Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 293 bits (751), Expect = 4e-84 Identities = 180/378 (47%), Positives = 229/378 (60%), Gaps = 25/378 (6%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA L L +V K Y G G ++ I L I +GEFL+LVGPSGCGKST + +AGLET+ Sbjct: 1 MATLELRNVNKTY---GAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETI 57 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T G + + D+ ++G+S +DRDIAMVFQSYALYP SVR N+ FGL+ +P +I V Sbjct: 58 TGGAIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRK-MPQADIDAEV 116 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 +L I LL+RKPGQLSGGQQQRVA+GRA+ R P+++L DEPLSNLDAKLR EMRT Sbjct: 117 ARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ + L TTVYVTHDQ EAMT+GD+VAV+ DG +QQ GTP + Y+ P N FVA FI Sbjct: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFI 236 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPL--SGATRDQLG---GASGL-----TLGIRPEDV- 289 G P MN L R DG L SG R +L +GL LG+RPE + Sbjct: 237 GSPPMNFVPLRLQ----RKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIM 292 Query: 290 -TVGERRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTV 348 GE S + AEV V EP G + V ++ D T+ + G+ T+ Sbjct: 293 LAAGEGDSAS-SIRAEVQVTEPTGPDTLVFVQLND----TKVCCRLAPDVAPQVGETLTL 347 Query: 349 SFPEDAIHLFDGETGDAL 366 F + LFD TG+ L Sbjct: 348 QFDPSKVLLFDANTGERL 365 Lambda K H 0.316 0.136 0.384 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: 447 Number of extensions: 18 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: 383 Length of database: 386 Length adjustment: 30 Effective length of query: 353 Effective length of database: 356 Effective search space: 125668 Effective search space used: 125668 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: 42 (22.0 bits) S2: 50 (23.9 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