Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 3608728 Dshi_2120 ABC transporter related (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Dino:3608728 Length = 376 Score = 136 bits (342), Expect = 7e-37 Identities = 82/243 (33%), Positives = 133/243 (54%), Gaps = 17/243 (6%) Query: 11 KRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLV 70 KR+GS +K + G+ ++I+GSSG GK+T LR + LE P G I L+ E++ Sbjct: 22 KRFGSFTAVKKADFEIGRGEFLAIMGSSGCGKTTTLRMLAGLEDPTEGAIYLDGEQVNGK 81 Query: 71 ANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREKA 130 A D MV+Q L+ +T EN+ E + + G+ K E R++A Sbjct: 82 ATWD---------------RDTPMVWQSLALFPFLTVQENV-EFALKMRGIGKEERRQRA 125 Query: 131 EHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLK 190 + +L+K+ + D +SGG++QRVA+ARAL EP+++L DEP SALD L + Sbjct: 126 DKWLDKMQITEFADRNINQLSGGQKQRVALARALVTEPKILLLDEPLSALDAHLKVRMQS 185 Query: 191 VMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFL 249 V+ L ++ G T V VTH M A +++++V + +G +E+ G P E+ P + + +FL Sbjct: 186 VLSNLQKDLGITFVYVTHSMSEAFSMADRVVIMSRGQIEQIGTPEEIYREPHNRFVAEFL 245 Query: 250 SGS 252 + Sbjct: 246 GSA 248 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: 175 Number of extensions: 7 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: 376 Length adjustment: 27 Effective length of query: 227 Effective length of database: 349 Effective search space: 79223 Effective search space used: 79223 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: 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