Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate GFF442 Psest_0447 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__psRCH2:GFF442 Length = 667 Score = 249 bits (636), Expect = 2e-70 Identities = 160/432 (37%), Positives = 220/432 (50%), Gaps = 35/432 (8%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 +++PD+G A ++E VK GD V D L + +DKA++EIP+P G V L +VG Sbjct: 242 VRIPDIGSS-GSANVIEVMVKAGDSVEADQSLITLESDKASMEIPAPKAGIVESLSIKVG 300 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQ---PE-KP 121 D ++ + G A P + EA +Q +A AP + PE K Sbjct: 301 DEARTGDLILTLRVQGTAPAKKPATKAEAAPQQ------------QAVAPNKQGVPEAKA 348 Query: 122 APKPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR-- 179 A PAPA K A PAVR+ ARE G++L V TGP GRI ED+ ++ Sbjct: 349 AATPAPAVSGPSKAGTKVHAGPAVRMLAREFGVELADVPATGPKGRILKEDVQAYVKNML 408 Query: 180 ---------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITY 224 G P+PA R VEEV M L + A + S +PH+T Sbjct: 409 HKVKQAPAEGATGGAGIPPIPA-IDFSRFGEVEEVAMTRLMQVGAANLHRSWLNVPHVTQ 467 Query: 225 VEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHR 284 E D+T LE R + KLT+LP L++A + E P N++ + R Sbjct: 468 FESADITELEAFRVAQKAIAEKAGVKLTVLPLLLKACAHLLKELPDFNSSLAPSGKALIR 527 Query: 285 HAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITI 344 VH+G A TP GL VPV+R+ + + + A E LA+ ART + D + G+ TI Sbjct: 528 KKYVHVGFAVDTPDGLMVPVIRNVDQKSLLQLAGEAAELAEKARTKKLSPDAMQGACFTI 587 Query: 345 SSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWD 404 SSLG IGG TP++N PEVAI+GV+K ++PVWDG F PR ++ LS S+DHRVI+G Sbjct: 588 SSLGHIGGTGFTPIVNAPEVAILGVSKATMQPVWDGKAFQPRLMLPLSLSYDHRVINGAA 647 Query: 405 AAVFVQRLKTLL 416 AA F +RL LL Sbjct: 648 AARFTKRLSELL 659 Score = 60.1 bits (144), Expect = 2e-13 Identities = 36/101 (35%), Positives = 56/101 (55%), Gaps = 4/101 (3%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 IK+PD+G + +A ++E VKPGD + + L + +DKA++EIPSP G V + +VG Sbjct: 127 IKVPDIGS-LGKASVIEIAVKPGDTIAAEQALITLESDKASMEIPSPAAGVVESISVKVG 185 Query: 66 DTVAVKAPLVRIETAG---EAGEAAPDSIPEALAEQVLDEP 103 D V ++ ++ A A AP S + +Q L EP Sbjct: 186 DEVGTGDLILVLKGAAPSKPAASKAPASQAASAPKQKLSEP 226 Score = 59.3 bits (142), Expect = 3e-13 Identities = 37/111 (33%), Positives = 57/111 (51%), Gaps = 5/111 (4%) Query: 6 IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65 I++PD+G G E E++E VK GD + D + + +DKA++EIP+P G V L ++G Sbjct: 5 IRVPDIGSG--EGEVIELFVKVGDRIEADQSILTLESDKASMEIPAPKAGVVKSLKVKLG 62 Query: 66 DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPP 116 D + L+ +E+ AAP +A AE + EA PP Sbjct: 63 DRLKEGDELLELESEDGQDSAAPS---QAAAEPAGAASGGPTDETEAPTPP 110 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: 650 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 426 Length of database: 667 Length adjustment: 35 Effective length of query: 391 Effective length of database: 632 Effective search space: 247112 Effective search space used: 247112 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