Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Miya:8502073 Length = 596 Score = 133 bits (335), Expect = 1e-35 Identities = 103/295 (34%), Positives = 150/295 (50%), Gaps = 24/295 (8%) Query: 140 TLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTALAPKLGVPVSAGIGLVVAALFWLY 199 T PLAA WGG +VLAG GL LA G+ S G GL+ W Sbjct: 312 TTYTPLAAMLHQWGGYA-ARAAVLAG---KGLFVALLA---GLLYSVGKGLL--GFQWHV 362 Query: 200 AAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLALGRQSDMLIV 259 + + L P P+ GG +L++ V AI VS +G+ + +GR S + Sbjct: 363 VFENLRSLLIWHFPTGRPDEMFLGLGGLAYSLLMAVIAISVSFFIGLAVGVGRSSSNRVF 422 Query: 260 KSLSVGIIEFVRGVPLITLLFTASLLLQYFLPP--GTNFDLILRVVILVTLFAAAYIAEV 317 + + IE +RG PLI ++F + +F+P GT ++ +T F AYIAE+ Sbjct: 423 RIPCLLYIELIRGNPLIIVIFW----VYFFIPVMFGTTLNVFWSATWALTAFTGAYIAEI 478 Query: 318 IRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFV 377 +R G+ +P GQ EAA + GL Y QA R I++PQALK IP IV FI +FKDT+L + Sbjct: 479 VRTGIQNIPAGQVEAAYSTGLTYLQAMRRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVL 538 Query: 378 GLFD---PLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERKL 429 G+ + +GI+N + E Y VA ++F+ +SMS ++ LER+L Sbjct: 539 GVLELTFVAQGINNRLMIHP------MEIYGTVAFLYFICCYSMSVFAARLERRL 587 Score = 78.2 bits (191), Expect = 7e-19 Identities = 50/153 (32%), Positives = 80/153 (52%), Gaps = 6/153 (3%) Query: 233 IGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPP 292 I + + ++L LG +L L R S ++ + +IEF R PL+ LF LP Sbjct: 67 ISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQLFFWYFAFPAILPD 126 Query: 293 GTNFDLILR------VVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRL 346 L I ++++ A+++AEVIR GL ++P+G EAA + GL Y+Q R Sbjct: 127 NAREALFSIQFEFWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEAAYSSGLSYFQVLRT 186 Query: 347 IIMPQALKISIPGIVSSFIGLFKDTTLVAFVGL 379 II+P A + IP + S F+ K+++L VG+ Sbjct: 187 IILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGV 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: 698 Number of extensions: 40 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: 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