Align ABC transporter (characterized, see rationale)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Burk376:H281DRAFT_03228 Length = 383 Score = 342 bits (876), Expect = 1e-98 Identities = 188/372 (50%), Positives = 244/372 (65%), Gaps = 16/372 (4%) Query: 1 MIKLKLDNVNKQLG-GMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGD 59 M + L V K G G ++RDV LEI EF VF+GPSGCGKSTLLR+IAGL+ + GD Sbjct: 1 MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 LLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQ 119 L I G+ +ND+ +RGV MVFQSYAL+PHM+V++N++FGLKLAKT K + +V + A+ Sbjct: 61 LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120 Query: 120 ILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARL 179 ILQL+ LL+R+PK LSGGQRQRVA+GRA+ R+P + LFDEPLSNLDA+LR Q R EIARL Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 HDRLG-STMIYVTHDQVEAMTLADKIVVLNGGR-------VEQVGSPRELYERPASRFVA 231 H + ++++YVTHDQ+EAMTLADKIV+L+ G+ + Q+G+P ELY RP SRFVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFVA 240 Query: 232 GFLGSPRMNFLSARLQTPGETSLVDTL--VWGITSLPFDSSNLAAGTPLSLGIRPEH--- 286 GF+GSPRMNFL R+ + +V TL +P D + L ++LG+RPEH Sbjct: 241 GFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADGAALQVSQAVTLGVRPEHLEF 300 Query: 287 --VSLKAADGTAGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDL 344 +S D V+ VE LG +YVHL+ LI + GDR L + Sbjct: 301 ADLSSSHDDAVLSRTVSLVEQLGEHSYVHLDQPGGVALIAKAPGDTRLAPGDRANLRVPR 360 Query: 345 DNLHLFDADGVA 356 HLF DG A Sbjct: 361 HATHLFTEDGFA 372 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: 377 Number of extensions: 14 Number of successful extensions: 5 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: 383 Length adjustment: 30 Effective length of query: 351 Effective length of database: 353 Effective search space: 123903 Effective search space used: 123903 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