Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate WP_086510782.1 BZY95_RS15415 sugar ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >NCBI__GCF_002151265.1:WP_086510782.1 Length = 310 Score = 430 bits (1105), Expect = e-125 Identities = 203/286 (70%), Positives = 239/286 (83%) Query: 16 LQRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQYMRLMDNDRWW 75 LQ WLPKLVLAPS I L YG+++WTF+LS TNS +PSY++VG QY RLM NDRWW Sbjct: 24 LQAWLPKLVLAPSAAISLFFVYGFMLWTFVLSLTNSRMLPSYEFVGFAQYARLMANDRWW 83 Query: 76 VASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWKWL 135 VAS NL +FGG+F++I L LG+ LA+LLDQRIR+EG +RT+YLYPMALS IVTG WKWL Sbjct: 84 VASTNLVVFGGLFVAICLALGLVLAILLDQRIRQEGALRTIYLYPMALSFIVTGVVWKWL 143 Query: 136 LNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVDQS 195 LNPGLG+ M+R WG+E FR DWLVD D VY LVIAAVWQASGFVMA+FLAGLRG+D S Sbjct: 144 LNPGLGIQAMVRSWGFENFRFDWLVDPDMAVYTLVIAAVWQASGFVMALFLAGLRGIDDS 203 Query: 196 IIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSSDL 255 I++AAQ+DGASLP IY ++V+P LRPV FSA MIL+HIAIKSFDLV A+T GGPGY+SDL Sbjct: 204 ILKAAQLDGASLPRIYWRVVIPCLRPVVFSAVMILSHIAIKSFDLVVALTGGGPGYASDL 263 Query: 256 PAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKRH 301 PA FMY+ F+R Q+G+GSASAMLMLG VL IL+PYLYSELR +RH Sbjct: 264 PATFMYAHAFTRAQIGLGSASAMLMLGGVLAILIPYLYSELRSRRH 309 Lambda K H 0.329 0.141 0.448 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: 405 Number of extensions: 10 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: 302 Length of database: 310 Length adjustment: 27 Effective length of query: 275 Effective length of database: 283 Effective search space: 77825 Effective search space used: 77825 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 (21.8 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