Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 122 bits (307), Expect = 6e-33 Identities = 88/260 (33%), Positives = 137/260 (52%), Gaps = 25/260 (9%) Query: 3 KLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHA----- 57 K+ + ++ YG + ++ VS+ +V + IG SG GKSTFLR +N + A Sbjct: 28 KMAARGVNVFYGEKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVE 87 Query: 58 GKILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAP-V 116 G+I L+ E + K+ D QL R+R+ MVFQ N + + EN+ P + Sbjct: 88 GEITLDGENIYD--------KSMDVVQL---RARVGMVFQKPNPFPK-SIYENVAYGPRI 135 Query: 117 HVLGMSKTEAREKAEHYLNKVG----VAHRKDAYPGHMSGGEQQRVAIARALAMEPEVML 172 H L +K + + E L + G V R + +SGG+QQR+ IARA+A++PEV+L Sbjct: 136 HGLARAKGDMDQIVERSLKRAGLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVIL 195 Query: 173 FDEPTSALDPELVGDVLKVMQALAQEGR-TMVVVTHEMGFAREVSNQLVFLHKGVVEESG 231 DEP SALDP + +++ L GR +V+VTH M A VS + F H G + E G Sbjct: 196 MDEPCSALDPIATAKIEELIHEL--RGRYAIVIVTHNMQQAARVSQRTAFFHLGTLVEYG 253 Query: 232 NPREVLVNPQSERLQQFLSG 251 ++ P+ ER + +++G Sbjct: 254 ETDQIFTAPRQERTKDYITG 273 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: 10 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: 276 Length adjustment: 25 Effective length of query: 229 Effective length of database: 251 Effective search space: 57479 Effective search space used: 57479 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