Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_062737234.1 AYX06_RS17570 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >NCBI__GCF_001580365.1:WP_062737234.1 Length = 255 Score = 236 bits (601), Expect = 4e-67 Identities = 131/247 (53%), Positives = 169/247 (68%), Gaps = 13/247 (5%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 LE++DL +G EVL+ VSL AG IIG SGSGKST LR IN L +P +G +LL Sbjct: 19 LEIRDLTLAFGDIEVLRNVSLSVPAGTTTCIIGPSGSGKSTLLRGINRLHEPKSGDVLLG 78 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 + + L DG +R R+ MVFQHFNL+ TA+EN+ AP +V M + Sbjct: 79 GQSV-LGVKPDG------------LRRRIGMVFQHFNLFPDHTALENVALAPTNVKRMPR 125 Query: 124 AEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 A+AR A +LA+VG++ R D P +SGG+QQRVAIARALAMEPEVMLFDE TSALDPE Sbjct: 126 AQARTLAHKHLAEVGLAERADHRPRDLSGGQQQRVAIARALAMEPEVMLFDEATSALDPE 185 Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 LV VL +M L+ G TMVVVTHEM FAR+V++Q+VF+ +G V E+G P+++ NP S+ Sbjct: 186 LVKGVLDLMAGLSHSGMTMVVVTHEMHFARKVADQVVFMDEGKVVEAGTPQQIFDNPGSD 245 Query: 244 RLQQFLS 250 RL++FLS Sbjct: 246 RLRRFLS 252 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: 208 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: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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 24 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