Align Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= SwissProt::P0AAF6 (242 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 131 bits (330), Expect = 1e-35 Identities = 82/208 (39%), Positives = 128/208 (61%), Gaps = 17/208 (8%) Query: 20 DITLDCPQGETLVLLGPSGAGKSSLLRVLNLLEMPRSGTLNIAGNH-FDFTKTPSDKAIR 78 DI L QGE + L GPSG+GK+S LR+++ L P G L++ G FD + K + Sbjct: 20 DIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGEQWFDAS---FGKNVS 76 Query: 79 DLRRNVGMVFQQYNLWPHLTVQQNLIEAPCRVLGLSKDQALARAEKLLERLRLKPYSDRY 138 RR +G +FQ Y+L+P++TV++N+ A L +KD+A +LLE + L D Sbjct: 77 PGRRKLGYLFQDYSLFPNMTVKENIAFA----LKNAKDKAYLM--ELLESMGLLHLQDTL 130 Query: 139 PLHLSGGQQQRVAIARALMMEPQVLLFDEPTAALDP----EITAQIVSIIRELAETNITQ 194 P HLSGGQQQRVA+ARAL ++P +LL DEP +ALDP ++ I++I R+ A +T Sbjct: 131 PKHLSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIHRKYA---LTT 187 Query: 195 VIVTHEVEVARKTASRVVYMENGHIVEQ 222 ++V+H+ K + R++ +++G ++ Q Sbjct: 188 ILVSHDAGEIIKLSDRIIELDHGKVLRQ 215 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: 131 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: 242 Length of database: 290 Length adjustment: 25 Effective length of query: 217 Effective length of database: 265 Effective search space: 57505 Effective search space used: 57505 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: 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