Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate 3608244 Dshi_1648 ABC transporter related (RefSeq)
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__Dino:3608244 Length = 373 Score = 148 bits (374), Expect = 1e-40 Identities = 87/238 (36%), Positives = 137/238 (57%), Gaps = 9/238 (3%) Query: 19 IEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVD 78 +++T + K YGD VL +INL + +GE IV GPSG GKST++R I LE+ G + +D Sbjct: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 Query: 79 GIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAMHFL 138 G + ND + +R + MVFQ + L+PH+T+ EN + A + + K + E + Sbjct: 64 G-TVVND---VPPAQRGIAMVFQSYALYPHMTVRENMSFA-LKIAKKSQAEIDAAVEAAA 118 Query: 139 ERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMVG 198 E++++ + + P LSGGQ+QRVAI RS+ PK+ LFDEP S LD + + + Sbjct: 119 EKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAAL-RVATRLEIA 177 Query: 199 LAEEGM---TMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLFL 253 +E M TM+ VTH+ A +A R++ + G I + SP E ++ P++E F+ Sbjct: 178 QLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFI 235 Lambda K H 0.322 0.136 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: 235 Number of extensions: 8 Number of successful extensions: 4 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: 258 Length of database: 373 Length adjustment: 27 Effective length of query: 231 Effective length of database: 346 Effective search space: 79926 Effective search space used: 79926 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 (21.9 bits) S2: 48 (23.1 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