Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate 349868 BT0340 trimethylamine corrinoid protein 2 (TCP 2) (NCBI ptt file)
Query= reanno::Phaeo:GFF1319 (233 letters) >FitnessBrowser__Btheta:349868 Length = 602 Score = 186 bits (472), Expect = 9e-52 Identities = 96/213 (45%), Positives = 141/213 (66%) Query: 15 DEDLVQQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFV 74 +ED ++ ++D + G E E + G P ++ ++ M VG F+DG FV Sbjct: 389 EEDRMKPLYDAIVAGKLEPAVEVTKDAIAAGVLPQDIINGYMITAMGEVGQRFQDGKAFV 448 Query: 75 PEVLLAANAMKGGMAILKPLLAETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEV 134 P++L+A AMKG + +LKPLLA + +G +VIGTVKGD+HDIGKNLV+ M+EG GFEV Sbjct: 449 PQLLMAGRAMKGALELLKPLLAGNASATIGKIVIGTVKGDLHDIGKNLVASMLEGCGFEV 508 Query: 135 VDIGINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGA 194 ++IGI+ + ++EA++E++ DIL MSALLTTTM YM+ VI + E G RD V++GGA Sbjct: 509 INIGIDVTCDKFVEAVKENKADILCMSALLTTTMTYMQDVIRALEEAGIRDQVKVMIGGA 568 Query: 195 PLNEEFGKAIGADGYCRDAAVAVEMAKDFVARK 227 P+++ F IGADGY +A AV +AK + ++ Sbjct: 569 PVSQGFADEIGADGYSDNANTAVAVAKVLMGKR 601 Lambda K H 0.318 0.138 0.390 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: 375 Number of extensions: 25 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 233 Length of database: 602 Length adjustment: 30 Effective length of query: 203 Effective length of database: 572 Effective search space: 116116 Effective search space used: 116116 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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