Align LacG, component of Lactose porter (characterized)
to candidate WP_011427707.1 RHE_RS23250 sn-glycerol-3-phosphate ABC transporter permease UgpE
Query= TCDB::P29824 (273 letters) >NCBI__GCF_000092045.1:WP_011427707.1 Length = 282 Score = 138 bits (348), Expect = 1e-37 Identities = 86/275 (31%), Positives = 140/275 (50%), Gaps = 13/275 (4%) Query: 11 DIVQYSVLSLAAFLSIFPFIWMVIGTTNTTSQIIRGKV----------TFGTALFDNIAS 60 + + + VL L + IFP I +++ + + G V + T L + S Sbjct: 9 NFLAHIVLILGVTIVIFPVYIAFIASSHGPNDFLSGLVPLAPGPHLIENYSTMLSSGMTS 68 Query: 61 FFAQVDVPLVFWNSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVPFA 120 A P++ NS +A+ + +S L+ + FR R + +I +TLM+P Sbjct: 69 SGAPPIGPMLL-NSFIMAVGVAVGKIAISILSAFAIVYFRFPFRTLAFWMIFITLMLPVE 127 Query: 121 ALMIPLFMLMGQAGLLNTHIAIMLPMIASAFIIFYFRQASKAFPTELRDAAKVDGLKEWQ 180 ++P + ++ G+LN + +++P+IASA F FRQ P EL +AA+VDG + Sbjct: 128 VRIVPTYKVVADLGMLNNYGGLIIPLIASATATFLFRQFFLTVPDELMEAARVDGAGPMK 187 Query: 181 IFFYIYVPVMRSTYAAAFVIVFMLNWNNYLWPLIVLQSNDTKTITLVVSSLASA--YSPE 238 F I +P+ + AA F+I+F+L WN YLWPLIV T+ + + +A+ P Sbjct: 188 FFRDILLPLSVTNIAALFIILFVLGWNQYLWPLIVTTDQSLYTVVMGIQRMAAVADAEPR 247 Query: 239 YGTVMIGTILATLPTLLVFFAMQRQFVQGMLGSVK 273 + VM ILA LP +LV AMQR FV+G++ + K Sbjct: 248 WNLVMAAVILAALPPVLVIVAMQRLFVKGLVETEK 282 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: 251 Number of extensions: 13 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: 282 Length adjustment: 25 Effective length of query: 248 Effective length of database: 257 Effective search space: 63736 Effective search space used: 63736 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 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