Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 176 bits (447), Expect = 4e-49 Identities = 102/246 (41%), Positives = 149/246 (60%), Gaps = 14/246 (5%) Query: 7 QDLHKRY--GSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNN 64 QD+ K Y G H L GVSL AG+V +IG+SG+GKST +R IN LE P AG+++++ Sbjct: 5 QDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQVIVDG 64 Query: 65 EELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKA 124 +++ AL A L+ +R R+ M+FQHFNL S T +N+ P+ + G A Sbjct: 65 DDV-------AALGVAG---LRALRRRVGMIFQHFNLLSGKTVAQNVA-FPLKLAGRPAA 113 Query: 125 EAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPEL 184 E + + L +VG+S YP +SGG++QRV IARALA P+V+L DE TSALDPE Sbjct: 114 EVKARTAELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALDPET 173 Query: 185 VGDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 +L ++ L +E G T+V++THEM R V +++ L G V E G EV ++P S+ Sbjct: 174 TEQILDLIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHPASD 233 Query: 244 RLQQFL 249 ++F+ Sbjct: 234 TARRFV 239 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: 193 Number of extensions: 10 Number of successful extensions: 4 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: 332 Length adjustment: 26 Effective length of query: 228 Effective length of database: 306 Effective search space: 69768 Effective search space used: 69768 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: 48 (23.1 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