Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 160 bits (405), Expect = 5e-44 Identities = 87/243 (35%), Positives = 149/243 (61%), Gaps = 2/243 (0%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 LLEI ++ K F V AL V + + G V+AL+G+NGAGKSTL+KII+G ++PD G++ Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMMEESK 122 GK ++F +P A+ GI I+Q+L L+P + I NI++ RE N + +N ++M + Sbjct: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182 +LL L+I + D +V NLS +RQ V +A+AV + + +++MDEPT+A++ E + Sbjct: 143 ELLARLRINL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242 + +LK +G G++ ITH + + + +AD + V G I ++ + N + + +M L Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 Query: 243 GKV 245 ++ Sbjct: 262 SQL 264 Score = 91.7 bits (226), Expect = 3e-23 Identities = 57/242 (23%), Positives = 121/242 (50%), Gaps = 17/242 (7%) Query: 4 LLEIRDVHKSFGAVKALDGV----SMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRG 59 LL +RD+ LDGV S +++ GE++ + G G+G++ + + I G G Sbjct: 276 LLTVRDL--------TLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSG 327 Query: 60 DLVFEGKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLA--REVTNKIFLNK 114 + +GK V + P+ A G + +D L P L + N+ +A T F+ + Sbjct: 328 QITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQ 387 Query: 115 KKMMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSV 174 K + + + L+++ P + ++ LSGG +Q +AR + + +++++DEPT + V Sbjct: 388 KALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDV 447 Query: 175 VEARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEIT 234 ++ L L +G+ V++I+ + + ++DR+ V+ G+++ + E E++ Sbjct: 448 GAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVM 507 Query: 235 EV 236 ++ Sbjct: 508 QL 509 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: 242 Number of extensions: 10 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: 251 Length of database: 517 Length adjustment: 29 Effective length of query: 222 Effective length of database: 488 Effective search space: 108336 Effective search space used: 108336 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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