Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 204 bits (520), Expect = 2e-57 Identities = 115/314 (36%), Positives = 183/314 (58%), Gaps = 6/314 (1%) Query: 24 SLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNI 83 ++ +V E G LLGPSGCGK+T L +I+GL + GRI+ +DVT+L R + Sbjct: 18 AVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRIMIGERDVTHLPPAQRQL 77 Query: 84 AQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTAD 143 A VFQ ++ +TV +N+ F L R V EA+ ++R+ ++++ L++ +RK L+ Sbjct: 78 AMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDILGLSALLQRKPGELSGG 137 Query: 144 QKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTE 203 Q+Q+++LGR LV + L DEPL+ +D ++ +R +++ L + G TMVYVTHDQTE Sbjct: 138 QQQRVALGRALVA-EAAVCLMDEPLSNLDAKLRHEMRREIRALQQTLGMTMVYVTHDQTE 196 Query: 204 ALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPA-RIEGSTVKVGD 262 A++ A+++++M G+IVQ TP+EL+ RP+ TF G FIG+P MN + GS G Sbjct: 197 AMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPMNLVRLDDARGSVCVAGS 256 Query: 263 ETLTLEYAPKTSGTAKTELGIRPEFIRLGREGMPITISKVEDIGRQKIVRARFADQPIAI 322 + T+ +A LGIRPE IR+ EG + VE +G ++ R + +++ Sbjct: 257 RSGTVSVV----DSADYVLGIRPEHIRIVPEGWRAVVESVEYLGSGSVLGCRVGGEELSV 312 Query: 323 VVPEDADIPADARV 336 VV I A + Sbjct: 313 VVDGVPTIAVGAEI 326 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: 276 Number of extensions: 9 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: 350 Length adjustment: 29 Effective length of query: 327 Effective length of database: 321 Effective search space: 104967 Effective search space used: 104967 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