Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_900177295.1:WP_085124759.1 Length = 518 Score = 147 bits (370), Expect = 6e-40 Identities = 80/235 (34%), Positives = 137/235 (58%), Gaps = 1/235 (0%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 LLE+R V + F V ALD V ++ GEV L G+NGAGKST+I +I+G +P G+ F Sbjct: 23 LLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRF 82 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123 G+ V NS + AR LGI ++Q+ +L+P + + N+FL E T L+++ + + + Sbjct: 83 RGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDRADA 142 Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183 +L L + + +V +L+ ++Q V +A+A ++++DEPTA+L+ E ++ +L Sbjct: 143 ILKRLGFPLRPRD-RVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKL 201 Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMT 238 +K +G+GV+ ITH + + + DRI VL G+ + + T E+ +MT Sbjct: 202 IEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMT 256 Score = 80.1 bits (196), Expect = 8e-20 Identities = 61/237 (25%), Positives = 112/237 (47%), Gaps = 12/237 (5%) Query: 6 EIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEG 65 E+ V + A ++ S+ + GE+V L G G+GKS + + G K G + +G Sbjct: 274 ELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKG 333 Query: 66 KKVIFNSPNDARSLGIETI---YQDLALIPDLPIYYNIFLAREVT----NKIFLNKKKMM 118 ++V P G + +D L+ P+ N+ L N L+++ Sbjct: 334 EEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTLAPFGNGALLDRRGET 393 Query: 119 EESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178 + ++L + L ++ P I VE SGG +Q V +A++ ++ DEPT + V Sbjct: 394 DRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPTVGVDVGTRV 453 Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITE 235 + E R+L + G G+L+I+ ++ + +++R YV RG++ + E +EITE Sbjct: 454 AIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRV-----QAELAGDEITE 505 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: 243 Number of extensions: 12 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: 518 Length adjustment: 29 Effective length of query: 222 Effective length of database: 489 Effective search space: 108558 Effective search space used: 108558 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