Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_900105005.1:WP_090275879.1 Length = 334 Score = 163 bits (413), Expect = 4e-45 Identities = 97/255 (38%), Positives = 147/255 (57%), Gaps = 17/255 (6%) Query: 4 LEVQDLHKRY--GSHEV--LKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 +E Q ++K Y G ++ L L AG V IIG SG+GKST LR IN LE+P G+ Sbjct: 2 IEFQQVNKAYRVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNGR 61 Query: 60 ILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVL 119 I++ E+ + N +G L+R R R+ M+FQHFNL S T +N+ P+ + Sbjct: 62 IMVAGEDTTAL-NAEG---------LRRFRQRVGMIFQHFNLLSSATVADNVA-LPLRLA 110 Query: 120 GMS-KTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178 G + + + + L++VG++ YP +SGG++QRV IARALA EP ++L DE TS Sbjct: 111 GSANRQQIAARVASLLDRVGLSDHASKYPAQLSGGQKQRVGIARALATEPSILLCDEATS 170 Query: 179 ALDPELVGDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVL 237 ALDP G VL+++ + +E T+V++THEM R V +Q+ + G + E G +V Sbjct: 171 ALDPHTTGQVLQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTVADVF 230 Query: 238 VNPQSERLQQFLSGS 252 ++PQ + F+ GS Sbjct: 231 LHPQHPTTRSFVFGS 245 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: 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: 334 Length adjustment: 26 Effective length of query: 228 Effective length of database: 308 Effective search space: 70224 Effective search space used: 70224 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 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