Pedo557:CA265_RS19585 Length = 562 Score = 203 bits (516), Expect = 1e-56 Identities = 139/434 (32%), Positives = 214/434 (49%), Gaps = 22/434 (5%) Query: 2 GTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGRVIALG 61 G VI+MP + + + E ++ WH KVGD V +D VLADV TDKA +++ G ++ +G Sbjct: 134 GVTVIRMPLLSDTMTEGVIAEWHKKVGDKVKDDDVLADVETDKATMEVMGYATGTLLHIG 193 Query: 62 GEPGEVMAVGSELIRIEVEGAGNLKESAQQAPTPTPAAQAPKPAPVATPEPVLEKTAAPR 121 E G V + + EG ++ P P A++ + AP A + + PR Sbjct: 194 VEKGAAAKVNGIIAIVGPEGT-DVSGILAGGSAPAPKAESAE-APKAEKSATVAEIETPR 251 Query: 122 CAPQAPVARDPDERPLASPAVRKHALDLGIQLRLVQGSGPAGRVLHEDLEAYLAQGPSVQ 181 + + D R ASP +K A D GI L V GS GR++ +D+E + + Sbjct: 252 TSSCGTTTDNGDSRVKASPLAKKIAKDKGIDLAQVAGSAEGGRIIKKDIENFKPSAAPAK 311 Query: 182 AKGGSGYAERHDEQQIPVIG---------------MRRKIAQRMQEATQRAAHFSYVEEI 226 A+ S A PVI MR+ IA+R+ E+ A HF I Sbjct: 312 AESASAPAAEKAAAPAPVIPQYVGEVKFTEAPVSQMRKVIAKRLAESLFTAPHFYLTISI 371 Query: 227 DITALEELRVHLNEKHGASRGKLTLLPFLVRALVVALRDFPQMNARYDDEAQVIHRSGAV 286 D+ R +N + K++ +++A+ VAL+ P +N+ + + I + Sbjct: 372 DMDNAMAARTAIN---AVAPVKVSFNDIVIKAVAVALKKHPAVNSSWGGDK--IRFNEHT 426 Query: 287 HVGVATQSDVGLMVPVVRHAEARSLWDNAAEISRLATAARTGKASRDELSGSTITLTSLG 346 ++GVA + GL+VPVVR A+ +SL +AE+ A+ K + GST T+++LG Sbjct: 427 NIGVAMAVEDGLLVPVVRFADGKSLSHISAEVKDFGGKAKAKKLQPADWEGSTFTVSNLG 486 Query: 347 ALGGIVSTPVLNLPEVAIVGVNKIVERPVVIKGQIVIRKMMNLSSSFDHRVVDGMDAAQF 406 G T ++N P+ AI+ V I + PVV G +V +M L+ DHRVVDG AQF Sbjct: 487 MFGIDEFTSIINSPDGAILSVGAIQQVPVVKNGAVVPGNVMKLTLGCDHRVVDGATGAQF 546 Query: 407 IQALRGLLEQPATL 420 +Q L+GLLE+P L Sbjct: 547 LQTLKGLLEEPIRL 560 Score = 57.4 bits (137), Expect = 1e-12 Identities = 38/108 (35%), Positives = 56/108 (51%), Gaps = 4/108 (3%) Query: 5 VIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGRVIALGGEP 64 VIKMP + + + E L+ WH KVGD V VLA+V TDKA +D+ S G ++ +G E Sbjct: 4 VIKMPKMSDTMTEGVLAKWHKKVGDKVKSGDVLAEVETDKATMDMESYWDGTLLYVGVEE 63 Query: 65 GEVMAVGSELIRIEVEG----AGNLKESAQQAPTPTPAAQAPKPAPVA 108 G + V + + I EG A E + + +P ++ AP A Sbjct: 64 GTAVPVDAIMAVIGKEGEDYKAALEAEQSGSQESGSPKSERKDEAPKA 111 Lambda K H 0.317 0.133 0.375 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: 562 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 423 Length of database: 562 Length adjustment: 34 Effective length of query: 389 Effective length of database: 528 Effective search space: 205392 Effective search space used: 205392 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 (21.6 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