Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate RR42_RS26120 RR42_RS26120 dihydrolipoamide acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Cup4G11:RR42_RS26120 Length = 540 Score = 224 bits (571), Expect = 5e-63 Identities = 154/436 (35%), Positives = 225/436 (51%), Gaps = 41/436 (9%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 +++PD+G+ + ++E VK GD VR + L ++ +DKAT+++P+P+ G V + +VG Sbjct: 113 VRIPDIGD-FKDIPVIEIFVKVGDTVRAEDALLSLESDKATMDVPAPLGGVVREIRVKVG 171 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 DTV+ + ++ + T G+A A + P A AV++ L A A P A Sbjct: 172 DTVSEGSIIMALAT-GDAPAVAATAAPGAAP--------AVAAALAAPAAPAATAAATAA 222 Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISRGAEPLP 185 A + A ASPAVR ARE+G+DL +V G+G GRI D++ F G P Sbjct: 223 AASGGVDEAAFALAYASPAVRKLARETGVDLGKVRGSGEHGRILRADVEAFARTGGPAAP 282 Query: 186 A--------------------QTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYV 225 A + + VE + +++ + + IPH+T Sbjct: 283 AARPAAAPAGGGAGLDLLAWPKVDFAKFGPVERKELSRIKKISGANLHRNWVVIPHVTTH 342 Query: 226 EEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRH 285 +E D+T LE R MN++ + K+++LPF+M+A V T+ P NA+ D V+ ++ Sbjct: 343 DEADITDLELFRVQMNKELEKSGVKISMLPFMMKAAVATLKAFPEFNASLDGDTLVLKQY 402 Query: 286 AAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITIS 345 HIG A TP GL VPV+R + + I D A E+ LA AR G D+++G T TIS Sbjct: 403 --YHIGFAADTPNGLMVPVIRDVDKKSIPDIAREMGELAKLAREGKLKPDQMSGGTFTIS 460 Query: 346 SLGAIGGIASTPVINHPEVAIVGVNKIAVRPVW-----DGAQFVPRKIMNLSSSFDHRVI 400 SLG IGGI TP+IN PEVAI+GV K W DG + R + LS S+DHRVI Sbjct: 461 SLGGIGGINFTPIINAPEVAIMGVCK----SFWKQHSSDGKNWASRLTLPLSLSWDHRVI 516 Query: 401 DGWDAAVFVQRLKTLL 416 DG AA F LL Sbjct: 517 DGAAAARFNVHFANLL 532 Score = 57.4 bits (137), Expect = 1e-12 Identities = 40/128 (31%), Positives = 64/128 (50%), Gaps = 27/128 (21%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 IK+PD+G+ + ++E VK GD V+ + L ++ +DKAT+E+P+P G V + ++G Sbjct: 7 IKVPDIGD-FRDVPVIELFVKVGDLVKAEDPLVSLESDKATMEVPAPHGGVVKQIHVKLG 65 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V+ + L++ E AG AG AA + P Q KP+ Sbjct: 66 DAVSEGSVLMQFEGAG-AGTAAAE-------------------------PAQATKPSVSA 99 Query: 126 APAPREAP 133 P+P AP Sbjct: 100 PPSPVSAP 107 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: 550 Number of extensions: 24 Number of successful extensions: 7 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: 540 Length adjustment: 34 Effective length of query: 392 Effective length of database: 506 Effective search space: 198352 Effective search space used: 198352 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: 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