Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_772 (248 letters) >FitnessBrowser__Miya:8502073 Length = 596 Score = 149 bits (375), Expect = 2e-40 Identities = 82/235 (34%), Positives = 131/235 (55%), Gaps = 4/235 (1%) Query: 3 YNWDWGVFFKSTGVGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVS 62 Y + W + F + L GL T+ I++ + +ALLLG++LG+ R R + Sbjct: 35 YEFKWSMLFTRNETYGVVMGAEILKGLANTVRISLISSALALLLGTMLGLARLSLFRPLR 94 Query: 63 GIATCYVELFRNVPLLVQLFIWYFLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFT 122 ATC +E FRN PLL+QLF WYF P +LP + +E L F + L ++T Sbjct: 95 VTATCVIEFFRNTPLLIQLFFWYFAFPAILPDNARE----ALFSIQFEFWCATIGLSIYT 150 Query: 123 TARVCEQVRTGIQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKN 182 + + E +R G+Q++P+G AA + G Q+ ++LP A+R IIPPL SEFLN KN Sbjct: 151 ASFMAEVIRAGLQSIPKGLLEAAYSSGLSYFQVLRTIILPLAFRAIIPPLGSEFLNNMKN 210 Query: 183 SSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEKKV 237 SS+A ++G+ EL +Q + FEA + AT++Y +L++ + ++ V ++ Sbjct: 211 SSLAMVVGVAELTWHAQQVESLTFKGFEATSAATVLYLSLSLIISFILNGVNGRM 265 Score = 101 bits (252), Expect = 3e-26 Identities = 65/226 (28%), Positives = 113/226 (50%), Gaps = 15/226 (6%) Query: 14 TGVGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFR 73 TG E++ L GL +++ +AV A ++ +G +GV R+ NR+ Y+EL R Sbjct: 377 TGRPDEMFLG--LGGLAYSLLMAVIAISVSFFIGLAVGVGRSSSNRVFRIPCLLYIELIR 434 Query: 74 NVPLLVQLFIWYFLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTG 133 PL++ +F YF +P + T + F S L FT A + E VRTG Sbjct: 435 GNPLIIVIFWVYFFIPVMF------------GTTLNVFWSATWALTAFTGAYIAEIVRTG 482 Query: 134 IQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLME 193 IQ +P GQ AA + G Q ++LPQA + +IP + +F+ +FK++S+A ++G++E Sbjct: 483 IQNIPAGQVEAAYSTGLTYLQAMRRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLE 542 Query: 194 LLAQTKQ-TAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEKKVA 238 L + + E + +YF S+ + +E++++ Sbjct: 543 LTFVAQGINNRLMIHPMEIYGTVAFLYFICCYSMSVFAARLERRLS 588 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: 393 Number of extensions: 23 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 248 Length of database: 596 Length adjustment: 30 Effective length of query: 218 Effective length of database: 566 Effective search space: 123388 Effective search space used: 123388 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: 50 (23.9 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