Align LacG, component of Lactose porter (characterized)
to candidate GFF261 PGA1_c02730 sn-glycerol-3-phosphate transport system permease protein UgpE
Query= TCDB::P29824 (273 letters) >FitnessBrowser__Phaeo:GFF261 Length = 293 Score = 133 bits (334), Expect = 5e-36 Identities = 80/273 (29%), Positives = 138/273 (50%), Gaps = 15/273 (5%) Query: 15 YSVLSLAAFLSIFPFIWMVIGTTNTTSQIIRG----------KVTFGTALFDNIASFFAQ 64 ++VL L + + P I +V+ TT +II+ F A+F+ A Sbjct: 22 HTVLILGSLFMLVPLIMVVMTTTVPDVEIIKYGPQLKIGDQFDENFEKAMFEASGFSGAN 81 Query: 65 VDVPLVFWNSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVPFAALMI 124 ++F NS + + ++++ +A Y FR + + VI TL++P ++ Sbjct: 82 TGTRMLF-NSFVLGIGFALGKIVIAMMAAYAIVYFRLRFASLAFWVIFTTLLLPLEVRIL 140 Query: 125 PLFMLMGQAGLLNTHIAIMLPMIASAFIIFYFRQASKAFPTELRDAAKVDGLKEWQIFFY 184 P + ++ Q G+LNT+ +++P+IASA F+FRQ ++ P EL +AA++DG + F Sbjct: 141 PSYEVVQQLGMLNTYQGLIIPLIASATATFFFRQYFRSIPEELVEAARIDGAGPVKFFID 200 Query: 185 IYVPVMRSTYAAAFVIVFMLNWNNYLWPLIVLQSNDTKT----ITLVVSSLASAYSPEYG 240 I VP+ ++ AA F+I+F+ WN YLWP ++ D T I + +L PE+G Sbjct: 201 ILVPLSKTMIAAMFIIMFVFGWNQYLWPTMITTEEDMYTLVRGIKQITQTLEGTNVPEFG 260 Query: 241 TVMIGTILATLPTLLVFFAMQRQFVQGMLGSVK 273 + ++A LP + V Q FV+G+ S K Sbjct: 261 RANLLAVIAILPPVAVVIFFQSWFVKGLTESDK 293 Lambda K H 0.331 0.140 0.416 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: 244 Number of extensions: 11 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: 273 Length of database: 293 Length adjustment: 26 Effective length of query: 247 Effective length of database: 267 Effective search space: 65949 Effective search space used: 65949 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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