Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate GFF3853 PGA1_78p00170 putative sn-glycerol-3-phosphate transport system permease protein UgpA
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__Phaeo:GFF3853 Length = 310 Score = 267 bits (683), Expect = 2e-76 Identities = 126/293 (43%), Positives = 193/293 (65%) Query: 8 SKASPFDALQRWLPKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQYMR 67 ++ P L+ K+ P +L LV F G WT SFT S +P +K+VG QY R Sbjct: 16 ARPRPPRVLRNLNAKIASVPMILTALVVFMGGTAWTVAHSFTKSRLLPKWKFVGFDQYER 75 Query: 68 LMDNDRWWVASKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIV 127 L ++RW ++ +NL ++G + +++ +G LA LLD++IR EG RT++LYP ALS +V Sbjct: 76 LWSSNRWLISVENLLIYGLCSLVLTMAIGFTLAALLDRKIRFEGAFRTIFLYPFALSFVV 135 Query: 128 TGTAWKWLLNPGLGLDKMLRDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLA 187 TG AW+W+LNP G+ ++R WGWE F D L + + V++ ++IA +WQ SGFVM + LA Sbjct: 136 TGLAWQWILNPDFGIQNVVRSWGWESFAFDPLNNPETVIFGVLIAGLWQGSGFVMVIMLA 195 Query: 188 GLRGVDQSIIRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAG 247 GLRG+D+ I +AA+VDG + Y+++++P +RPVF +A +I+A IK +DLV A T G Sbjct: 196 GLRGIDEDIWKAARVDGIGVTKTYVRVIIPMMRPVFVTALVIIASGIIKLYDLVVAQTNG 255 Query: 248 GPGYSSDLPAMFMYSFTFSRGQMGIGSASAMLMLGAVLTILVPYLYSELRGKR 300 GPG SS++PA ++ ++ F +G G A++ +ML +V+ ILVP+ Y E GK+ Sbjct: 256 GPGISSEVPAKYVINYMFEAQNLGQGFAASTMMLLSVIIILVPWAYLEFGGKK 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: 308 Number of extensions: 15 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: 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 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