Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 206400 DVU0968 amino acid ABC transporter, ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >MicrobesOnline__882:206400 Length = 246 Score = 218 bits (556), Expect = 7e-62 Identities = 115/234 (49%), Positives = 162/234 (69%), Gaps = 14/234 (5%) Query: 19 LKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLVANKDGALK 78 L+ VSL A G+V+ IIG SGSGKSTFLRC+N LE +G+IL+ ++ Sbjct: 22 LRDVSLDVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADSGEILIEGRDI----------- 70 Query: 79 AADPK-QLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREKAEHYLNKV 137 DPK ++ +R+ + MVFQ FNL+ H++ +EN+ A + V S+ E+ +K L KV Sbjct: 71 -LDPKCEINEVRAEVGMVFQSFNLFPHLSVLENVALAQMTVRKRSRAESEKKGMELLTKV 129 Query: 138 GVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLKVMQALAQ 197 G+A + YP +SGG+QQRVAIAR+LAM+P++MLFDEPTSALDPE+VG+VL VM+ LA+ Sbjct: 130 GIADKHAVYPDQLSGGQQQRVAIARSLAMDPKIMLFDEPTSALDPEMVGEVLDVMRNLAR 189 Query: 198 EGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS-ERLQQFLS 250 EG TMVVVTHEMGFAREV++++VF+ G + E P+++ + +R + FLS Sbjct: 190 EGMTMVVVTHEMGFAREVADRVVFMDHGAILEIATPKDLFTTGATHDRTKLFLS 243 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: 192 Number of extensions: 6 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: 246 Length adjustment: 24 Effective length of query: 230 Effective length of database: 222 Effective search space: 51060 Effective search space used: 51060 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: 46 (22.3 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