Align Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized)
to candidate Synpcc7942_0564 Synpcc7942_0564 ATPase
Query= SwissProt::P0AAF6 (242 letters) >FitnessBrowser__SynE:Synpcc7942_0564 Length = 237 Score = 145 bits (366), Expect = 7e-40 Identities = 86/226 (38%), Positives = 137/226 (60%), Gaps = 9/226 (3%) Query: 3 IQLNGINCFYG----AHQALFDITLDCPQGETLVLLGPSGAGKSSLLRVLNLLEMPRSGT 58 + + ++ FYG Q LFD+ D GE ++L GPSG GK++LL ++ L ++GT Sbjct: 7 VSIRNLDHFYGHDSLQKQVLFDVGFDLNPGEIVLLTGPSGCGKTTLLTLIGGLRSVQAGT 66 Query: 59 LNIAGNHFDFTKTPSDKAIRDLRRNVGMVFQQYNLWPHLTVQQNLIEAPCRVLGLSKDQA 118 L++ G S + ++RRN+G +FQ +NL LT QN+ L+ D+ Sbjct: 67 LSVLGQELHGA---SQRQRVEVRRNIGYIFQAHNLLRFLTASQNVQMTLDLQADLNWDER 123 Query: 119 LARAEKLLERLRLKPYSDRYPLHLSGGQQQRVAIARALMMEPQVLLFDEPTAALDPEITA 178 +AR+ ++LE + L + D YP +LSGGQ+QRVAIARAL+ P+++L DEPTAALD + Sbjct: 124 IARSHQMLEAVGLGDHLDYYPENLSGGQKQRVAIARALVGRPKLVLADEPTAALDRQSGR 183 Query: 179 QIVSIIRELA-ETNITQVIVTHEVEVARKTASRVVYMENGHIVEQG 223 +V ++++LA E T ++VTH+ + A R++ ME+G +V+ G Sbjct: 184 DVVDLMQQLAKEQGCTILLVTHDNRIL-DIADRILEMEDGRLVKGG 228 Lambda K H 0.320 0.135 0.391 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: 147 Number of extensions: 6 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: 242 Length of database: 237 Length adjustment: 23 Effective length of query: 219 Effective length of database: 214 Effective search space: 46866 Effective search space used: 46866 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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