Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate BPHYT_RS30865 BPHYT_RS30865 sugar ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__BFirm:BPHYT_RS30865 Length = 256 Score = 217 bits (553), Expect = 2e-61 Identities = 111/244 (45%), Positives = 169/244 (69%), Gaps = 7/244 (2%) Query: 1 MSDLLEI---RDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPD 57 MSD+LE D+ K FGAV ALDGVS+ + +GE++ +LGDNGAGKSTLIKI++G+H+ Sbjct: 1 MSDVLEALRGEDIVKRFGAVTALDGVSLTLKQGEILGVLGDNGAGKSTLIKILTGFHQQT 60 Query: 58 RGDLVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNK---IFLNK 114 G L G++ + S + ARSLGIE +YQDLAL L IY+N+FL RE+ + L+ Sbjct: 61 SGKLFVGGEETMLRSVDHARSLGIECVYQDLALANSLSIYHNMFLNREIIRRGPFRLLDN 120 Query: 115 KKMMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSV 174 + M E + + L+ + + +P +++ VE LSGGQRQA+AVARAV +AK++L+DEP AA+ Sbjct: 121 RAMRERAAECLEEIGVHVPSVDLPVEQLSGGQRQAIAVARAVNSNAKILLLDEPLAAMGA 180 Query: 175 VEARKVLELARNLKKK-GLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233 EA +++L LK K GL +++I HN Q ++ADR+ ++ RG++ + ++ T+VEE+ Sbjct: 181 REAGLIIDLILRLKAKGGLSIVMIMHNYAQTLDIADRVMLMQRGRVTYQREAASTSVEEL 240 Query: 234 TEVM 237 E++ Sbjct: 241 MEIV 244 Lambda K H 0.318 0.137 0.371 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: 146 Number of extensions: 7 Number of successful extensions: 3 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: 251 Length of database: 256 Length adjustment: 24 Effective length of query: 227 Effective length of database: 232 Effective search space: 52664 Effective search space used: 52664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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