Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate 3607838 Dshi_1246 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q88P36 (281 letters) >FitnessBrowser__Dino:3607838 Length = 282 Score = 179 bits (453), Expect = 8e-50 Identities = 97/281 (34%), Positives = 162/281 (57%), Gaps = 7/281 (2%) Query: 4 PVDKPVLSLSRMAIHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGNLLSWPAVITGI-- 61 P++K + +++ ++ +A++L+L+PL+ + + S K D GN WPA G Sbjct: 5 PIEKAPRA-AQLTYQGMIPLALILWLLPLIAVAIFSVKPAGDFAAGNYWGWPAEFAGFEN 63 Query: 62 -GWVKAWGAVSGYFWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFL 120 V + Y NS MIT+P V+ + A+ + G+ L ++RFRG+ L F + + G F+ Sbjct: 64 YARVFTDSEMPRYILNSFMITIPTVIGAVALSCMTGFALGIYRFRGNLLIFFMFIAGNFV 123 Query: 121 PFQTVLLPASFTLGKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDG 180 PFQ +++P +GL +T GLVL H+ + F TLF RNF ++P L++AAR++G Sbjct: 124 PFQILMVPVRDLTVDMGLYNTKTGLVLFHIAFQTGFCTLFMRNFIRALPYELIEAARVEG 183 Query: 181 AGFFTIFRRIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSG-DSQPITVALNNLVNTS 239 + IF ++LP+ P I + FT IWND+ + VV + G ++QP+T + + N Sbjct: 184 VAEWRIFWFVVLPLMKPAIAALSVLIFTFIWNDYFWAVVLTQGPNAQPVTAGITSF-NAQ 242 Query: 240 TGAKEYNVDMAAAMIAGLPTLLVYVVAGKYFVRGLTAGAVK 280 G YN+ A ++IA LP ++++ + K+F+ GLT GAVK Sbjct: 243 FGI-AYNMLSAGSLIAALPPVMMFFLMQKHFIAGLTLGAVK 282 Lambda K H 0.329 0.142 0.443 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: 204 Number of extensions: 10 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: 281 Length of database: 282 Length adjustment: 26 Effective length of query: 255 Effective length of database: 256 Effective search space: 65280 Effective search space used: 65280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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