Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Phaeo:GFF1915 Length = 363 Score = 209 bits (532), Expect = 9e-59 Identities = 119/330 (36%), Positives = 190/330 (57%), Gaps = 8/330 (2%) Query: 25 LKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNIA 84 LK ++ + G LLG SGCGK+TLLN I+GL + + G+I + ++VT + R +A Sbjct: 28 LKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAGLQEATEGQIWINDENVTWREPKDRGLA 87 Query: 85 QVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTADQ 144 VFQ +Y MTV NLAF LR V +A+ D+ V + ++ L R+ L+ Q Sbjct: 88 MVFQSYALYPKMTVRGNLAFGLRMNKVPKAEADKLVDEAARVLQLEELLDRRPGELSGGQ 147 Query: 145 KQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTEA 204 +Q++++GR LVR V+ LFDEPL+ +D ++ LR +LKRLH++ G TM+YVTHDQ EA Sbjct: 148 RQRVAIGRALVRK-VDVFLFDEPLSNLDAKLRAELRVELKRLHQELGATMIYVTHDQVEA 206 Query: 205 LTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARI-EGSTVKVGDE 263 LT A+++ VM DG + Q+ +P E++ RP++ +V F+G P MNF+ + E ++ D Sbjct: 207 LTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVGLPSMNFVNGVVTESGAIQTEDF 266 Query: 264 TLTLEYAPKTSGTA---KTELGIRPEFIR-LGREGMPITISKVEDIGRQKIVRARFADQP 319 L L+ S A + E+GIRPE + G + + VE +G ++++ + + Sbjct: 267 ELALDQCNLASTPAPGTEVEIGIRPEHVHPANAGGFMLDVGMVELLGSERLIWGKVGNTS 326 Query: 320 IAIVVPEDADIPA--DARVTFDPSAISIYA 347 I + D I + R+ P A S+++ Sbjct: 327 IVMRDDPDTTIRSGDQVRINLKPGAFSVFS 356 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: 285 Number of extensions: 15 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: 363 Length adjustment: 29 Effective length of query: 327 Effective length of database: 334 Effective search space: 109218 Effective search space used: 109218 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