Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate 3608829 Dshi_2221 ABC transporter related (RefSeq)
Query= reanno::Smeli:SMc02121 (258 letters) >FitnessBrowser__Dino:3608829 Length = 259 Score = 213 bits (541), Expect = 4e-60 Identities = 115/246 (46%), Positives = 155/246 (63%), Gaps = 10/246 (4%) Query: 19 IEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVD 78 IEI +++K YG VL+ +++R RG+ + + G SGSGKST++RC N LE+ Q+G ++ Sbjct: 9 IEIRDLHKAYGALEVLKGVSIRAERGDVVSLIGSSGSGKSTLLRCCNLLEDSQRGDVLFC 68 Query: 79 GIELT----------NDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKK 128 G +T D K++ +R + MVFQ FNL+ H+TILEN AP+ V P K Sbjct: 69 GEPVTWTGSGLDRRPADKKQVIRIRTNLSMVFQQFNLWAHMTILENVMEAPVTVLGEPPK 128 Query: 129 EAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEM 188 E E A L++V I ++ YP QLSGGQQQR AIAR L M PK LLFDEPTSALDPE+ Sbjct: 129 EVEARARALLDKVGIGDKCDAYPAQLSGGQQQRAAIARGLAMEPKALLFDEPTSALDPEL 188 Query: 189 VKEVLDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHER 248 +EV+ + LA EG TM+ VTH+M A V++ V+F+ QG I E+ P F P+ R Sbjct: 189 EQEVVKVIKDLAAEGRTMLIVTHDMRLAADVSDHVVFLHQGLIEEEGPPDILFGQPKSAR 248 Query: 249 TKLFLS 254 K FLS Sbjct: 249 LKQFLS 254 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: 170 Number of extensions: 5 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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