Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF2209 HP15_2163 sugar ABC transporter, ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Marino:GFF2209 Length = 366 Score = 365 bits (937), Expect = e-105 Identities = 190/364 (52%), Positives = 251/364 (68%), Gaps = 14/364 (3%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA I L + H+Y P DY+++++DH W+ GGAYALLGPSGCGK+T+LNIISGL+Q Sbjct: 1 MAEIQLKSLAHSYSDMPTGPDDYAIRQLDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQ 60 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 PS G +LFDGK V LS + RNIAQVFQFPVIYD+MTVYDNLAFPL+N V + + RV Sbjct: 61 PSEGDVLFDGKRVNELSPRDRNIAQVFQFPVIYDSMTVYDNLAFPLKNNKVPASKIKARV 120 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 +I E++++ +KA+ LTAD+KQK+S+GRGLVR DV+AILFDEPLTVIDP +KW LR Sbjct: 121 HEIAEVLEIEDKLYKKAKNLTADEKQKVSMGRGLVREDVSAILFDEPLTVIDPQLKWKLR 180 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 +LK++H+QF TMVYVTHDQ EA TFA+K+ VMY GQIVQ GTP ELFE+P+HTFVG+F Sbjct: 181 RKLKQIHEQFDITMVYVTHDQLEASTFADKIAVMYGGQIVQFGTPTELFEQPNHTFVGFF 240 Query: 241 IGSPGMNFMPAR------IEGSTVKVGDETLTLEYAPKTSGTAKTELGIRPEFIRLGREG 294 IGSPGMN + + GSTV V E+ ++ +T T ++GIRPEF+ + Sbjct: 241 IGSPGMNLIEVQRCPRGVCFGSTV-VSLESWQVDVLQRTRST-NIKIGIRPEFVEVSSVA 298 Query: 295 MPIT----ISKVEDIGRQKIVRARFADQPIAIVVPED--ADIPADARVTFDPSAISIYAD 348 T + VED+G KIV + + + + E+ A I + ++F + +Y D Sbjct: 299 SDDTFEAEVLDVEDLGTYKIVTVQLDHEKMKVRQSEEFAASIGSKVHLSFPRQWLKLYVD 358 Query: 349 SWRV 352 + V Sbjct: 359 EFLV 362 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: 390 Number of extensions: 10 Number of successful extensions: 1 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: 366 Length adjustment: 29 Effective length of query: 327 Effective length of database: 337 Effective search space: 110199 Effective search space used: 110199 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