Align D-xylose ABC transporter, periplasmic D-xylose-binding protein (characterized)
to candidate N515DRAFT_3231 N515DRAFT_3231 xylose-binding protein
Query= CharProtDB::CH_003787 (330 letters) >FitnessBrowser__Dyella79:N515DRAFT_3231 Length = 341 Score = 394 bits (1012), Expect = e-114 Identities = 194/337 (57%), Positives = 255/337 (75%), Gaps = 9/337 (2%) Query: 3 IKNILLTLCTSLLLTNVAAHA---------KEVKIGMAIDDLRLERWQKDRDIFVKKAES 53 +K + + +L+ T +A A + KIG +IDD+RLERW +DRD FV AE Sbjct: 1 MKRLFARVLLALVATGLAVAALTACSGKASDQPKIGFSIDDMRLERWTRDRDYFVAAAEK 60 Query: 54 LGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYD 113 LGAKV+VQSA+GNE+ Q+ Q+EN+I+RGV+VLVI+P+N +VL NV+ EAK+ GIKV++YD Sbjct: 61 LGAKVYVQSADGNEQRQVQQLENLISRGVNVLVIVPFNSKVLDNVIAEAKRNGIKVISYD 120 Query: 114 RMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLK 173 R+I AD+D YISFDNEKVGELQA+ ++D VP+GNYFL+GGSP DNNAK+ R GQ+KVL+ Sbjct: 121 RLILGADVDAYISFDNEKVGELQAQGVLDAVPKGNYFLLGGSPTDNNAKILREGQLKVLQ 180 Query: 174 PYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQ 233 P +D G +K+VG QW W AL+I+E+ALTAN+N I +VASNDATAGGAIQAL+AQ Sbjct: 181 PAIDRGDVKIVGQQWTPEWDASKALRIVEDALTANHNDIQGIVASNDATAGGAIQALAAQ 240 Query: 234 GLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTL 293 L+GKVA+SGQDADLAG++R+ GTQ MTVYKP+ +A TAAE+AV+L G+ P + Sbjct: 241 QLAGKVAVSGQDADLAGVRRVVDGTQAMTVYKPLKTIATTAAELAVKLAKGEAPTYTGKM 300 Query: 294 NNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL 330 NNG KDV S LL P + K+ + DTVIKDGF+ ++ Sbjct: 301 NNGKKDVDSVLLQPTLLTKDKVDDTVIKDGFYTREQI 337 Lambda K H 0.314 0.132 0.366 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: 387 Number of extensions: 12 Number of successful extensions: 1 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: 330 Length of database: 341 Length adjustment: 28 Effective length of query: 302 Effective length of database: 313 Effective search space: 94526 Effective search space used: 94526 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: 49 (23.5 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