Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate AZOBR_RS27075 AZOBR_RS27075 arginine ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__azobra:AZOBR_RS27075 Length = 254 Score = 245 bits (626), Expect = 6e-70 Identities = 127/248 (51%), Positives = 168/248 (67%), Gaps = 4/248 (1%) Query: 3 KLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62 K+EV L K++G VL+ ++LK G V+++IG SGSGKST LRC+NLL P+ G+I + Sbjct: 5 KIEVAGLRKQFGELVVLRDITLKVDPGAVVALIGPSGSGKSTLLRCLNLLVVPNGGRIRI 64 Query: 63 NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122 + K PK + RS MVFQHFNL+ HMT + N+ME PV M Sbjct: 65 GGDAFDFETGK----ALPRPKAQAKFRSNTGMVFQHFNLFPHMTVLGNVMEGPVSAKNMP 120 Query: 123 KAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182 KA+A LAKVG++ + +AYP +SGG++QRVAIARALAMEPEVMLFDE TSALDP Sbjct: 121 KAQAEAIGRRLLAKVGLADKAEAYPDRLSGGQKQRVAIARALAMEPEVMLFDEATSALDP 180 Query: 183 ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242 ELV +VL VM+ LA EG TM++VTHE+ FAREV+++++F+ GV+ E G R+V+ PQ Sbjct: 181 ELVSEVLGVMRDLAAEGMTMIIVTHEIAFAREVADRVIFMRDGVIVEEGPARDVIDRPQQ 240 Query: 243 ERLQQFLS 250 E + FLS Sbjct: 241 EATRAFLS 248 Lambda K H 0.317 0.131 0.364 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: 184 Number of extensions: 7 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: 254 Length adjustment: 24 Effective length of query: 230 Effective length of database: 230 Effective search space: 52900 Effective search space used: 52900 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: 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