Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_086511415.1 BZY95_RS18770 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >NCBI__GCF_002151265.1:WP_086511415.1 Length = 673 Score = 241 bits (616), Expect = 4e-68 Identities = 161/433 (37%), Positives = 228/433 (52%), Gaps = 33/433 (7%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 I++PD+ G ++ ++E V GD V E+ L + +DKA++++PSP GK++ L + G Sbjct: 244 IRVPDLS-GSSDVPIIEIAVSAGDEVNEEDPLITLESDKASMDVPSPYKGKLIELTVKEG 302 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAP---PQPEKPA 122 DTV+ + IE AG A P AEQ P + + A P P PE A Sbjct: 303 DTVSEGDLIGYIEVAGSKPAAKKADKP---AEQKAAAPSSAKADKPASTPGGTPSPE--A 357 Query: 123 PKPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR--- 179 A PR+ + A PAVR+ ARE G+DL V +GP R+ ED+ ++ + Sbjct: 358 QMAAHKPRDGKLVHA----GPAVRMLARELGVDLGLVKPSGPKDRVLKEDVHAYVKQVMA 413 Query: 180 ----------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHIT 223 G P+P Q + VEE M L + A + S +PH+T Sbjct: 414 GQAKAPAAAPTATGGAGIPPVPDQD-FSQFGEVEEKPMGRLLKMGATNLHRSWLNVPHVT 472 Query: 224 YVEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIH 283 +E D+T LE R M + + + AKLT LPFL++A + + P N + I Sbjct: 473 QFDEADITELEAFRKAMKAEAEAQGAKLTPLPFLIKACAFALRKFPQFNVSLKSDGETIV 532 Query: 284 RHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTIT 343 VHIGIA TP GL VPV+R A+ + + D A E LA A++ R+E+TG T Sbjct: 533 WKKYVHIGIAVDTPDGLMVPVIRDADKKSLIDLAKESVELAGKAQSKKLKREEMTGGCFT 592 Query: 344 ISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGW 403 ISSLG+IGG A TP++N PEVAI+GV+K ++PVW+GA F PR +M LS S+DHR ++G Sbjct: 593 ISSLGSIGGTAFTPIVNAPEVAILGVSKAQMKPVWNGADFEPRLMMPLSLSYDHRAVNGA 652 Query: 404 DAAVFVQRLKTLL 416 DAA F L L Sbjct: 653 DAARFTAFLAAAL 665 Score = 72.4 bits (176), Expect = 4e-17 Identities = 48/131 (36%), Positives = 73/131 (55%), Gaps = 10/131 (7%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 IK+PD+G G E++E V GD V E+ L + +DKA++++PSP GK++ L + G Sbjct: 130 IKVPDLG-GSENVEIIEVAVAEGDEVAEEDTLITLESDKASMDVPSPYGGKLVSLTVKEG 188 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 DTV+ + +E AGE GE P+ PEA+ + EP +A+AP + E + +P Sbjct: 189 DTVSEGDVIGTMEIAGEGGEDEPE--PEAV--ETTAEPAE-----QAEAPAEEEAVSGEP 239 Query: 126 APAPREAPDLS 136 PDLS Sbjct: 240 ERREIRVPDLS 250 Score = 62.4 bits (150), Expect = 4e-14 Identities = 43/127 (33%), Positives = 68/127 (53%), Gaps = 8/127 (6%) Query: 1 MGEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWL 60 M IIK+PD+G G + E++E V GD ++ + L + +DKA++++PSP GKV+ + Sbjct: 1 MSSEIIKVPDIG-GSEDVEIIEIAVSEGDVIQPEDTLITLESDKASMDVPSPKGGKVVRV 59 Query: 61 GAEVGDTVAVKAPLVRIETAGEAGEAAPDSIPEA-LAEQVLDEPVAVSSRLEAKAPPQPE 119 + GDTV+ +V +E G + S +A AE +E +S+ A E Sbjct: 60 LVKEGDTVSEGDDIVELEVEGSGSSSDAGSEEQAEPAEPKREEASGQASQAAA------E 113 Query: 120 KPAPKPA 126 KPA K A Sbjct: 114 KPAAKKA 120 Lambda K H 0.317 0.133 0.384 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: 709 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 426 Length of database: 673 Length adjustment: 35 Effective length of query: 391 Effective length of database: 638 Effective search space: 249458 Effective search space used: 249458 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 24 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