Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate AO353_20825 AO353_20825 ABC transporter permease
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20825 Length = 325 Score = 199 bits (507), Expect = 6e-56 Identities = 125/332 (37%), Positives = 189/332 (56%), Gaps = 18/332 (5%) Query: 18 TASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLA 77 TA + G R+ F LA A LL MI FS S +F+ D ++ VLA Sbjct: 3 TALSAGKRSSNFYGLGTYLGLAGA-LLAMIALFSVLSSHFLSYDTFSTLANQIPDLMVLA 61 Query: 78 IACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMP-LP---LGIAAAIFFGALSGWIS 133 + T+V+I GIDLSVG+++ V + WG LP LG+AAA A++G I+ Sbjct: 62 VGMTFVLIIGGIDLSVGSVLALAGSTVSVAILGWGWSVLPAALLGMAAA----AVAGTIT 117 Query: 134 GMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLP 193 G + ++P FI +LG++ + +G++ ++G+R Y D F+ ++ G + PS Sbjct: 118 GSITVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAYIGDA--FAWLSNPITFG-ISPSFI 174 Query: 194 IPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAIC 253 I A+L++F+ A +L +TVFGRY +G+NEEA+RL+G+ +K+ V++ G + Sbjct: 175 I--ALLVIFI----AQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLA 228 Query: 254 GIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNG 313 GIA L SRL +A P G G EL IAAVVIGGTSL GG G+++ T G I+SVL G Sbjct: 229 GIAALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAG 288 Query: 314 LRIMSVAQEWQTVVTGVIIILAVYLDILRRRR 345 L + + + ++TG +I++AV LD R +R Sbjct: 289 LAQIGATEPTKRIITGAVIVVAVVLDTYRSQR 320 Lambda K H 0.326 0.139 0.398 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: 249 Number of extensions: 12 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: 347 Length of database: 325 Length adjustment: 28 Effective length of query: 319 Effective length of database: 297 Effective search space: 94743 Effective search space used: 94743 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 (21.7 bits) S2: 49 (23.5 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