Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate GFF3013 HP15_2957 sugar ABC transporter, permease protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__Marino:GFF3013 Length = 308 Score = 449 bits (1154), Expect = e-131 Identities = 211/289 (73%), Positives = 249/289 (86%) Query: 14 DALQRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQYMRLMDNDR 73 DALQRWLPKLV+AP+ +++ VG YGY++WT +LSFT+SSF+P Y +VG QY +LM NDR Sbjct: 20 DALQRWLPKLVVAPTFVLIGVGIYGYMLWTGVLSFTSSSFLPVYDFVGFDQYAKLMANDR 79 Query: 74 WWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWK 133 W AS NL +FGG+F+ LV+GV LA+ LDQRIR+EG IRT+YLYPMALSMIVTGT WK Sbjct: 80 WLTASINLGIFGGLFVLSCLVIGVILAIFLDQRIRQEGAIRTIYLYPMALSMIVTGTVWK 139 Query: 134 WLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVD 193 W+LNP LGL+K++ DWGW F DWLV D +Y +V+AAVWQASGFVMA+FLAGLRGVD Sbjct: 140 WILNPSLGLEKLMHDWGWTSFSFDWLVSSDMAIYTIVMAAVWQASGFVMALFLAGLRGVD 199 Query: 194 QSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSS 253 SIIRAA+VDGASLP IY KI+LPSLRPVFFSA M+LAHIAIKSFDLV AMTAGGPGYS+ Sbjct: 200 SSIIRAARVDGASLPLIYWKIILPSLRPVFFSAVMVLAHIAIKSFDLVMAMTAGGPGYST 259 Query: 254 DLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKRHD 302 DLPA+FMY+ TF+RGQMG+GSASAMLMLGA+L ++VPYLYSELR KRHD Sbjct: 260 DLPAVFMYAHTFTRGQMGLGSASAMLMLGAILALIVPYLYSELREKRHD 308 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: 435 Number of extensions: 11 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: 308 Length adjustment: 27 Effective length of query: 275 Effective length of database: 281 Effective search space: 77275 Effective search space used: 77275 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