Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate SMc02260 SMc02260 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__Smeli:SMc02260 Length = 284 Score = 311 bits (796), Expect = 1e-89 Identities = 155/247 (62%), Positives = 196/247 (79%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 + V DLHKR+G EVLKGVSL A GDVI+IIG SGSGKST LRCIN+LE P AG+I ++ Sbjct: 35 IAVTDLHKRFGPLEVLKGVSLSARQGDVIAIIGGSGSGKSTLLRCINMLELPSAGQISVH 94 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 EE+++ + G L AD KQ+QR+R++L MVFQ FNLW HMT ++N++EAPVHVLG +K Sbjct: 95 GEEIRMKPDGHGGLMPADRKQVQRIRTQLGMVFQSFNLWQHMTILQNVIEAPVHVLGKTK 154 Query: 124 AEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 AEA E AE L +VG+ ++DAYP +SGG+QQR AIARALA++P VMLFDEPTSALDPE Sbjct: 155 AEAVETAEALLRRVGLYEKRDAYPAFLSGGQQQRAAIARALAIQPLVMLFDEPTSALDPE 214 Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 LVG+VL V+ LA+E RTMV+VTHEM FAR+V+N +VFLH GV+EE G P + P+SE Sbjct: 215 LVGEVLSVIGDLAREERTMVLVTHEMKFARDVANHIVFLHNGVIEEQGPPEAIFGAPKSE 274 Query: 244 RLQQFLS 250 RL++F+S Sbjct: 275 RLKKFIS 281 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: 221 Number of extensions: 4 Number of successful extensions: 1 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: 284 Length adjustment: 25 Effective length of query: 229 Effective length of database: 259 Effective search space: 59311 Effective search space used: 59311 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