Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 162 bits (411), Expect = 1e-44 Identities = 85/240 (35%), Positives = 141/240 (58%), Gaps = 3/240 (1%) Query: 14 GANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDV 73 G + K +++E D G LLGPSGCGKTT+L +I+GL P+ G I G+ + Sbjct: 49 GLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIKGRRI 108 Query: 74 TNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWA 133 + RN+ +FQ ++ T+++N+AF L+ R V+ ++ +V LEM+ L Sbjct: 109 NDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVRLPGVE 168 Query: 134 RRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFT 193 +R A L+ Q+Q+I+L R +V + + +L DEPL+ +D ++ +R ++ + +Q T Sbjct: 169 KRYASQLSGGQQQRIALARAIV-IEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQLNLT 227 Query: 194 MVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARI 253 ++VTHDQ EAL+ + K+VVM DG+ Q GTP ++++ P + FV F+G NF AR+ Sbjct: 228 TLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGH--ANFFDARV 285 Lambda K H 0.321 0.137 0.405 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: 347 Number of extensions: 19 Number of successful extensions: 2 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: 356 Length of database: 406 Length adjustment: 30 Effective length of query: 326 Effective length of database: 376 Effective search space: 122576 Effective search space used: 122576 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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