Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate Pf6N2E2_2891 Glucose ABC transport system, inner membrane component 1
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2891 Length = 297 Score = 549 bits (1414), Expect = e-161 Identities = 262/297 (88%), Positives = 283/297 (95%) Query: 6 VFSKASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQY 65 VFSKASPFDALQRWLPKLVLAPSM IVLVGFYGYI+WTF+LSFT S+F+P+YKW GL QY Sbjct: 1 VFSKASPFDALQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTTSTFLPNYKWAGLAQY 60 Query: 66 MRLMDNDRWWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSM 125 RLMDNDRWWVASKNLALFGG+FI I+LV+GV LAV LDQRIR+EGFIRT+YLYPMALSM Sbjct: 61 ARLMDNDRWWVASKNLALFGGLFIGITLVIGVLLAVFLDQRIRREGFIRTIYLYPMALSM 120 Query: 126 IVTGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMF 185 IVTGTAWKWLLNPG+GLDK+LRDWGWEGFRLDWL+D DRVVYCLVIAAVWQASGF+MAMF Sbjct: 121 IVTGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMF 180 Query: 186 LAGLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMT 245 LAGLRGVDQSIIRAAQ+DGAS+P IY K+VLPSLRPVFFSA MILAHIAIKSFDLVAAMT Sbjct: 181 LAGLRGVDQSIIRAAQIDGASMPRIYWKVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMT 240 Query: 246 AGGPGYSSDLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKRHD 302 AGGPGYSSDLPAMFMYSFTFSRGQMG+GSASA+LMLGA+L I+VPYLYSELR KRHD Sbjct: 241 AGGPGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKRHD 297 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: 490 Number of extensions: 8 Number of successful extensions: 1 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: 297 Length adjustment: 27 Effective length of query: 275 Effective length of database: 270 Effective search space: 74250 Effective search space used: 74250 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 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