Align arginine/ornithine transport protein (characterized)
to candidate AZOBR_RS15675 AZOBR_RS15675 ABC transporter permease
Query= CharProtDB::CH_107317 (229 letters) >FitnessBrowser__azobra:AZOBR_RS15675 Length = 224 Score = 101 bits (251), Expect = 1e-26 Identities = 59/197 (29%), Positives = 104/197 (52%), Gaps = 12/197 (6%) Query: 9 IVDGAWLTLQLALLSMLLAIVLGLLGAAFRLSPVRWLAWCGDLYATVVRGIPDLVLILLI 68 ++ GAWLT+QL++ +M+L +++ +L A + S + + W + Y VVR P LV I LI Sbjct: 17 LLQGAWLTVQLSIGAMVLGLIVAILCALGKTSGPKPVRWVINAYIEVVRNTPFLVQIFLI 76 Query: 69 FYGGQGLLNWVAPQLGYDDYIDLNPFVSGVGTLGFIFGAYLSETFRGAFMAIPKGQGEAG 128 F+G P +G + L+P ++ + + GAY +E R +I KGQ EAG Sbjct: 77 FFG--------LPTMG----VRLSPDLAALIAMVVNVGAYATEIIRAGIESIQKGQIEAG 124 Query: 129 YGYGMSHRQVFFRIQVPQMIRLAIPGFTNNWLVLVKATALISVVGLQDMMFKAKQASDAT 188 G+ QVF I + +R P T+ +++L+ +++++S + ++ A T Sbjct: 125 LALGLKPLQVFRYIVIKPALRTVYPALTSQFILLMLSSSVVSAISADELTSVANNIQSQT 184 Query: 189 REPFTYYLAVAGLYLLV 205 F Y+ V G+YL++ Sbjct: 185 FRSFEIYIVVTGIYLML 201 Lambda K H 0.328 0.144 0.442 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: 91 Number of extensions: 4 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: 229 Length of database: 224 Length adjustment: 22 Effective length of query: 207 Effective length of database: 202 Effective search space: 41814 Effective search space used: 41814 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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