Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_108402665.1 B9Z44_RS13465 dihydrolipoyllysine-residue acetyltransferase
Query= reanno::Smeli:SMc03203 (426 letters) >NCBI__GCF_003063475.1:WP_108402665.1 Length = 552 Score = 231 bits (588), Expect = 5e-65 Identities = 160/435 (36%), Positives = 232/435 (53%), Gaps = 42/435 (9%) Query: 2 GEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLG 61 G I +PD+G+ + ++E VKPGD ++ + L V +DKA++EIPS G + L Sbjct: 116 GPIEIHVPDIGD-FKDVAVIEVFVKPGDSIKVEQSLITVESDKASMEIPSSHAGVLKELK 174 Query: 62 AEVGDTVAVKAPLVRIE---TAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQP 118 +VGDTV + L +E +A A AA S A+A + P V++ + A A Sbjct: 175 VKVGDTVNIGDLLAILEGTVSAAAAPVAAAASAVAAVAPAAVAAPTTVAAAVAAVA---- 230 Query: 119 EKPAPKPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLF-- 176 AP AP AP L P ASP+VR ARE G+ L ++ G+G GRIT +D+ F Sbjct: 231 ---APAHAPG---APTLGL-PHASPSVRKFARELGVPLEELKGSGVKGRITQDDVQTFTK 283 Query: 177 -ISRGAEPLPAQT--------------GLV--------RKTAVEEVRMIGLRRRIAEKMS 213 + GA AQ GL+ + VE M +++ + Sbjct: 284 AVMSGATQTKAQAAKGGASAGGDGAGLGLIPWPKVDFAKFGPVERKEMGRIKKISGANLL 343 Query: 214 LSTSRIPHITYVEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNA 273 + IP +T ++ D+T LE R + N++ + K+T+L FL++A V + + P N+ Sbjct: 344 RNAVMIPAVTNHDDCDITDLEAFRVSTNKENEKSGVKVTMLAFLIKACVAALKKYPEFNS 403 Query: 274 TFDDHAGVIHRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTAT 333 + D A V + HIG A TP GL VPV+R + +G+ + E++ LA AR G Sbjct: 404 SLDGDALVYKNYW--HIGFAADTPNGLMVPVIRDCDKKGVLQISQEMSELAKKARDGKLG 461 Query: 334 RDELTGSTITISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSS 393 E+TG+T TISSLG IGG TP+IN PEVAI+GV K + PVW+G +FVPR ++ LS Sbjct: 462 PAEMTGATFTISSLGGIGGKYFTPIINAPEVAILGVCKSTMEPVWNGKEFVPRLMLPLSL 521 Query: 394 SFDHRVIDGWDAAVF 408 ++DHRVIDG AA F Sbjct: 522 TWDHRVIDGAAAARF 536 Score = 62.8 bits (151), Expect = 3e-14 Identities = 52/155 (33%), Positives = 76/155 (49%), Gaps = 28/155 (18%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 +K+PD+G+ E ++E VK GD V+ + L V +DKA++EIPS G V L +G Sbjct: 6 VKVPDIGD-FDEVAVIELLVKVGDTVKAEQSLITVESDKASMEIPSSTAGVVKELRVNLG 64 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125 D V + ++ +E AG A A P + P A A PVA + PAP Sbjct: 65 DKVKEGSVVLVVEAAGAA--AGPAAAPAAAA------PVAAA-------------PAPVA 103 Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVA 160 A AP ++A P AS + + + G D + VA Sbjct: 104 AAAP-----VAAAPSASGPIEIHVPDIG-DFKDVA 132 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: 500 Number of extensions: 16 Number of successful extensions: 6 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: 552 Length adjustment: 34 Effective length of query: 392 Effective length of database: 518 Effective search space: 203056 Effective search space used: 203056 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