Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SM_b21216 SM_b21216 sugar ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Smeli:SM_b21216 Length = 360 Score = 213 bits (543), Expect = 5e-60 Identities = 130/356 (36%), Positives = 203/356 (57%), Gaps = 17/356 (4%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 M+ + + +IR YG + +LK +D G LLG SGCGK+TLLNII+GL + Sbjct: 1 MSALEIRNIRKRYG------EVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAE 54 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 PS G IL + V + + R+IA VFQ +Y ++V N+ F L R V +A+ D+ V Sbjct: 55 PSGGDILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAV 114 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 RD ++ + + RK L+ Q+Q++++GR LVRN LFDEPL+ +D ++ +R Sbjct: 115 RDTARLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNP-QVFLFDEPLSNLDAKLRMEMR 173 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 ++LKRLH+ T+VYVTHDQ EA+T A ++ VM DG+I Q+ P E+++RP+ +V F Sbjct: 174 TELKRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGF 233 Query: 241 IGSPGMNFMPARIEGSTVKVG--DETLTLEYAPKTSGTA--KTELGIRPEFIRL--GREG 294 +GSP MN + A + + +K+ +E L L A + A + ++GIRPE +RL G E Sbjct: 234 VGSPPMNILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEA 293 Query: 295 MPIT--ISKVEDIGRQKIVRARFADQPIAIVVPEDADIPADA--RVTFDPSAISIY 346 +T + VE G + + A Q I +P + + TFD +A+ ++ Sbjct: 294 QRLTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLF 349 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: 288 Number of extensions: 13 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: 360 Length adjustment: 29 Effective length of query: 327 Effective length of database: 331 Effective search space: 108237 Effective search space used: 108237 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: 49 (23.5 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