Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_084456399.1 G494_RS0104020 hypothetical protein
Query= reanno::Smeli:SMc03203 (426 letters) >NCBI__GCF_000429965.1:WP_084456399.1 Length = 427 Score = 242 bits (617), Expect = 2e-68 Identities = 151/429 (35%), Positives = 237/429 (55%), Gaps = 40/429 (9%) Query: 8 MPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVGDT 67 +PD G+ V E ++E ++PG V ++ L ++ ++KA ++IP+P++G + + G Sbjct: 3 IPDFGD-VQEITVIEIFIRPGQRVEQEEALISLESEKAVMDIPAPLSGTIEEVLLREGQQ 61 Query: 68 VAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKP---APK 124 V L+ + TA E E PD+ PE A EA P +P P AP+ Sbjct: 62 VK-SGQLIALLTA-ERQEDRPDTPPEQTAAPA-----------EAPEPTEPAAPGGAAPR 108 Query: 125 PAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR----- 179 P P P+ A + A A+P+VR AR+ GIDL V +GP GR+ EDL+L + + Sbjct: 109 PGPPPK-AQEPGAPVHATPSVRAYARKLGIDLSLVQASGPKGRLLKEDLELLLRQAIRRH 167 Query: 180 ---GAEPLPAQTGLV----RKTAVEEVRMIG---------LRRRIAEKMSLSTSRIPHIT 223 G PA L ++ EE + G +++ E++ S IPH+T Sbjct: 168 QEDGNRAAPAGAALAAMDGKEYGEEEYALYGEISQLPLGRIQKISGERLHTSWLNIPHVT 227 Query: 224 YVEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIH 283 + E+ D++ LE+ R +NR+ + ++ +L++L F+++A+ T+A P VN++ VI Sbjct: 228 HFEQADISELEEFRQQLNRENEGKEPRLSLLVFVLKAVAATLAHFPLVNSSLAAGDRVIL 287 Query: 284 RHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTIT 343 +H H+G+A TP GL VPV+R E +G+ + EL L+ AAR G E+ G + T Sbjct: 288 KHH-YHLGVAVDTPQGLLVPVIRDVERKGVLEINRELRELSQAAREGRLQPGEMEGGSFT 346 Query: 344 ISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGW 403 ISSLG +GG TP+IN P+ AI+G+ K +++PVWDG+ F PR I+ S S+DHR+IDG Sbjct: 347 ISSLGKLGGTNFTPIINAPQAAILGLAKSSIQPVWDGSAFTPRLILPFSLSYDHRIIDGA 406 Query: 404 DAAVFVQRL 412 +AA F L Sbjct: 407 EAARFCAAL 415 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: 427 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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 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