Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_039469450.1 H744_RS03175 sugar ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_000940995.1:WP_039469450.1 Length = 497 Score = 152 bits (383), Expect = 2e-41 Identities = 85/244 (34%), Positives = 150/244 (61%), Gaps = 3/244 (1%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +LE+R + K+F VKALD V + + KG V+AL+G+NGAGKSTL+K++ G ++ D G + + Sbjct: 5 ILEMRGITKTFPGVKALDNVQLTLKKGRVMALMGENGAGKSTLMKVLFGTYQRDEGTIRY 64 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLARE-VTNKI-FLNKKKMMEES 121 +G+ V F+ ++ GI I+Q+L+ + I NI+L RE +T + ++ KKM ++ Sbjct: 65 QGELVDFSGAKESLESGISMIHQELSPVLHRNIAENIWLGREPLTGPLRLIDHKKMFADT 124 Query: 122 KKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVL 181 + LL L + + D + +L+ Q V +A+A+ F +K+I+MDEPT+AL+ E + Sbjct: 125 EALLQRLDLDL-DPRTLMSDLTVATMQMVEIAKAISFESKIIIMDEPTSALTDKEVAHLF 183 Query: 182 ELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFA 241 E+ LK +G+ ++ I+H + + +++ D I V G I ++ +TN +E+ ++M Sbjct: 184 EIIEKLKSQGVAMVYISHKMDEIFKICDDITVFRDGCYIGEREARDTNHDELVQMMVGRD 243 Query: 242 LGKV 245 LG V Sbjct: 244 LGDV 247 Score = 87.4 bits (215), Expect = 5e-22 Identities = 59/227 (25%), Positives = 118/227 (51%), Gaps = 11/227 (4%) Query: 23 VSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLGIE 82 V+ ++++GE++ + G GAG++ LI+ + G + + G++ G++V +P DA S + Sbjct: 274 VNFKLHEGEILGIAGLVGAGRTELIETLFGVREKETGEIWINGEEVEIKAPQDAISHKMA 333 Query: 83 TIYQDL---ALIPDLPIYYNIFLAREVTNKI----FLNKKKMMEESKKLLDSLQIRIPDI 135 + +D L L I+ N +A K L+ ++M +S++ L+++ P + Sbjct: 334 FLTEDRRHSGLYLMLDIFANTSIAHLDAYKSRVANVLDVRQMRSDSEEHCKKLKVKTPHM 393 Query: 136 NMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGLGVL 195 + ++NLSGG +Q V +AR + ++ +DEPT + V ++ +L R L G ++ Sbjct: 394 SEAIDNLSGGNQQKVLLARWMLTKPDILFLDEPTRGIDVGAKSEIYKLMRLLTGMGKSLV 453 Query: 196 IITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242 +I+ + + ++DR+ V+ G + K E E E + S AL Sbjct: 454 MISSELPEVIGMSDRVLVMHEGNL----KGELDGTEATQEKIMSMAL 496 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: 251 Number of extensions: 7 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: 497 Length adjustment: 29 Effective length of query: 222 Effective length of database: 468 Effective search space: 103896 Effective search space used: 103896 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 Sep 24 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