Align ABC transporter (characterized, see rationale)
to candidate H281DRAFT_02629 H281DRAFT_02629 carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-)
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Burk376:H281DRAFT_02629 Length = 381 Score = 342 bits (876), Expect = 1e-98 Identities = 185/368 (50%), Positives = 242/368 (65%), Gaps = 10/368 (2%) Query: 1 MIKLKLDNVNKQL-GGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGD 59 M + L + K G +LRD++LEI EF VF+GPSGCGKSTLLR++AGL+ GD Sbjct: 1 MAAISLRGIQKTFDGNAPVLRDLNLEIGEHEFCVFLGPSGCGKSTLLRIVAGLEDQTDGD 60 Query: 60 LLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQ 119 + I GR +N + ERGV MVFQSYAL+PHM+VY+N++FGLKLA+T K + +V + A Sbjct: 61 VSIGGRTMNSVPAAERGVAMVFQSYALFPHMTVYENMAFGLKLARTPKAEIDRKVREAAH 120 Query: 120 ILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARL 179 +LQLD LL RKP+ELSGGQRQRVA+GRA+ REP + LFDEPLSNLDA+LR Q R EIARL Sbjct: 121 VLQLDALLARKPRELSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDAALRGQTRIEIARL 180 Query: 180 HDRLG-STMIYVTHDQVEAMTLADKIVVLNG-------GRVEQVGSPRELYERPASRFVA 231 H R ++++YVTHDQ+EAMTLADKIV+L+ G + Q+G+P ELY RP S+FVA Sbjct: 181 HQRYAQASVVYVTHDQIEAMTLADKIVLLHAGAETQRLGSIAQIGAPLELYHRPRSKFVA 240 Query: 232 GFLGSPRMNFLSARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKA 291 GF+GSPRMNF+ ++ + S+ ++ + D L G ++LGIRPEHV Sbjct: 241 GFIGSPRMNFIDGVVERIADDSVEVSMPGTALRVLVDGRRLKPGQRVTLGIRPEHVRFDG 300 Query: 292 ADGTAGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFD 351 T V E LG +Y+H + LI + + G+R+ L L D HLFD Sbjct: 301 GTQTLAVNALLTEQLGEHSYLHADHA-GGTLIAKAPGDLHVRNGERLALHLPADACHLFD 359 Query: 352 ADGVALSR 359 DG+AL R Sbjct: 360 EDGIALHR 367 Lambda K H 0.320 0.137 0.394 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: 398 Number of extensions: 12 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: 381 Length of database: 381 Length adjustment: 30 Effective length of query: 351 Effective length of database: 351 Effective search space: 123201 Effective search space used: 123201 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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