Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__psRCH2:GFF4241 Length = 335 Score = 168 bits (425), Expect = 2e-46 Identities = 97/252 (38%), Positives = 148/252 (58%), Gaps = 17/252 (6%) Query: 4 LEVQDLHKRY--GSHEV--LKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 +E +HK Y G +V L+ L+ A+G+V +IG SG+GKST LR IN LE+P G+ Sbjct: 2 IEFHQVHKTYRTGGRDVPALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGGR 61 Query: 60 ILLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVL 119 IL+N E++ A D L+R R R+ M+FQHFNL T +N+ P+ + Sbjct: 62 ILVNGEDVT----------ALDADGLRRFRQRVGMIFQHFNLLMSKTVADNVA-MPLRLA 110 Query: 120 GM-SKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178 G+ S+ E + L +VG+ YP +SGG++QRV IARALA EP ++L DE TS Sbjct: 111 GIRSRREIDARVAALLERVGLKEHARKYPAQLSGGQKQRVGIARALATEPSILLCDEATS 170 Query: 179 ALDPELVGDVLKVMQALAQEGR-TMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVL 237 ALDP+ VL+++ + +E + T+V++THEM R V +++ + G + E G EV Sbjct: 171 ALDPQTTASVLQLLAEINRELKLTIVLITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVF 230 Query: 238 VNPQSERLQQFL 249 ++P+ Q+F+ Sbjct: 231 LHPKHPTTQRFV 242 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: 218 Number of extensions: 8 Number of successful extensions: 4 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: 335 Length adjustment: 26 Effective length of query: 228 Effective length of database: 309 Effective search space: 70452 Effective search space used: 70452 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