Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 8502445 DvMF_3151 ABC transporter related (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__Miya:8502445 Length = 242 Score = 217 bits (553), Expect = 2e-61 Identities = 118/249 (47%), Positives = 160/249 (64%), Gaps = 11/249 (4%) Query: 1 MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKI 60 M +E D+HK YG VLKG++ K G+V+ I G SGSGKS+F+RC+N LE G+I Sbjct: 1 MAMIEFHDVHKWYGEFHVLKGITQKVEKGEVLVICGPSGSGKSSFIRCLNRLEPIQKGQI 60 Query: 61 LLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLG 120 LL + + K D +L R+ + +VFQ FNL+ H++ + N+ AP V Sbjct: 61 LLEGKSIHD--------KGVDVNEL---RTEVGIVFQQFNLYPHLSVLHNVTLAPTKVRK 109 Query: 121 MSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSAL 180 M KA+A A L +VG+ + YP +SGG+QQRVAIARALAM+P+VMLFDEPTSAL Sbjct: 110 MPKAKAESIAMELLERVGIHDQARKYPVELSGGQQQRVAIARALAMQPKVMLFDEPTSAL 169 Query: 181 DPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNP 240 DPE++ +VL M+ LA+ G TM+ VTHEMGFAREV++++VF+ G V E P +P Sbjct: 170 DPEMINEVLNAMKDLARAGMTMLCVTHEMGFAREVADRVVFMDGGKVIEEAPPDVFFSSP 229 Query: 241 QSERLQQFL 249 + ER Q FL Sbjct: 230 KHERTQAFL 238 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: 202 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: 242 Length adjustment: 24 Effective length of query: 230 Effective length of database: 218 Effective search space: 50140 Effective search space used: 50140 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