Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate Dsui_1577 Dsui_1577 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__PS:Dsui_1577 Length = 555 Score = 249 bits (636), Expect = 1e-70 Identities = 157/437 (35%), Positives = 235/437 (53%), Gaps = 30/437 (6%) Query: 2 GEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLG 61 G +K+PD+G+ + ++E VK GD V+++ L ++ +DKAT+++PS G V + Sbjct: 119 GPVEVKVPDIGD-FKDVPVIEVFVKVGDTVKQEDALCSLESDKATMDVPSSAAGVVKEVR 177 Query: 62 AEVGDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKP 121 +VGD V+ + +V +E G AG A + A A P + L+ AP +P P Sbjct: 178 VKVGDKVSEGSVVVVLE--GAAGAVAAVAAAPAAAAPAPAAPAVIPPELDGPAPTKPFTP 235 Query: 122 APKPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFIS--- 178 AP AP L K ASP+VR ARE G+DL +V TGP RI ED+ +I Sbjct: 236 APAAAPYGLA---LGGKVHASPSVRAFARELGVDLSKVTATGPKSRIQAEDVKAYIKGVM 292 Query: 179 RGAEPLPAQTG-------------------LVRKTAVEEVRMIGLRRRIAEKMSLSTSRI 219 G P Q G + +E + +++ ++ + I Sbjct: 293 SGQTVAPTQVGGGGITGGGSLDLLPWPKVDFAKFGPIEAKPLSRIKKISGANLARNWVMI 352 Query: 220 PHITYVEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHA 279 P +TY E+ D+T LE R +N++ + KLT+L F+++A VK + + P +N + D Sbjct: 353 PAVTYHEDADITDLEAFRVQLNKENEKSGQKLTMLAFIIKACVKVLQQFPELNTSLDGDN 412 Query: 280 GVIHRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTG 339 V ++ HIG A TP GL VPV++ A+ +G+ + A E LA AR G ++ G Sbjct: 413 LVYKKY--YHIGFAADTPNGLVVPVLKDADKKGVLEIAKETGELAKLARDGKLKPADMQG 470 Query: 340 STITISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRV 399 +T TISS+G IGG A +P++N PEVAI+GV+K +++PVW+G +FVPR I+ LS S DHRV Sbjct: 471 ATFTISSVGGIGGTAFSPIVNAPEVAILGVSKSSMKPVWNGKEFVPRLIVPLSLSADHRV 530 Query: 400 IDGWDAAVFVQRLKTLL 416 IDG A F L LL Sbjct: 531 IDGALATRFNAELAKLL 547 Score = 67.8 bits (164), Expect = 8e-16 Identities = 48/133 (36%), Positives = 73/133 (54%), Gaps = 14/133 (10%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 +K+PD+G+ + ++E VKPGD V+ + L ++ +DKAT+++PS G V + +VG Sbjct: 7 VKVPDIGD-FKDVPVIEIFVKPGDTVKVEDPLCSLESDKATMDVPSSAAGVVKEVKIKVG 65 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D VA + +V +E+A +G AA P+A A PVA A A P P AP P Sbjct: 66 DKVAEGSVVVILESAA-SGAAAAAPAPQAAA----PAPVAA-----APAAPAPVAAAPAP 115 Query: 126 A---PAPREAPDL 135 A P + PD+ Sbjct: 116 AASGPVEVKVPDI 128 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: 559 Number of extensions: 29 Number of successful extensions: 5 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: 426 Length of database: 555 Length adjustment: 34 Effective length of query: 392 Effective length of database: 521 Effective search space: 204232 Effective search space used: 204232 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