Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate GFF3910 PGA1_65p00130 putative amino-acid ABC transporter, ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__Phaeo:GFF3910 Length = 251 Score = 206 bits (523), Expect = 5e-58 Identities = 109/246 (44%), Positives = 160/246 (65%), Gaps = 8/246 (3%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 + + L K +G VL G+ L G+ I IIG SG+GKST LRC+N L+ P AG + + Sbjct: 10 ISITGLRKTFGDSVVLDGIDLTIQPGERIVIIGPSGTGKSTLLRCLNFLDAPDAGLVRIG 69 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 + ++ D A A ++ +R R + VFQ++ L+++ TA ENIMEA + V + Sbjct: 70 DLDV------DAA--RASKAEILALRRRTAFVFQNYALFANKTAAENIMEALITVQKQPR 121 Query: 124 AEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 AEA +A LA+ G++ + DAYP +SGG+QQRV I RA+A+ E+MLFDEPTSALDPE Sbjct: 122 AEAEARAREILAETGLADKADAYPASLSGGQQQRVGIGRAMALGAELMLFDEPTSALDPE 181 Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 VG+VL +M +A+E +TM++VTHEM FARE+++++VF+ G + E G P ++ PQ Sbjct: 182 WVGEVLALMHKVAEERQTMLIVTHEMQFAREIADRVVFMEGGRIVEQGPPTQIFDAPQDP 241 Query: 244 RLQQFL 249 R + FL Sbjct: 242 RTRAFL 247 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: 160 Number of extensions: 5 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: 251 Length adjustment: 24 Effective length of query: 230 Effective length of database: 227 Effective search space: 52210 Effective search space used: 52210 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