Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Echvi_4044 Echvi_4044 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Cola:Echvi_4044 Length = 249 Score = 131 bits (329), Expect = 2e-35 Identities = 79/249 (31%), Positives = 133/249 (53%), Gaps = 16/249 (6%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRC-INLLEQPHAGKILL 62 +EV+ L K +G +VL GV L G+ + ++G SG+GKS ++ + LL Q +L Sbjct: 6 VEVRGLKKSFGELDVLMGVDLDLYKGENVVVLGKSGTGKSVLIKIMVGLLTQDEGTMNVL 65 Query: 63 NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPV--HVLG 120 E L A K L +R ++ FQ L+ MT EN+ E P+ +V G Sbjct: 66 GKEVSNLGA-----------KDLNELRLKIGFSFQASALYDSMTVRENL-EFPLVRNVKG 113 Query: 121 MSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSAL 180 +S+TE + E L VG++ + P +SGG+++R+ IAR L ++PE+ML+DEPT+ L Sbjct: 114 LSRTEKDKMVEEVLEAVGLSQTINQMPSELSGGQRKRIGIARTLILKPEIMLYDEPTAGL 173 Query: 181 DPELVGDVLKVMQALAQEGRT-MVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVN 239 DP D+ ++ + + T +++TH++ AR+ +++ L G G EV Sbjct: 174 DPITCSDINNLINEVRENYNTSSIIITHDLTCARDTGDRVAVLLDGQFGAEGKFEEVFKT 233 Query: 240 PQSERLQQF 248 P+ +R++ F Sbjct: 234 PEDQRVKSF 242 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: 129 Number of extensions: 5 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: 249 Length adjustment: 24 Effective length of query: 230 Effective length of database: 225 Effective search space: 51750 Effective search space used: 51750 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: 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