Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_057508907.1 ABB28_RS12160 methionine ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >NCBI__GCF_001431535.1:WP_057508907.1 Length = 335 Score = 162 bits (411), Expect = 6e-45 Identities = 95/254 (37%), Positives = 143/254 (56%), Gaps = 16/254 (6%) Query: 4 LEVQDLHKRYG----SHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 +E Q LHK Y + L+ + L G+V IIG SG+GKST +R IN LE P G+ Sbjct: 2 IEFQRLHKSYAVAGRAISALQPLDLTIQEGEVFGIIGHSGAGKSTLIRMINRLEDPSGGR 61 Query: 60 ILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVL 119 +L+ E++ A + L+ +R R+ M+FQHFNL S T N+ P+ + Sbjct: 62 LLIAGEDVT----------ALETAGLRTLRRRIGMIFQHFNLLSSRTVASNVA-FPLELA 110 Query: 120 GMSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSA 179 G +A+ + L VG+ D YP +SGG++QRV IARALA P+++L DE TSA Sbjct: 111 GTPRAQIDARVAELLQTVGLQAHADKYPAQLSGGQKQRVGIARALATGPQILLCDEATSA 170 Query: 180 LDPELVGDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLV 238 LDP+ VL ++ + +E G T+V++THEM R V +++ L G + E G +V + Sbjct: 171 LDPQTTASVLALLSKINRELGLTIVLITHEMDVIRRVCDRVAVLDAGEMVEMGPVTDVFL 230 Query: 239 NPQSERLQQFLSGS 252 +PQ ++F+S S Sbjct: 231 HPQHPTTRRFVSES 244 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: 195 Number of extensions: 7 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: 335 Length adjustment: 26 Effective length of query: 228 Effective length of database: 309 Effective search space: 70452 Effective search space used: 70452 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