Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 337 bits (863), Expect = 4e-97 Identities = 190/368 (51%), Positives = 239/368 (64%), Gaps = 15/368 (4%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA VTL+ + K +G +EV+HG+DLEV D EF+A VGPSGCGKST LR+IAGLEE SGG + Sbjct: 1 MAGVTLRGVRKSFGRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDL 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 IGG++VND PP AR I+MVFQSYALYPHMT +NM F L ++ I RV AA + Sbjct: 61 SIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARL 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L + LL+R+P LSGGQRQRVA+GRAIVR+P VFLFDEPLSNLDA LR Q+R EI KL Sbjct: 121 LQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKLK 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 A ++ATMIYVTHDQVEAMTL+DRIV++ G +EQ GTP +++ RP +FVAGFIGSP MN Sbjct: 181 ADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPAMN 240 Query: 241 MEEAV---LTDGKLAFASGATLPLPPRFRSLV-REGQKVTFGLRPDDVYPSGHGLHAGDA 296 + V LTDG + +PL G +T G+RP+ H G A Sbjct: 241 FLDVVSEGLTDGSVRVWLPGGVPLDIAVDGAAPAAGTPLTLGVRPE---------HVGLA 291 Query: 297 DAVHEIELPVTITEPLGNETLVFTQF-NGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLF 355 D + + E LG ET +G+ + R+ RP+ GE + ++ AHLF Sbjct: 292 DGGAGLLATILAVERLGGETHCHAALEDGQRLLVRLDGDRPVAAGERLRLNLRGETAHLF 351 Query: 356 DGETGRAL 363 G G+ L Sbjct: 352 -GPDGQRL 358 Lambda K H 0.320 0.137 0.397 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: 419 Number of extensions: 17 Number of successful extensions: 2 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: 365 Length of database: 358 Length adjustment: 29 Effective length of query: 336 Effective length of database: 329 Effective search space: 110544 Effective search space used: 110544 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: 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