Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate 206098 DVU0674 ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= uniprot:B2TBJ8 (250 letters) >MicrobesOnline__882:206098 Length = 271 Score = 114 bits (286), Expect = 2e-30 Identities = 77/210 (36%), Positives = 117/210 (55%), Gaps = 12/210 (5%) Query: 15 LLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMFLV 74 LL + TL + SL+L LL+ V V +R+S AR Y+ R +PLL+Q+F+ Sbjct: 69 LLQGLGVTLQVAAGSLVLALLLAAVAVALRLSCLRTGRLVARLYVESVRNTPLLVQLFVT 128 Query: 75 YYGMGQ-FGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAGYS 133 Y+ + FG+ R + AV++L + Y AEI+R G+ AVP GQ EA S Sbjct: 129 YFAIAPVFGLGRMA-----------SAVMALGVFEGAYMAEILRAGIAAVPQGQWEASRS 177 Query: 134 IGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQQTYR 193 +G+ +VI P ALR+ LP + +AV LVK ++LAS + + E+T AQ II +T+ Sbjct: 178 LGMDEPGTYVQVILPQALRRALPPLTGQAVSLVKDSSLASAIAIHELTMQAQTIIAETFL 237 Query: 194 TTEVFICAALIYLFLNFVIVRLLGMLETRL 223 T EV++ A IYL + + + +LE R+ Sbjct: 238 TFEVWLLTAAIYLCVTLSLSAVARLLERRM 267 Lambda K H 0.331 0.143 0.431 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: 139 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 250 Length of database: 271 Length adjustment: 24 Effective length of query: 226 Effective length of database: 247 Effective search space: 55822 Effective search space used: 55822 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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