Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 7026313 Shewana3_3455 ABC transporter related (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__ANA3:7026313 Length = 656 Score = 137 bits (345), Expect = 6e-37 Identities = 78/247 (31%), Positives = 144/247 (58%), Gaps = 19/247 (7%) Query: 4 LEVQDLHKRYGSHE----VLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 LEV ++ + + E VLK ++L A G++++I+G+SGSGKST + + L++P G Sbjct: 6 LEVSACYRSFQAGEQQLTVLKDINLSIARGEMVAIVGASGSGKSTLMNILGCLDKPSKGS 65 Query: 60 ILLNNEELKLVANKDGALKAADPKQLQRMR-SRLSMVFQHFNLWSHMTAMENIMEAPVHV 118 ++ ++ + D +L ++R +FQ ++L + A+ N+ E P Sbjct: 66 YFIDGQDTSQM----------DVDELAKLRREHFGFIFQRYHLLGDLNAVGNV-EVPAVY 114 Query: 119 LGMSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178 G + E RE+AE L+++G+ R D P +SGG+QQRV++ARAL +V+L DEPT Sbjct: 115 AGKDRLERRERAESLLSRLGLGERLDHKPNQLSGGQQQRVSVARALMNGGDVILADEPTG 174 Query: 179 ALDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVV--EESGNPREV 236 ALD ++++++Q L +EG+T+++VTH+M A+ +++++ + GV+ +E + Sbjct: 175 ALDSHSGEEMMRLLQELHREGQTIIIVTHDMHVAQH-ADRIIEIKDGVIISDEPNPASNI 233 Query: 237 LVNPQSE 243 P++E Sbjct: 234 AAAPKTE 240 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: 342 Number of extensions: 13 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: 656 Length adjustment: 31 Effective length of query: 223 Effective length of database: 625 Effective search space: 139375 Effective search space used: 139375 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: 50 (23.9 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