Align ABC transporter for Lactose, permease component 2 (characterized)
to candidate Ac3H11_4786 Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
Query= reanno::Smeli:SM_b21654 (272 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4786 Length = 283 Score = 121 bits (303), Expect = 2e-32 Identities = 77/259 (29%), Positives = 131/259 (50%), Gaps = 12/259 (4%) Query: 26 FPFIWMVLGATNSSIDIIKGKL--LPGAAFATNVANFF--------TLVNVPLVFWNSAK 75 FP + +T+++ DI++ + +PG F + + V + W S Sbjct: 25 FPLYLAFVASTHTAQDIVQVPMPMVPGGNFWQTYHDTLFGGGSGAGSTAPVARMMWVSFV 84 Query: 76 IAIVATVLTLAVSSLAGYGFEMFRSRRRERVYRAMLLTLMIPFAALMIPLFVMMGKAGLI 135 AIV T+ +A+S L+ + FR + + + +TLM+P + P + ++ G++ Sbjct: 85 TAIVITLGKIAISLLSAFAIVYFRFPFKGICFWLIFITLMLPVEVRIGPTYEVVSNLGML 144 Query: 136 NTHLAVVLPSIGSAFVIFYFRQSTKAFPSELRDAAKVDGLKEWQIFLFIYVPVMRSTYAA 195 N++ + +P I SA F FRQ P EL +AA+VDG + F I VP+ R++ AA Sbjct: 145 NSYAGLTVPLIASATATFLFRQFFLTVPDELVEAARVDGAGPMRFFKDILVPLSRTSIAA 204 Query: 196 AFVIVFMTAWNNYLWPLIVLQTNETKTITLVISSLASA--YYPDYGVVMVGTILATLPTL 253 FVI F+ WN YLWPL+V + + + + I + + ++ +VM +LA LP Sbjct: 205 LFVIQFIYGWNQYLWPLLVTTSEDMYPVVIGIKRMIAGGDAGNEWNIVMATALLAMLPPA 264 Query: 254 AVFFFMQRQFVQGMLGSVK 272 V MQR FV+G++ + K Sbjct: 265 FVVVVMQRWFVKGLVDTEK 283 Lambda K H 0.331 0.141 0.422 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: 18 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: 272 Length of database: 283 Length adjustment: 25 Effective length of query: 247 Effective length of database: 258 Effective search space: 63726 Effective search space used: 63726 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