Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate YP_001312850.1 Smed_4110 transketolase domain-containing protein
Query= reanno::Smeli:SMc03202 (337 letters) >NCBI__GCF_000017145.1:YP_001312850.1 Length = 692 Score = 254 bits (649), Expect = 5e-72 Identities = 143/337 (42%), Positives = 200/337 (59%), Gaps = 21/337 (6%) Query: 3 RMTMIEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFRCTQGLQAKYGKTRCFDTPISESG 62 R+ M+ A+R +D M+ ++ VV+FGED+G GGV T GLQ KYG R FDT +SE G Sbjct: 373 RINMVTAIRRTLDHEMSVNERVVLFGEDIGAKGGVHAVTLGLQEKYGVVRVFDTSLSEEG 432 Query: 63 IVGTAIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTGGG 122 I+G A+GMA GL P EIQF Y PA +QL + IR+R++ F PI+VRM G Sbjct: 433 IIGRAVGMALAGLVPVPEIQFRKYAEPAIEQL-NDCGTIRWRTSNRFAAPIIVRMAGGFF 491 Query: 123 IFGGQTHSQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGPFD 182 G HSQ+ E F H G K+ VPSN DA GLL +A+ DPV+F E + + + P Sbjct: 492 KCGDPWHSQTNEVAFVHQPGWKIAVPSNAEDAVGLLRTALRGNDPVIFFEHRAMLDHP-- 549 Query: 183 GHHERPVTAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAEETGI 242 W++ P + +P GKA+ R+G +T++ +G MV AAAE GI Sbjct: 550 ---------WARR---PYPGDAFGLPFGKAKFTREGGDITIVTWGAMVPRCEAAAE--GI 595 Query: 243 DAEVIDLRSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYHLESPV 302 A+VIDLRSL+P D E ++ S ++T RC++VHE T+GFGAE+AA+V + F L++P+ Sbjct: 596 SADVIDLRSLMPWDSEAVIASVRRTRRCLIVHEDLGTAGFGAEIAAVVAQEAFIDLDAPI 655 Query: 303 VRLTGWDTPYPH---AQEWDYFPGPARVGRALAEAME 336 RLT D P PH +W P P R+ + + + +E Sbjct: 656 SRLTMPDIPSPHNPVLLDW-VVPSPERIRKKINDLLE 691 Lambda K H 0.321 0.138 0.424 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: 629 Number of extensions: 25 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: 337 Length of database: 692 Length adjustment: 34 Effective length of query: 303 Effective length of database: 658 Effective search space: 199374 Effective search space used: 199374 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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