Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SMc02474 SMc02474 ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Smeli:SMc02474 Length = 356 Score = 208 bits (530), Expect = 2e-58 Identities = 126/324 (38%), Positives = 187/324 (57%), Gaps = 16/324 (4%) Query: 21 KDYSLKEVDHEWN----DGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNL 76 K Y+ EV H + +G AL+GPSGCGK+TLL +I+GL + S G +L GK V L Sbjct: 11 KSYAALEVVHGVSLSIAEGEFIALVGPSGCGKSTLLRMIAGLEEISDGEVLIGGKVVNPL 70 Query: 77 STQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRK 136 + + RNIA VFQ +Y M+V +N+ F L+ G++ ++D++V + M+ L RK Sbjct: 71 TPRERNIAMVFQSYALYPHMSVAENMGFNLKLSGLSRPEIDKKVGEAARMLALTELLDRK 130 Query: 137 AQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVY 196 L+ Q+Q+ ++GR +VR D LFDEPL+ +D ++ +R+++K LH++ T +Y Sbjct: 131 PSQLSGGQRQRAAMGRAIVR-DPAVFLFDEPLSNLDAKLRVQMRTEIKALHQKVATTSIY 189 Query: 197 VTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARIEGS 256 VTHDQ EA+T A+++VV+ G+I Q+GTP EL+ P++ FV FIGSP MN + ++ Sbjct: 190 VTHDQIEAMTLADRIVVLNGGRIEQVGTPLELYRTPANLFVAGFIGSPAMNVLDGTVDAD 249 Query: 257 ----TVKVGDETLTLEYAP--KTSGTAKTELGIRPEFIRLGREGMPIT--ISKVEDIGRQ 308 V++GD + + AP K +G+RPE G EG I VE G Q Sbjct: 250 DGEPAVRLGDGS-AIRIAPERKVRPGQAVRIGLRPEHFVAGGEGNAIAGQTLLVEPTGAQ 308 Query: 309 KIVRARFADQPIAIVVPEDADIPA 332 V FA + I VV D D PA Sbjct: 309 THVLFEFAGEQITAVV--DGDHPA 330 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: 309 Number of extensions: 16 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: 356 Length adjustment: 29 Effective length of query: 327 Effective length of database: 327 Effective search space: 106929 Effective search space used: 106929 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