Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Synpcc7942_0249 Synpcc7942_0249 ATPase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__SynE:Synpcc7942_0249 Length = 261 Score = 213 bits (542), Expect = 3e-60 Identities = 113/245 (46%), Positives = 157/245 (64%), Gaps = 12/245 (4%) Query: 7 QDLHKRYGSH-EVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNE 65 + + K YG+ + L GVSL G+V+ ++G SGSGKSTFLR +N LE G+I + Sbjct: 25 EGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGH 84 Query: 66 ELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTE 125 L + D + + +R + MVFQ FNL+ H+T ++N+M APV V + Sbjct: 85 RL-----------SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQ 133 Query: 126 AREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELV 185 A A L +V +A + D YPG +SGG+QQRVAIARALAM+P ++LFDEPTSALDPE+V Sbjct: 134 AEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMV 193 Query: 186 GDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERL 245 +VL VM+ LA EG TM+V THE+GFAREV++++V + G + E P PQS+R Sbjct: 194 REVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRA 253 Query: 246 QQFLS 250 +QFL+ Sbjct: 254 KQFLA 258 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: 195 Number of extensions: 7 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: 261 Length adjustment: 24 Effective length of query: 230 Effective length of database: 237 Effective search space: 54510 Effective search space used: 54510 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