Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate HSERO_RS16725 HSERO_RS16725 ABC transporter permease
Query= reanno::Smeli:SM_b21653 (298 letters) >FitnessBrowser__HerbieS:HSERO_RS16725 Length = 299 Score = 125 bits (313), Expect = 2e-33 Identities = 92/283 (32%), Positives = 140/283 (49%), Gaps = 11/283 (3%) Query: 13 DVNGWLFVAPALGLITLFMVYPIAWSLWMSFQSGR-GMTLKFAGFANIVRLWNDPVFIKA 71 +V G LF+APA+ L+ +F+ YP+ +W+ F + G F G N L D + + Sbjct: 10 NVLGMLFMAPAVILLVVFLTYPLGLGIWLGFTDTKIGGEGSFIGLDNFTYLAGDSLAQLS 69 Query: 72 LTNTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMF 131 L NT+ Y V + +L L LA LLN + + FR + LP + ++ F ++ Sbjct: 70 LFNTVFYTVSASILKFMLGLWLAILLNK-NVPLKTFFRAIVLLPWIVPTALSALAFWWLY 128 Query: 132 -ATDGIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKS 190 A +++ L +GL I +L P+ A+ + A WR + I LA LQ I S Sbjct: 129 DAQFSVISWALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAISLLAGLQTISPS 188 Query: 191 IYEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNAT 250 +YE A IDG W + H+T+PLL P+I S + T F +Y LT +GGP NAT Sbjct: 189 LYEAAAIDGATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDFQLIYVLT--RGGPLNAT 246 Query: 251 LTLSLYIYNLTFRFMPN--LGY-AATVSYVIVVLVALLAFVQF 290 ++ + R +P LG AA +Y+I L+A + F F Sbjct: 247 HLMATLSFQ---RAIPGGALGEGAALATYMIPFLLAAIMFSYF 286 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: 14 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: 299 Length adjustment: 27 Effective length of query: 271 Effective length of database: 272 Effective search space: 73712 Effective search space used: 73712 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