Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 209 bits (533), Expect = 7e-59 Identities = 125/352 (35%), Positives = 198/352 (56%), Gaps = 29/352 (8%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA+++L +++ Y N K + +D E NDG ++GPSGCGK+TLL +++GL Sbjct: 1 MAKLSLRNVQKTYAGNVKV-----VHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEA 55 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 S G + K V +L R+IA VFQ +Y M+VYDN+A+ L+ RG+ ++++++RV Sbjct: 56 ISGGEVHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRV 115 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 + +++LA RK + L+ Q+Q++++GR +VR LFDEPL+ +D ++ +R Sbjct: 116 KHAAGILELAPLLERKPRALSGGQRQRVAMGRAIVREPA-VFLFDEPLSNLDAKLRVQMR 174 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 +LK LH++ T +YVTHDQ EA+T A++++V+ G + QIGTP E++ RP+ TFV F Sbjct: 175 LELKELHRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASF 234 Query: 241 IGSPGMNFMP-ARIEGSTVKVGDETLTLEYAPKTSGTAKT--------------ELGIRP 285 IGSP MN +P R G G+ + +E P G T LG+RP Sbjct: 235 IGSPPMNLVPVTRTNGGQ---GEAQMRVEQKPGAQGAPATLGHLPMGLHLPERALLGLRP 291 Query: 286 EFIR--LGREGM-PITISKVEDIGRQKIVRARFADQPIAIVVPEDADIPADA 334 E I E + I + VE +G QP +VV D+++P + Sbjct: 292 EHIEPCAAHEAIAEIEVRLVEALGADSYAYGTLGGQP--VVVRLDSNMPVSS 341 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: 18 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: 367 Length adjustment: 29 Effective length of query: 327 Effective length of database: 338 Effective search space: 110526 Effective search space used: 110526 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