Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate Pf6N2E2_2889 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2889 Length = 386 Score = 296 bits (757), Expect = 9e-85 Identities = 181/377 (48%), Positives = 229/377 (60%), Gaps = 23/377 (6%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA L L +V K Y G G ++ I L I DGEFL+LVGPSGCGKST + +AGLET+ Sbjct: 1 MATLELRNVNKTY---GVGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETI 57 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T G + + D+ ++G+S +DRDIAMVFQSYALYP SVR N+ FGL+ + I + V Sbjct: 58 TGGAIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRK-MNQAAIDEEV 116 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 +L I LL+RKPGQLSGGQQQRVA+GRA+ R P+++L DEPLSNLDAKLR EMRT Sbjct: 117 TRVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E++ + L TTVYVTHDQ EAMT+GD+VAV+ DG +QQ GTP D Y P NLFVA FI Sbjct: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFI 236 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPL--SGATRDQLGGA---SGL-----TLGIRPEDVT 290 G P MN L R DG L SG R +L +GL LG+RPE + Sbjct: 237 GSPPMNFIPLRLQ----RKDGRLLALLDSGQARCELPMGMQDAGLEDREVILGMRPEQIM 292 Query: 291 V-GERRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVS 349 + G +G T AEV V EP G + V + D T+ + G+ T+ Sbjct: 293 LAGSEPNGLPTIRAEVQVTEPTGPDTLVFVNLND----TKVCCRLAPDVAPQPGETLTLQ 348 Query: 350 FPEDAIHLFDGETGDAL 366 F + LFD ++G+ L Sbjct: 349 FDPSKVLLFDAQSGERL 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: 478 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