Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate SMa2195 SMa2195 ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Smeli:SMa2195 Length = 254 Score = 243 bits (621), Expect = 2e-69 Identities = 128/241 (53%), Positives = 173/241 (71%), Gaps = 3/241 (1%) Query: 11 KRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLV 70 K YGS VL ++L+ A G+VIS+IG SGSGKST LRC+N LE+ G I ++ E + Sbjct: 13 KSYGSMTVLNDINLEIATGEVISLIGPSGSGKSTLLRCVNHLERIERGSITVDGELIGY- 71 Query: 71 ANKDGALKAADPKQL-QRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREK 129 + G L P++L R R+ + MVFQ+FNL+ H TA+EN++EAPVHV G+++ +A + Sbjct: 72 -RRVGNLAHELPEKLVARQRAGIGMVFQNFNLFGHKTALENVIEAPVHVRGLARRDAEAQ 130 Query: 130 AEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVL 189 A L +VG+A + +YP +SGG+QQRVAIARALAM+P+V+LFDEPTSALDPELVG+VL Sbjct: 131 ATALLERVGLADKMQSYPRMLSGGQQQRVAIARALAMKPKVLLFDEPTSALDPELVGEVL 190 Query: 190 KVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFL 249 VM++LA EG TM+VVTHEM FAREV N++ F+ G + E G P E+ P +R + FL Sbjct: 191 DVMRSLAAEGLTMMVVTHEMSFAREVCNRIAFMQAGEIVECGAPSEIFDKPAFQRTRSFL 250 Query: 250 S 250 S Sbjct: 251 S 251 Lambda K H 0.317 0.131 0.366 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: 195 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: 254 Length adjustment: 24 Effective length of query: 230 Effective length of database: 230 Effective search space: 52900 Effective search space used: 52900 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