Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 17340 b3270 putative transport system permease protein (VIMSS)
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__Keio:17340 Length = 367 Score = 268 bits (684), Expect = 3e-76 Identities = 162/416 (38%), Positives = 228/416 (54%), Gaps = 67/416 (16%) Query: 14 PRPAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQAAAPWLLHGVW-NANSLTE 72 PRPA + A+ W+R+NLFS N+ LT+ +WL+ P LL+ + AN + Sbjct: 10 PRPASHNSSRAMVWVRKNLFSSWSNSLLTI----GCIWLMWELIPPLLNWAFLQANWVGS 65 Query: 73 CRAIIAERWGPEATGACWAVIRVRWNQFLFGFYPVDQYWRLFVTFAGLFLALAPVLFDAL 132 RA + GACW I R+ QF++G YP DQ WR+ Sbjct: 66 TRADCTK------AGACWVFIHERFGQFMYGLYPHDQRWRI------------------- 100 Query: 133 PRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFTALAPKLGVPVSAGIGLVV 192 +++L G + +F + P G ++A + Sbjct: 101 --------------------------NLALLIGLVSIAPMFWKILPHRGRYIAAWAVIYP 134 Query: 193 AALFWLYAAAPIEAALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLALGR 252 ++WL AL V++ Q+GG L L+I I +LP GILLALGR Sbjct: 135 LIVWWLMYGGFF----------ALERVETRQWGGLTLTLIIASVGIAGALPWGILLALGR 184 Query: 253 QSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPPGTNFDLILRVVILVTLFAAA 312 +S M IV+ LSV IEF RGVPLIT+LF +S++L F+ GT+ D ++R ++ V LF +A Sbjct: 185 RSHMPIVRILSVIFIEFWRGVPLITVLFMSSVMLPLFMAEGTSIDKLIRALVGVILFQSA 244 Query: 313 YIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTT 372 Y+AEV+RGGL ALP+GQYEAA++L L YW+ Q L+I+PQALK+ IPG+V++ I LFKDT+ Sbjct: 245 YVAEVVRGGLQALPKGQYEAAESLALGYWKTQGLVILPQALKLVIPGLVNTIIALFKDTS 304 Query: 373 LVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFSMSRYSMYLERK 428 LV +GLFD + D AW G E Y+F ALI+++F FSMSRYS YLE++ Sbjct: 305 LVIIIGLFDLFSSVQQAT-VDPAWLGMSTEGYVFAALIYWIFCFSMSRYSQYLEKR 359 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: 618 Number of extensions: 39 Number of successful extensions: 6 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: 367 Length adjustment: 31 Effective length of query: 403 Effective length of database: 336 Effective search space: 135408 Effective search space used: 135408 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: 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