Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 3608829 Dshi_2221 ABC transporter related (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Dino:3608829 Length = 259 Score = 276 bits (705), Expect = 4e-79 Identities = 140/249 (56%), Positives = 183/249 (73%), Gaps = 1/249 (0%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 +E++DLHK YG+ EVLKGVS++A GDV+S+IGSSGSGKST LRC NLLE G +L Sbjct: 9 IEIRDLHKAYGALEVLKGVSIRAERGDVVSLIGSSGSGKSTLLRCCNLLEDSQRGDVLFC 68 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 E + + + AD KQ+ R+R+ LSMVFQ FNLW+HMT +EN+MEAPV VLG Sbjct: 69 GEPVTWTGSGLDR-RPADKKQVIRIRTNLSMVFQQFNLWAHMTILENVMEAPVTVLGEPP 127 Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 E +A L+KVG+ + DAYP +SGG+QQR AIAR LAMEP+ +LFDEPTSALDPE Sbjct: 128 KEVEARARALLDKVGIGDKCDAYPAQLSGGQQQRAAIARGLAMEPKALLFDEPTSALDPE 187 Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 L +V+KV++ LA EGRTM++VTH+M A +VS+ +VFLH+G++EE G P + P+S Sbjct: 188 LEQEVVKVIKDLAAEGRTMLIVTHDMRLAADVSDHVVFLHQGLIEEEGPPDILFGQPKSA 247 Query: 244 RLQQFLSGS 252 RL+QFLS + Sbjct: 248 RLKQFLSAT 256 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: 208 Number of extensions: 4 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: 259 Length adjustment: 24 Effective length of query: 230 Effective length of database: 235 Effective search space: 54050 Effective search space used: 54050 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