Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 212 bits (539), Expect = 1e-59 Identities = 121/346 (34%), Positives = 204/346 (58%), Gaps = 13/346 (3%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA I L +R YGA K+ + +D E DG ++GPSGCGK+TLL +++GL + Sbjct: 1 MAAIHLKQVRKTYGAGTKAVD--VIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEE 58 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 S G+I+ + V +L + R+IA VFQ +Y MTVY N+A+ L+ +G++++++D RV Sbjct: 59 ISSGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARV 118 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 + +++L + R + L+ Q+Q++++GR +VR LFDEPL+ +D ++ +R Sbjct: 119 QRAAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPA-VFLFDEPLSNLDAKLRVQMR 177 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 ++++LH T +YVTHDQ EA+T ++++VM G QIGTPAE++ RP+ TFV F Sbjct: 178 LEIQKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASF 237 Query: 241 IGSPGMNFMPARI--EGSTVKV--GDETLTLEYAPKTSGTAKTE--LGIRPEFIRLGREG 294 IGSP MN + ++ +G++ +V G+ + L +G A E LG+RPE + +G Sbjct: 238 IGSPPMNLLQGKLSADGASFEVSKGNASDILRLPQPLTGAAGQERILGVRPEHLLPILDG 297 Query: 295 ----MPITISKVEDIGRQKIVRARFADQPIAIVVPEDADIPADARV 336 + + + VE +G + +V AR Q + + P + + R+ Sbjct: 298 SAAQLSLEVELVEALGAELLVHARCGGQALVLRCPANVQVRTGQRI 343 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: 271 Number of extensions: 7 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: 364 Length adjustment: 29 Effective length of query: 327 Effective length of database: 335 Effective search space: 109545 Effective search space used: 109545 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