Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__PS:Dsui_2943 Length = 356 Score = 134 bits (338), Expect = 3e-36 Identities = 83/246 (33%), Positives = 133/246 (54%), Gaps = 14/246 (5%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA + L + YGA+ D + G LLGPSGCGKTTLL I+G Sbjct: 1 MAHLELADVMQRYGAHTVVDG------IGFHIEAGVIACLLGPSGCGKTTLLRCIAGFED 54 Query: 61 PSHGRILFDGKDVTN----LSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADV 116 + G I DG+ V+ L+ + R I VFQ ++ +TV DN+AF L+ +G + Sbjct: 55 IAAGSIALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKG---GER 111 Query: 117 DRRVRDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMK 176 +RV +L+++ LA + L+ Q+Q+++L R L +L DEP + +D ++ Sbjct: 112 QQRVAAMLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAP-RLVLLDEPFSNLDVDLR 170 Query: 177 WVLRSQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTF 236 L +++ + K+ G T + VTHDQ EA A+++ VM++G+I Q TP L+ +P++ F Sbjct: 171 ERLSLEVREILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRF 230 Query: 237 VGYFIG 242 V F+G Sbjct: 231 VADFVG 236 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: 282 Number of extensions: 14 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: 356 Length adjustment: 29 Effective length of query: 327 Effective length of database: 327 Effective search space: 106929 Effective search space used: 106929 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