Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate H281DRAFT_02573 H281DRAFT_02573 amino acid ABC transporter ATP-binding protein, PAAT family
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__Burk376:H281DRAFT_02573 Length = 252 Score = 268 bits (686), Expect = 6e-77 Identities = 140/246 (56%), Positives = 177/246 (71%), Gaps = 11/246 (4%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 +E+ +HKR+ + EVLKGVSL AG+V+ +IG SGSGKST LRCIN E AG I + Sbjct: 2 IEINAIHKRFYNQEVLKGVSLSVKAGEVVCLIGPSGSGKSTVLRCINGFETYDAGSITI- 60 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 DG A+ K + +R R+ MVFQ FNL++H TA+EN+ME PV+V Sbjct: 61 ----------DGVRVDANAKNIHELRMRVGMVFQRFNLFAHRTALENVMEGPVYVRRTPV 110 Query: 124 AEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 A+ARE+A L KVG+SHR +AYP +SGG+QQRVAIARALAMEPE +LFDEPTSALDPE Sbjct: 111 AQAREQARQLLDKVGLSHRMNAYPSELSGGQQQRVAIARALAMEPEALLFDEPTSALDPE 170 Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 LVG+VL VM++LA++G TMVVVTHEM FAREV++++ FLH G + E+G R VL PQ Sbjct: 171 LVGEVLNVMRSLARDGMTMVVVTHEMAFAREVADRVCFLHGGTICETGPARGVLTEPQHP 230 Query: 244 RLQQFL 249 R Q+FL Sbjct: 231 RTQEFL 236 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: 223 Number of extensions: 8 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: 252 Length adjustment: 24 Effective length of query: 230 Effective length of database: 228 Effective search space: 52440 Effective search space used: 52440 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