Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_019867231.1 METMI_RS0115610 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >NCBI__GCF_000384075.1:WP_019867231.1 Length = 371 Score = 231 bits (588), Expect = 2e-65 Identities = 113/247 (45%), Positives = 175/247 (70%), Gaps = 11/247 (4%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 ++V L K + VL +S + G+VI+IIG SG+GKSTFLRC+NLLEQP G I ++ Sbjct: 2 IKVGHLSKSFAGTTVLADISTEIKKGEVIAIIGPSGTGKSTFLRCLNLLEQPSGGTIEID 61 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 ++ K AD + ++R +++MVFQ FNL+SH++ ++N+ AP+ + GMS Sbjct: 62 GMDI--------LDKKAD---IAKIRQKMNMVFQSFNLFSHLSVLDNLTLAPIRLKGMST 110 Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 +A+ KA L VG+A + D+YP +SGG++QRVAIAR LAMEPE++LFDEPTSALDP Sbjct: 111 QDAQAKALELLRLVGLAEKADSYPDELSGGQKQRVAIARCLAMEPEIILFDEPTSALDPT 170 Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 ++ +VL V++ LA++G TM +VTHEM FA++VSN+++++ +G++ E G+P ++ NPQ E Sbjct: 171 MISEVLSVIRRLAKDGMTMAIVTHEMDFAKDVSNRVLYMDEGLIYEEGSPAQIFDNPQKE 230 Query: 244 RLQQFLS 250 + + F++ Sbjct: 231 KTKAFIN 237 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: 202 Number of extensions: 7 Number of successful extensions: 2 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: 371 Length adjustment: 27 Effective length of query: 227 Effective length of database: 344 Effective search space: 78088 Effective search space used: 78088 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