Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate WP_011423480.1 RHE_RS00425 sugar ABC transporter permease
Query= reanno::Smeli:SM_b21653 (298 letters) >NCBI__GCF_000092045.1:WP_011423480.1 Length = 315 Score = 155 bits (392), Expect = 1e-42 Identities = 95/282 (33%), Positives = 157/282 (55%), Gaps = 8/282 (2%) Query: 16 GWLFVAPALGLITLFMVYPIAWSLWMSFQSGRGM-TLKFAGFANIVRLWN-DPVFIKALT 73 G+LF+ P L + P SL++SF + + ++ G AN VR+ DP F A+ Sbjct: 32 GYLFLLPWLVGFFGLTLGPALISLYLSFTDFDMLQSPRWVGMANYVRIATADPKFSAAMD 91 Query: 74 NTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCV-SSLVAYSVLFKGMFA 132 T+TY V VP + AL++A LN L G V+R +LP + VA +VL++ +FA Sbjct: 92 VTLTYVVFSVPFKLTFALLVAMALNRG-LRGLTVYRAIFYLPSLLGGSVAIAVLWRQLFA 150 Query: 133 TDGIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSIY 192 +DG+VN+ L G+ W++HP ++ ++ W++ G MI +LA L+ I + +Y Sbjct: 151 SDGLVNAALSQFGIEGPS--WISHPNYSIYTLVALSVWQF-GSPMIIFLAGLRQIPQDMY 207 Query: 193 EVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNATLT 252 E A +DG + + +T+PLL PVI F V+ TI + F + ++ G GGP N+TL Sbjct: 208 EAASLDGASKFRQFYKITLPLLTPVIFFNAVVQTIEAFKAFTPAFIISGGTGGPINSTLF 267 Query: 253 LSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQFFAAR 294 +LY+Y F +GYA+ +++++VV++A+ F +R Sbjct: 268 YTLYLYQEAFGNF-RMGYASALAWILVVIIAIFTAFSFLTSR 308 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: 285 Number of extensions: 15 Number of successful extensions: 5 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: 315 Length adjustment: 27 Effective length of query: 271 Effective length of database: 288 Effective search space: 78048 Effective search space used: 78048 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 24 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