Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 3607646 Dshi_1055 ABC transporter related (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Dino:3607646 Length = 366 Score = 132 bits (331), Expect = 1e-35 Identities = 82/249 (32%), Positives = 137/249 (55%), Gaps = 21/249 (8%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 +EV+ L K YG + L+ V L AAG+ ++G SG GK+T LR I +P G++LL+ Sbjct: 9 VEVKGLSKHYGPVKALRQVDLTIAAGEYFVLLGPSGGGKTTLLRTIGGFHRPTEGQVLLH 68 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 ++ L + +MVFQ + L+ HMT ++N+ + V GM K Sbjct: 69 GRDMS---------------HLPPDKRPTTMVFQAYALFPHMTVLQNVSYG-LKVAGMDK 112 Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 A+EKA ++ VG+A + P +SGG+QQRV +ARAL ++ +++L DEP +ALD + Sbjct: 113 ATAQEKAAAMMDVVGLAGFAERKPHELSGGQQQRVQLARALVLDRDILLLDEPLAALDAQ 172 Query: 184 LVGDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242 L D+ ++ L ++ G T + VTH A V++++ + G + E G R++ P Sbjct: 173 LRKDMCLELKHLQEKVGITFIHVTHNQEEAMTVADRIALVADGQLVEQGAARDIYRAP-- 230 Query: 243 ERLQQFLSG 251 +++F +G Sbjct: 231 --IKKFTAG 237 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: 198 Number of extensions: 10 Number of successful extensions: 4 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: 366 Length adjustment: 27 Effective length of query: 227 Effective length of database: 339 Effective search space: 76953 Effective search space used: 76953 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: 48 (23.1 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