Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 14261 b0115 dihydrolipoamide acetyltransferase (NCBI)
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Keio:14261 Length = 630 Score = 228 bits (582), Expect = 3e-64 Identities = 147/435 (33%), Positives = 223/435 (51%), Gaps = 45/435 (10%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 + +PD+G E E+ E VK GD V + L V DKA++E+P+P G V L VG Sbjct: 209 VNVPDIGGD--EVEVTEVMVKVGDKVAAEQSLITVEGDKASMEVPAPFAGVVKELKVNVG 266 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAP-PQPEKPAPK 124 D V + ++ E G A AAP ++ EA AP P + AP Sbjct: 267 DKVKTGSLIMIFEVEGAAPAAAP-------------------AKQEAAAPAPAAKAEAPA 307 Query: 125 PAPAPR-----EAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR 179 APA + E + A A+P +R ARE G++L +V GTG GRI ED+ ++ Sbjct: 308 AAPAAKAEGKSEFAENDAYVHATPLIRRLAREFGVNLAKVKGTGRKGRILREDVQAYVKE 367 Query: 180 G---AEPLPAQTG-------------LVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHIT 223 AE PA TG + +EEV + +++ +S + IPH+T Sbjct: 368 AIKRAEAAPAATGGGIPGMLPWPKVDFSKFGEIEEVELGRIQKISGANLSRNWVMIPHVT 427 Query: 224 YVEEVDMTALEDLRATMNRD--RKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGV 281 + ++ D+T LE R N + ++ K+T + F+M+A+ + + P N++ + Sbjct: 428 HFDKTDITELEAFRKQQNEEAAKRKLDVKITPVVFIMKAVAAALEQMPRFNSSLSEDGQR 487 Query: 282 IHRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGST 341 + ++IG+A TP GL VPV + +GI + + EL ++ AR G T E+ G Sbjct: 488 LTLKKYINIGVAVDTPNGLVVPVFKDVNKKGIIELSRELMTISKKARDGKLTAGEMQGGC 547 Query: 342 ITISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVID 401 TISS+G +G P++N PEVAI+GV+K A+ PVW+G +FVPR ++ +S SFDHRVID Sbjct: 548 FTISSIGGLGTTHFAPIVNAPEVAILGVSKSAMEPVWNGKEFVPRLMLPISLSFDHRVID 607 Query: 402 GWDAAVFVQRLKTLL 416 G D A F+ + L Sbjct: 608 GADGARFITIINNTL 622 Score = 58.2 bits (139), Expect = 7e-13 Identities = 45/142 (31%), Positives = 65/142 (45%), Gaps = 26/142 (18%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 IK+PD+G E E+ E VK GD V + L V DKA++E+PSP G V + VG Sbjct: 5 IKVPDIGAD--EVEITEILVKVGDKVEAEQSLITVEGDKASMEVPSPQAGIVKEIKVSVG 62 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D A ++ ++A A +AAP A AE + ++ AP Sbjct: 63 DKTQTGALIMIFDSADGAADAAP-----AQAE-------------------EKKEAAPAA 98 Query: 126 APAPREAPDLSAKPLASPAVRL 147 APA A D++ + S V + Sbjct: 99 APAAAAAKDVNVPDIGSDEVEV 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: 627 Number of extensions: 19 Number of successful extensions: 6 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: 630 Length adjustment: 35 Effective length of query: 391 Effective length of database: 595 Effective search space: 232645 Effective search space used: 232645 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