Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate SMa2197 SMa2197 ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_772 (248 letters) >FitnessBrowser__Smeli:SMa2197 Length = 304 Score = 108 bits (271), Expect = 1e-28 Identities = 70/242 (28%), Positives = 113/242 (46%), Gaps = 11/242 (4%) Query: 2 NYNWDWGVFFKSTGVGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIV 61 N N+ W V V ++ L GL T+ + V +I ++LG+I +M N ++ Sbjct: 49 NPNFGWDV------VADYLFDSRILWGLSLTVWLTVVTMVIGVVLGTIFAIMAMADNVVI 102 Query: 62 SGIATCYVELFRNVPLLVQLFIWY---FLVPDLLPAD--IQEWYKQDLNPTTSAFLSVVV 116 S +A Y+ FR P+LVQL WY L P L W N S + V+ Sbjct: 103 STVANAYIWFFRGTPVLVQLIFWYNLGALFPQLSVGVPFTSLWVSVPTNTLISPVTAAVL 162 Query: 117 CLGLFTTARVCEQVRTGIQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEF 176 LGL A + E +R+G+ ++ GQ AA+++G + W +LLPQA +IIPP ++ Sbjct: 163 GLGLNEGAYMSEIIRSGLMSVDPGQRQAAKSLGMTNGKTLWRILLPQAMPVIIPPTGNQT 222 Query: 177 LNVFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEKK 236 + + K SS+ S+I L +LL + + +A + Y L + +E+ Sbjct: 223 IGMLKTSSLVSVISLADLLYSAQTIYSRNFQTIPLLIVACIWYLAATTILSAVQVRIERH 282 Query: 237 VA 238 A Sbjct: 283 FA 284 Lambda K H 0.326 0.140 0.433 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: 191 Number of extensions: 8 Number of successful extensions: 3 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: 248 Length of database: 304 Length adjustment: 25 Effective length of query: 223 Effective length of database: 279 Effective search space: 62217 Effective search space used: 62217 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: 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