Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate RR42_RS07370 RR42_RS07370 dihydrolipoamide acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Cup4G11:RR42_RS07370 Length = 554 Score = 254 bits (650), Expect = 4e-72 Identities = 157/436 (36%), Positives = 231/436 (52%), Gaps = 48/436 (11%) Query: 2 GEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLG 61 G +K+PD+G+ ++E HVKPGD + + L + +DKAT+++PSP G V + Sbjct: 122 GPVEVKVPDIGD-YDSVPVIEVHVKPGDTINAEDALVTLESDKATMDVPSPAAGVVKEVR 180 Query: 62 AEVGDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKP 121 +VGD VA ++ +E A A +AP A ++ A A P P Sbjct: 181 IKVGDNVAEGTLILILEGAASAAASAP----------------AAAAPAAAAAAPAPAPV 224 Query: 122 APKPAPAPREAPDLSAKPL--------ASPAVRLRARESGIDLRQVAGTGPAGRITHEDL 173 A PAP P AP +A ASP+VR ARE G+D+ +V GTGP GRIT +D+ Sbjct: 225 ASAPAPVPAAAPAAAAPVAGVTGTAAHASPSVRKFARELGVDVSRVPGTGPKGRITQDDV 284 Query: 174 DLFIS-----RGAEPLPA----------------QTGLVRKTAVEEVRMIGLRRRIAEKM 212 ++ A P A + R VE + +++ + Sbjct: 285 QAYVKGVMSGHAAAPAKAAAAPAGGGELNLLPWPKVDFTRFGEVESKPLSRIKKLSGANL 344 Query: 213 SLSTSRIPHITYVEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVN 272 + IPH+T +E D+T LE R +N++ + + K+T+L F+++A V + + P N Sbjct: 345 HRNWVMIPHVTNHDEADITELEAFRVQLNKEYEKQGVKVTMLAFMIKAAVAALKKFPNFN 404 Query: 273 ATFDDHAGVIHRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTA 332 A+ D V+ ++ +IG A TP GL VPV+++A+ +G+ + E+N LA AR G Sbjct: 405 ASLDGENLVLKQY--FNIGFAADTPNGLVVPVIKNADKKGVIEIGQEMNELAKLARDGKL 462 Query: 333 TRDELTGSTITISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLS 392 D++ G +ISSLG IGG TP+IN PEVAI+GV K +PVWDG QFVPR + LS Sbjct: 463 KPDQMQGGCFSISSLGGIGGTYFTPIINAPEVAIMGVCKSYQKPVWDGKQFVPRLTLPLS 522 Query: 393 SSFDHRVIDGWDAAVF 408 S+DHRVIDG +AA F Sbjct: 523 LSWDHRVIDGAEAARF 538 Score = 74.7 bits (182), Expect = 7e-18 Identities = 48/128 (37%), Positives = 66/128 (51%), Gaps = 19/128 (14%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 IK+PD+G+ A ++E HVKPGD + + L + +DKAT+++PSP G V + ++G Sbjct: 7 IKVPDIGDYDA-VPVIEVHVKPGDTINAEDALVTLESDKATMDVPSPQGGTVKEVRIKIG 65 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D VA LV +E AG+A A P A + A AP PAP P Sbjct: 66 DNVAEGTVLVMLEPAGQAATA--------------PAPAAAAPAPAAAAP----APAPTP 107 Query: 126 APAPREAP 133 APA AP Sbjct: 108 APAAASAP 115 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: 623 Number of extensions: 26 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: 554 Length adjustment: 34 Effective length of query: 392 Effective length of database: 520 Effective search space: 203840 Effective search space used: 203840 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