Align LacG, component of Lactose porter (characterized)
to candidate 8499893 DvMF_0658 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::P29824 (273 letters) >FitnessBrowser__Miya:8499893 Length = 277 Score = 116 bits (290), Expect = 6e-31 Identities = 63/198 (31%), Positives = 112/198 (56%), Gaps = 1/198 (0%) Query: 73 NSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVPFAALMIPLFMLMGQ 132 N+V + + A L++ +LA Y F + + ++ ++L+ LM+ L++ + M Sbjct: 75 NTVLLVTMVLAGQLVLCTLAAYAFAKYDFPGKGILFALVLMQLMIMPDVLVVENYRTMSA 134 Query: 133 AGLLNTHIAIMLPMIASAFIIFYFRQASKAFPTELRDAAKVDGLKEWQIFFYIYVPVMRS 192 G+L++ +AI LP +ASAF IF RQ K+ P EL +AA V+G QI + +YVP+ + Sbjct: 135 IGVLDSTLAIGLPYMASAFGIFLLRQTFKSIPKELDEAAAVEGASTLQILWKVYVPLGKP 194 Query: 193 TYAAAFVIVFMLNWNNYLWPLIVLQSNDTKTITLVVSSLASA-YSPEYGTVMIGTILATL 251 Y A ++ +WNN+LWPLIV + +++ +T+ + +S ++ + T++ + Sbjct: 195 VYLAYALVSVSYHWNNFLWPLIVTNTTNSRPLTVGLQVFSSTEQGVDWSIITAATLMTSG 254 Query: 252 PTLLVFFAMQRQFVQGML 269 P L+ F QRQFVQ + Sbjct: 255 PLLIGFLLFQRQFVQSFM 272 Lambda K H 0.331 0.140 0.416 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: 217 Number of extensions: 13 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: 273 Length of database: 277 Length adjustment: 25 Effective length of query: 248 Effective length of database: 252 Effective search space: 62496 Effective search space used: 62496 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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