Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__psRCH2:GFF16 Length = 278 Score = 242 bits (617), Expect = 7e-69 Identities = 126/241 (52%), Positives = 172/241 (71%), Gaps = 1/241 (0%) Query: 11 KRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLV 70 KRYG VL G+ L+ G+ ++IIG SGSGKST LR + LE G I ++ E L + Sbjct: 32 KRYGELTVLDGLDLQIEEGEKVAIIGPSGSGKSTLLRVLMTLEGIDEGVIEVDGEPLTHM 91 Query: 71 ANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKAEAREKA 130 + G L A+ + L+R+R ++ MVFQ FNL+ HM A++N+MEAPV VLG+SKAEAR +A Sbjct: 92 PDASGQLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQVLGLSKAEARGRA 151 Query: 131 ELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLK 190 E LA VG+ + + +P +SGG+QQRVAIARALAM P+VMLFDE TSALDPEL G+VL Sbjct: 152 EELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDPELCGEVLN 211 Query: 191 VMQALAQ-EGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFL 249 V++ L + TM++VTH+MGFARE ++++ F H+G + E G+P E+ NPQ ER ++FL Sbjct: 212 VIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDELFNNPQEERTREFL 271 Query: 250 S 250 S Sbjct: 272 S 272 Lambda K H 0.317 0.131 0.364 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: 199 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: 254 Length of database: 278 Length adjustment: 25 Effective length of query: 229 Effective length of database: 253 Effective search space: 57937 Effective search space used: 57937 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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