Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate CCNA_02006 CCNA_02006 lipoprotein releasing system ATP-binding protein lolD
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Caulo:CCNA_02006 Length = 228 Score = 132 bits (331), Expect = 8e-36 Identities = 87/232 (37%), Positives = 124/232 (53%), Gaps = 25/232 (10%) Query: 1 MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKI 60 +YK E DL VL+GV L G+V+ +IG SGSGKS+ L LLE+P AG + Sbjct: 14 VYKTEAGDL-------PVLRGVDLDVYPGEVVGLIGPSGSGKSSLLHSAGLLERPDAGLV 66 Query: 61 LLNNEELKLVANKDGALKAADPKQLQRMRSRLS---MVFQHFNLWSHMTAMENIMEAPVH 117 L + ++ + R R RL V+Q +L +A+EN+ P+ Sbjct: 67 ALEGRDCSKLSER------------ARTRIRLGTVGFVYQFHHLLPEFSALENVA-MPLT 113 Query: 118 VLGMSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPT 177 + G S+ EA +A L +G+ HR + P MSGGEQQRVAIARALA P+++L DEPT Sbjct: 114 IAGKSRREAEARARELLESLGLGHRLNHQPAQMSGGEQQRVAIARALANRPKLLLADEPT 173 Query: 178 SALDPELVGDVLKVM-QALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVE 228 LDP V + + Q ++G V+ TH M AR + +++V L G +E Sbjct: 174 GNLDPATSTAVFQALYQVCREQGVAAVIATHNMELARYM-DRVVALKDGHLE 224 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: 144 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: 228 Length adjustment: 23 Effective length of query: 231 Effective length of database: 205 Effective search space: 47355 Effective search space used: 47355 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