Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::Q52665 (434 letters) >MicrobesOnline__882:206177 Length = 596 Score = 129 bits (325), Expect = 2e-34 Identities = 91/252 (36%), Positives = 139/252 (55%), Gaps = 19/252 (7%) Query: 187 GIGLVVAALFWLYAAAPIEAALQSALPLALPEVDSDQF----GGFLLALVIGVTAIVVSL 242 G+ V A + + I L++ L P SD+ GG +L++ V AI VS Sbjct: 346 GLLFVTARGLYNFNWGVIADNLRTLLIWHFPNGQSDELFMGLGGLAYSLLMAVIAISVSF 405 Query: 243 PLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPP--GTNFDLIL 300 +G+++ +GR SD I + + IE +RG PLI ++F + +F+P T F++ Sbjct: 406 FIGLVVGIGRTSDNRICRIPCLLYIELIRGNPLIIVIFW----IYFFIPVLFNTFFNVFW 461 Query: 301 RVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGI 360 I +TLF AY+AE++R G+ +P GQ EAA + GL + Q R II+PQALK IP I Sbjct: 462 SATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTMRRIILPQALKQMIPAI 521 Query: 361 VSSFIGLFKDTTLVAFVGLFD---PLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFS 417 V FI +FKDT+L +G+ + +GI+N + M + E Y VA ++F+ +S Sbjct: 522 VGQFIAIFKDTSLAFVLGVLELTFVAQGINNRL---MVYP---MEIYGTVAFLYFICCWS 575 Query: 418 MSRYSMYLERKL 429 MS Y+ LER+L Sbjct: 576 MSVYAARLERRL 587 Score = 79.7 bits (195), Expect = 2e-19 Identities = 50/161 (31%), Positives = 85/161 (52%), Gaps = 8/161 (4%) Query: 226 GFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLL 285 G + + I + + ++L LG +L + R S ++ + ++EF R PL+ LF Sbjct: 60 GLGVTVRISLISSALALGLGTVLGIARLSLFAPLRLTATAVVEFFRNTPLLVQLFFWYFA 119 Query: 286 LQYFLPPGT-------NFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGL 338 LP NF+ + L +++ +A++AEVIR GL ++P+G EAA + GL Sbjct: 120 FPAILPENIRELLFTGNFEFWCATIGL-SVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGL 178 Query: 339 DYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGL 379 +Y Q R II+P A + IP + S F+ K+++L VG+ Sbjct: 179 NYVQVLRTIILPMAFRAIIPPLGSEFLNNMKNSSLAMVVGV 219 Lambda K H 0.329 0.143 0.457 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: 744 Number of extensions: 51 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 434 Length of database: 596 Length adjustment: 34 Effective length of query: 400 Effective length of database: 562 Effective search space: 224800 Effective search space used: 224800 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 (21.8 bits) S2: 52 (24.6 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