Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__HerbieS:HSERO_RS02210 Length = 372 Score = 337 bits (864), Expect = 3e-97 Identities = 182/369 (49%), Positives = 243/369 (65%), Gaps = 16/369 (4%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA V+++ L KRY EV+ I+LE++D EF+ VGPSGCGKST LRMIAGLEE+S G + Sbjct: 1 MAAVSIRNLAKRYDDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDGDL 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 +IG R++N++P R ++MVFQSYALYPHM++ +NM F LKIAG+ EI V AA I Sbjct: 61 DIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAAKI 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L + HLL+R+P LSGGQRQRVA+GRAI RQP VFLFDEPLSNLDA LR ++R E KLH Sbjct: 121 LHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAKLH 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 ++ TMIYVTHDQ+EAMTL+D+IV++ +G IEQVG+P+ ++ PA +FVAGFIGSP MN Sbjct: 181 DDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPKMN 240 Query: 241 MEE----AVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDA 296 + A+ DG G L S ++ GQKVT G+RP+ H A Sbjct: 241 FIDGTVAAIQADGVQVQLPGGGLQWAAVDGSTLQVGQKVTLGVRPE---------HLNIA 291 Query: 297 DAVHEIELPVTITEPLGNETLVFTQFNGRD--WVSRMLNPRPLRPGEAVPMSFDLARAHL 354 ++ T E LG+ + ++ + G + + R+ + G +P++ D AR HL Sbjct: 292 QGQAALQARCTALELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADPARCHL 351 Query: 355 FDGETGRAL 363 F G G+AL Sbjct: 352 F-GADGQAL 359 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: 390 Number of extensions: 19 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: 372 Length adjustment: 30 Effective length of query: 335 Effective length of database: 342 Effective search space: 114570 Effective search space used: 114570 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