Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 278 bits (710), Expect = 2e-79 Identities = 165/373 (44%), Positives = 226/373 (60%), Gaps = 20/373 (5%) Query: 1 MGQIQLTDLTKRFGDTV--AVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSG 58 M ++L ++ K +G + + ++ L I + EFL+LVGPSGCGKST + +AGLET T G Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 59 DIYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEV 118 I IG ++ P++RDIAMVFQ YALYP M+VR+NI FGL+ + A+ D V V Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRK-MPQADIDAEVARV 119 Query: 119 AETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQ 178 A+ L I LL+RKP +LSGGQQQRVA+GRA+ R P+++L DEPLSNLDAKLR EMRTE++ Sbjct: 120 AKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK 179 Query: 179 NLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEP 238 + +L TTVYVTH+Q EAMT+ D++AVM DG +QQ +P E Y+ P N FVA FIG P Sbjct: 180 LMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSP 239 Query: 239 MINLV--RGTRSESTFV-----GEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAP 291 +N V R R + V G+ ++DR D +LG+RPE I +A Sbjct: 240 PMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDR-DVILGLRPEQIMLAAGEG 298 Query: 292 DDAALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTI 351 D A+ ++ +V V EP G ++ + D V + G+ +T+ Sbjct: 299 DSAS----SIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQV-----GETLTLQF 349 Query: 352 PPDKIHLFDAETG 364 P K+ LFDA TG Sbjct: 350 DPSKVLLFDANTG 362 Lambda K H 0.317 0.135 0.386 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: 367 Number of extensions: 14 Number of successful extensions: 4 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: 41 (21.6 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