Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >MicrobesOnline__882:206177 Length = 596 Score = 139 bits (351), Expect = 2e-37 Identities = 80/204 (39%), Positives = 122/204 (59%), Gaps = 4/204 (1%) Query: 156 GGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSV 215 GGL +L++A + I + +G+V+ +GR S+ R+ C+ +IE RG PLI V+F Sbjct: 388 GGLAYSLLMAVIAISVSFFIGLVVGIGRTSDNRICRIPCLLYIELIRGNPLIIVIFWIYF 447 Query: 216 MLPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSM 275 +P+ F+ A I + LF AY+AE+VR G+Q IP GQ EAA + GL + ++M Sbjct: 448 FIPVLF--NTFFNVFWSATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTM 505 Query: 276 GLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYV 335 +ILPQALK +IP IV FIA+FKDTSL ++G+ +L + + + + E Y Sbjct: 506 RRIILPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLEL--TFVAQGINNRLMVYPMEIYG 563 Query: 336 FAALVFWIFCFGMSRYSMHLERKL 359 A +++I C+ MS Y+ LER+L Sbjct: 564 TVAFLYFICCWSMSVYAARLERRL 587 Score = 103 bits (258), Expect = 9e-27 Identities = 60/164 (36%), Positives = 95/164 (57%), Gaps = 8/164 (4%) Query: 157 GLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVM 216 GL +T+ I+ + AL LG VL + R S +R+ +EF+R PL+ LF Sbjct: 60 GLGVTVRISLISSALALGLGTVLGIARLSLFAPLRLTATAVVEFFRNTPLLVQLFFWYFA 119 Query: 217 LPLFLPEGM-------NFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGL 269 P LPE + NF+ A IG+ ++ SA++AEV+R GLQ+IPKG EAA + GL Sbjct: 120 FPAILPENIRELLFTGNFE-FWCATIGLSVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGL 178 Query: 270 GYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDL 313 Y + + +ILP A + +IP + + F+ K++SL +++G+ +L Sbjct: 179 NYVQVLRTIILPMAFRAIIPPLGSEFLNNMKNSSLAMVVGVAEL 222 Lambda K H 0.330 0.144 0.469 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: 659 Number of extensions: 38 Number of successful extensions: 5 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: 365 Length of database: 596 Length adjustment: 33 Effective length of query: 332 Effective length of database: 563 Effective search space: 186916 Effective search space used: 186916 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 (21.9 bits) S2: 51 (24.3 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