Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate PP_0225 PP_0225 sulfur compound ABC transporter - ATP-binding subunit
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__Putida:PP_0225 Length = 252 Score = 247 bits (631), Expect = 1e-70 Identities = 128/247 (51%), Positives = 178/247 (72%), Gaps = 7/247 (2%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 +EV+ L KR+ VL G+ L G+V++IIG SGSGK+TFLRC+NLLE P AG+I + Sbjct: 2 IEVKGLTKRFKGQTVLNGIDLTVQPGEVVAIIGPSGSGKTTFLRCLNLLETPDAGQIQIG 61 Query: 64 NEELKLVANKD-GALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122 + + AN+ G ++A ++R+R + VFQ+FNL+ H TA+EN++E PV V Sbjct: 62 --AISIDANRPLGGQQSA----IRRLRQQAGFVFQNFNLFPHRTALENVIEGPVIVKKTP 115 Query: 123 KAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182 + +A E LAKVG++ ++DAYP +SGG+QQRVAIARALAMEPEV+LFDEPTSALDP Sbjct: 116 REQAIELGRRLLAKVGLAGKEDAYPRRLSGGQQQRVAIARALAMEPEVILFDEPTSALDP 175 Query: 183 ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242 ELVG+VL ++ LA+E RTM++VTHEM FAR+V+N+++F KGV+ E G + + P+ Sbjct: 176 ELVGEVLATIRGLAEEKRTMIIVTHEMSFARDVANRVIFFDKGVIVEQGEAKALFAAPKE 235 Query: 243 ERLQQFL 249 ER +QFL Sbjct: 236 ERTRQFL 242 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: 181 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: 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