Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_028998012.1 H537_RS0111250 dihydrolipoyllysine-residue acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >NCBI__GCF_000430725.1:WP_028998012.1 Length = 559 Score = 243 bits (619), Expect = 1e-68 Identities = 159/435 (36%), Positives = 230/435 (52%), Gaps = 36/435 (8%) Query: 2 GEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLG 61 G +K+PD+G+ E ++E VKPGD ++ + L V +DKA++EIPS G V + Sbjct: 117 GTIEVKVPDIGD-FKEVAVIEVFVKPGDQIKVEQSLITVESDKASMEIPSSHAGTVKEVL 175 Query: 62 AEVGDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKP 121 ++GD V+ + +V +E G AG AAP P A A P A S + APP P Sbjct: 176 VKLGDKVSEGSLVVVLE--GAAGAAAPAPAPAAAAPAAA--PAATVSAPDV-APPATRTP 230 Query: 122 APKPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR-- 179 PA P ASP++RL+AR+ G+ L +V G+G GRIT +DL F+ Sbjct: 231 PTAALPAHEPTAAKGVLPHASPSIRLQARQLGVPLEEVKGSGLKGRITQDDLQNFVKSVM 290 Query: 180 --------GAEPLPAQT----------GLVRKTAVEEVRMIGLRRRIAEKMSLSTSR--- 218 A PA T GL+ V+ + + R+ ++ + Sbjct: 291 AGTTLTKAAAAKAPAATVGAAAGGAFPGLLPWPQVDFAKFGPVERKDLSRIKKISGANLH 350 Query: 219 -----IPHITYVEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNA 273 IPH+T ++ D+T LE R +N++ + K+T+L FL++A V + + P NA Sbjct: 351 RNWVVIPHVTNHDDADITELEAFRVQLNKENEKSGVKVTMLAFLIKAAVAALKKFPEFNA 410 Query: 274 TFDDHAGVIHRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTAT 333 + D V+ ++ HIG A TP GL VPV++ A+ +GI+ + E++ LA AR G Sbjct: 411 SLDGDQVVLKQY--FHIGFAADTPNGLMVPVIKDADKKGIFQISQEMSELAKKARDGKLG 468 Query: 334 RDELTGSTITISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSS 393 E+TG +ISSLG IGG TP+IN PEVAI+GV K + P WDG QFVPR + LS Sbjct: 469 PAEMTGGCFSISSLGGIGGRYFTPIINAPEVAILGVCKSTMEPKWDGKQFVPRLTLPLSL 528 Query: 394 SFDHRVIDGWDAAVF 408 S+DHR +DG AA F Sbjct: 529 SWDHRAVDGAAAARF 543 Score = 70.9 bits (172), Expect = 1e-16 Identities = 52/155 (33%), Positives = 78/155 (50%), Gaps = 27/155 (17%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 + +PD+G+ E ++E VKPGD V+E+ L V +DKA++EIPS +G V + A++G Sbjct: 6 VLVPDIGD-FKEVAVIEVLVKPGDTVKEEQSLITVESDKASMEIPSSRSGVVKEILAKIG 64 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V+ + +VR+ET G A AAP P A A P+P P Sbjct: 65 DKVSEGSLVVRMET-GAAEAAAPAPAPAAAA------------------------PSPAP 99 Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVA 160 A AP A A A + ++ + G D ++VA Sbjct: 100 AAAPAAAAPAPAPAAAGGTIEVKVPDIG-DFKEVA 133 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: 548 Number of extensions: 23 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: 559 Length adjustment: 34 Effective length of query: 392 Effective length of database: 525 Effective search space: 205800 Effective search space used: 205800 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