Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__psRCH2:GFF16 Length = 278 Score = 221 bits (562), Expect = 2e-62 Identities = 120/250 (48%), Positives = 162/250 (64%), Gaps = 12/250 (4%) Query: 19 IEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVD 78 + + K YG+ VL ++L++ GE++ + GPSGSGKST++R + LE +G I VD Sbjct: 25 VRFAGVTKRYGELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGIDEGVIEVD 84 Query: 79 GIELTN-----------DLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPK 127 G LT+ + + + VR +VGMVFQ FNLFPH+ L+N AP+ V + K Sbjct: 85 GEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQVLGLSK 144 Query: 128 KEAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPE 187 EA A L V + ++ +P QLSGGQQQRVAIAR+L MRPK++LFDE TSALDPE Sbjct: 145 AEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDPE 204 Query: 188 MVKEVLDTMVGLAE-EGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQH 246 + EVL+ + L E +TM+ VTH+MGFAR+ A+RV F QG+I EQ SP E F+NPQ Sbjct: 205 LCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDELFNNPQE 264 Query: 247 ERTKLFLSQI 256 ERT+ FLS + Sbjct: 265 ERTREFLSAV 274 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: 224 Number of extensions: 8 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: 258 Length of database: 278 Length adjustment: 25 Effective length of query: 233 Effective length of database: 253 Effective search space: 58949 Effective search space used: 58949 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: 47 (22.7 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