Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_038022060.1 HA49_RS08470 sulfate/thiosulfate ABC transporter ATP-binding protein CysA
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_000757425.2:WP_038022060.1 Length = 362 Score = 184 bits (466), Expect = 4e-51 Identities = 109/307 (35%), Positives = 178/307 (57%), Gaps = 18/307 (5%) Query: 4 ITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSH 63 I + I ++G P L ++D + + G ALLGPSG GKTTLL II+GL + Sbjct: 3 INIHQINKSFGKTPV------LNDIDLDISSGEMVALLGPSGSGKTTLLRIIAGLEHQNS 56 Query: 64 GRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPL----RNRGVAEADVDRR 119 GRI F +DV++L + R++ VFQ ++ MTV+DN+AF L R ++AD+ ++ Sbjct: 57 GRISFRDRDVSHLHARDRHVGFVFQHYALFRHMTVFDNIAFGLTVLPRRERPSQADIRKK 116 Query: 120 VRDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVL 179 V ++LEM+ L+ A R L+ QKQ+++L R L D + +L DEP +D ++ L Sbjct: 117 VLNLLEMVQLSHLAGRYPAQLSGGQKQRVALARALAV-DPHILLLDEPFGALDAQVRKEL 175 Query: 180 RSQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGY 239 R L++LH++ FT V+VTHDQ EA+ A+++VVM G + Q GTP +++++P+ FV Sbjct: 176 RRWLRQLHEELQFTSVFVTHDQEEAMEVADRIVVMSQGNVEQTGTPEQVWKQPASRFVLE 235 Query: 240 FIGSPGMNFMPARIEGSTVKVGDETLTLEYAPKTSGTAKTELGIRP---EFIRLGREGMP 296 F+G +N + ++ G+ ++V L++ P G + +L +RP + R E P Sbjct: 236 FLGE--INRLQGQLVGNKLQVAGHQWPLDFTPAVQG--EVDLFLRPWETDISRGQSEATP 291 Query: 297 ITISKVE 303 + + VE Sbjct: 292 LPVKVVE 298 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: 313 Number of extensions: 15 Number of successful extensions: 3 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: 362 Length adjustment: 29 Effective length of query: 327 Effective length of database: 333 Effective search space: 108891 Effective search space used: 108891 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 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