Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate HSERO_RS15495 HSERO_RS15495 ABC transporter permease
Query= reanno::Smeli:SM_b21653 (298 letters) >FitnessBrowser__HerbieS:HSERO_RS15495 Length = 291 Score = 152 bits (385), Expect = 7e-42 Identities = 96/277 (34%), Positives = 150/277 (54%), Gaps = 9/277 (3%) Query: 17 WLFVAPALGLITLFMVYPIAWSLWMSFQSG-RGMTLK-FAGFANIVRLWNDPVFIKALTN 74 WL ++PA+ L+ F YP +LW SF S +G+ F G N + +DPVF +AL N Sbjct: 11 WLLLSPAMVLLIAFTHYPALATLWHSFFSTPKGVRPSVFVGLENYRLMADDPVFWQALCN 70 Query: 75 TMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFATD 134 + + + +P+ I LA+++A L N +L GRGV R A F P V ++A + ++ + Sbjct: 71 NLWFALGTIPLAIALAILMA-LWVNEKLAGRGVLRLAYFTPTVLPMIAVANIWLFFYTPQ 129 Query: 135 -GIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSIYE 193 G++ A+GL + WL +P +++ W+ G+ MIFYLAALQ I + E Sbjct: 130 YGLLEQITGALGLPSHN--WLGNPQTVLGALMVVAVWKEAGFFMIFYLAALQQISPVLAE 187 Query: 194 VARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNATLTL 253 A ++G W + PLL P LF + + I +L D + +T KGGP NA+ L Sbjct: 188 AAALEGASRWQYFWRVQFPLLMPTTLFVLINALINAFRLVDHIVVMT--KGGPDNASSLL 245 Query: 254 SLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQF 290 YIY + F F + YAA ++ V++ L+ L+A V+F Sbjct: 246 LYYIYEVGFAFWDS-SYAAALTVVLLALLGLIALVKF 281 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: 247 Number of extensions: 16 Number of successful extensions: 6 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: 291 Length adjustment: 26 Effective length of query: 272 Effective length of database: 265 Effective search space: 72080 Effective search space used: 72080 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