Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate 3608622 Dshi_2015 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Smeli:SM_b21653 (298 letters) >FitnessBrowser__Dino:3608622 Length = 293 Score = 125 bits (313), Expect = 2e-33 Identities = 88/277 (31%), Positives = 139/277 (50%), Gaps = 11/277 (3%) Query: 18 LFVAPALGLITLFMVYPIAWSLWMSF--QSGRGMTLKFAGFANIVRLWNDPVFIKALTNT 75 L VAP + + LF YP ++W S G+++++ G N L++DP + + T Sbjct: 15 LLVAPQIVITALFFFYPAGQAIWQSLFIPDPFGLSMQWVGLGNFEFLFSDPFYRASFVTT 74 Query: 76 MTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFATD- 134 + ++ + + +AL LA LL + + G G +RT + P + VL+ MF T Sbjct: 75 AVFSILVTVVSMGVALYLA-LLADRLIKGSGTYRTLLIWPYAVAPAVAGVLWLFMFNTRV 133 Query: 135 GIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSIYEV 194 G+V L +G + + + A LV++A W YN +F+LA LQ I KS+ E Sbjct: 134 GVVTWYLGQLGYDWNHV---LNEEEAMGLVVVASAWGRISYNFLFFLAGLQAIPKSVIEA 190 Query: 195 ARIDGVPAWARLTHLTIPLLKPVILFTTVISTI-GTLQLFDEVYNLTEGKGGPSNATLTL 253 A IDG W R + PLL PV F V++ I + F ++ +T GGP AT L Sbjct: 191 AAIDGARFWTRFRTIVFPLLSPVTFFLLVVNIIYAFFETFGVIHTIT--SGGPQQATTIL 248 Query: 254 SLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQF 290 +Y+ F +LG +A S V++VLV++L +QF Sbjct: 249 VYKVYSDGF-VGQDLGSSAAQSVVLLVLVSILTVIQF 284 Lambda K H 0.330 0.142 0.447 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: 244 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: 298 Length of database: 293 Length adjustment: 26 Effective length of query: 272 Effective length of database: 267 Effective search space: 72624 Effective search space used: 72624 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 (21.9 bits) S2: 48 (23.1 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