Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_011383782.1 AMB_RS06945 phosphate ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_000009985.1:WP_011383782.1 Length = 259 Score = 134 bits (336), Expect = 2e-36 Identities = 89/254 (35%), Positives = 133/254 (52%), Gaps = 13/254 (5%) Query: 3 KLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62 K+ + L+ YG + L + L AG+V ++IG SG GKSTFLRCIN + G + Sbjct: 11 KISARGLNVHYGEKQALHDIDLDIPAGEVTALIGPSGCGKSTFLRCINRMNDMVDGAKVT 70 Query: 63 NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAP-VHVLGM 121 + L DG+ + ++R+R+ MVFQ N + + +N+ P +H L Sbjct: 71 GSLTL------DGSDVYDRSLDVVQLRARVGMVFQKPNPFPK-SIYDNVAYGPRIHGLAR 123 Query: 122 SKTEAREKAEHYLNKVG----VAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPT 177 + E E + L K G V R +SGG+QQR+ IARA+A+ PEV+L DEP Sbjct: 124 DQAELDEIVMNSLEKAGLLAEVESRLSESGTGLSGGQQQRLCIARAIAVAPEVILMDEPC 183 Query: 178 SALDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVL 237 SALDP V +++ L ++ T+V+VTH M A VS + F H G + E G E+ Sbjct: 184 SALDPIATAKVEELIDEL-RDNYTIVIVTHSMQQAARVSQRTAFFHLGKLIEVGGTEEIF 242 Query: 238 VNPQSERLQQFLSG 251 NP+ Q +++G Sbjct: 243 TNPKEPLTQGYITG 256 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: 148 Number of extensions: 9 Number of successful extensions: 3 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: 259 Length adjustment: 24 Effective length of query: 230 Effective length of database: 235 Effective search space: 54050 Effective search space used: 54050 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