Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 3608990 Dshi_2380 ABC transporter related (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__Dino:3608990 Length = 257 Score = 130 bits (327), Expect = 3e-35 Identities = 85/252 (33%), Positives = 142/252 (56%), Gaps = 17/252 (6%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 +E++ + K +G EVL+GV L G+ + IIG SG+GKS L+ + L P AG+IL++ Sbjct: 11 IELRGVSKAFGPKEVLRGVDLVIPKGESMVIIGGSGTGKSVMLKSVLGLISPDAGQILVD 70 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVH-VLGMS 122 ++++ V +D L +R M+FQ L+ + +N+ + L Sbjct: 71 GKDVEKV-ERDAFL------------ARFGMLFQGGALFDSLPVWQNVSFRLLRGALKRP 117 Query: 123 KAEAREKAELYLAKVGVSHR-KDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALD 181 +AEAR+ A L +VG++ D +P +SGG Q+RV +ARA+A EPE++ FDEPT+ LD Sbjct: 118 RAEARDIAIEKLRRVGLTPDVADQFPAELSGGMQKRVGLARAIAAEPEIIFFDEPTTGLD 177 Query: 182 PELVGDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNP 240 P + G + +++ + E G T + +TH+M R +++ + LH G + +G P + + Sbjct: 178 PIMSGVINDLIREIVVEMGATAMTITHDMTSVRAIADDVAMLHGGKIRWTG-PVSDMDHS 236 Query: 241 QSERLQQFLSGS 252 L QF+SGS Sbjct: 237 GDPYLTQFISGS 248 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: 155 Number of extensions: 10 Number of successful extensions: 3 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: 257 Length adjustment: 24 Effective length of query: 230 Effective length of database: 233 Effective search space: 53590 Effective search space used: 53590 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