Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >FitnessBrowser__SynE:Synpcc7942_0247 Length = 377 Score = 73.6 bits (179), Expect = 5e-18 Identities = 35/114 (30%), Positives = 63/114 (55%) Query: 106 GAYLSETFRGAFMAIPKGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKA 165 GA+++E RG +++P GQ EA AA G++ Q ++++VPQ +R+ +P + ++ K Sbjct: 257 GAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKN 316 Query: 166 TALISVVGLQDMMFKAKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKR 219 ++L VG D+ A+ + T P FL + YL I +V + L++R Sbjct: 317 SSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQR 370 Score = 24.3 bits (51), Expect = 0.004 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 1/66 (1%) Query: 5 YGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPDLVL 64 Y ++ G +L++ + L V+G + S L +L Y V+R P L+L Sbjct: 78 YARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTP-LLL 136 Query: 65 ILLIFY 70 L+++Y Sbjct: 137 QLIVWY 142 Lambda K H 0.329 0.144 0.421 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: 263 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 229 Length of database: 377 Length adjustment: 26 Effective length of query: 203 Effective length of database: 351 Effective search space: 71253 Effective search space used: 71253 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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