Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Dino:3607842 Length = 351 Score = 209 bits (533), Expect = 7e-59 Identities = 116/291 (39%), Positives = 169/291 (58%), Gaps = 4/291 (1%) Query: 28 VDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNIAQVF 87 VD DG +GPSGCGK+TLL +I+GL + S G I +DVT L R +A VF Sbjct: 22 VDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEGSIHIGARDVTRLDPSERGVAMVF 81 Query: 88 QFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTADQKQK 147 Q +Y MTV +N+ F L+ GV +A++ +V E++ L + RK + L+ Q+Q+ Sbjct: 82 QTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAASEILKLDDYLARKPKALSGGQRQR 141 Query: 148 ISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTEALTF 207 +++GR +VR LFDEPL+ +D ++ +R ++ RLHK+ G TM+YVTHDQ EA+T Sbjct: 142 VAIGRAIVRGP-EVFLFDEPLSNLDAELRVEMRVEIARLHKEIGATMIYVTHDQVEAMTL 200 Query: 208 AEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARIEGSTVKV-GDETLT 266 A+K+VV+ G++ Q+G P EL+ P + FV FIGSP MNF+ RIE V + G L Sbjct: 201 ADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPAMNFLDGRIENDAVHLAGLPPLP 260 Query: 267 LEYAPKTSGTAKTELGIRPEFIRLGREGMPITISKVEDIGRQKIVRARFAD 317 + A SG +G+RP+ I L G + E +G + R AD Sbjct: 261 VPGAAGRSG--PVTVGVRPQHIALEPGGDGYLVELTESLGGVSYLYLRGAD 309 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: 297 Number of extensions: 12 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: 351 Length adjustment: 29 Effective length of query: 327 Effective length of database: 322 Effective search space: 105294 Effective search space used: 105294 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