Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate 209035 DVU0105 glutamine ABC transporter, ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_16275 (244 letters) >MicrobesOnline__882:209035 Length = 244 Score = 278 bits (711), Expect = 7e-80 Identities = 140/242 (57%), Positives = 179/242 (73%), Gaps = 2/242 (0%) Query: 1 MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVVV 60 MI I+N++K YGD VL V+ GEV+VV GPSGSGKST ++C+N LE G ++V Sbjct: 4 MIEIRNLHKSYGDHHVLRGIDLTVRTGEVVVVIGPSGSGKSTALRCINRLEEITSGTIIV 63 Query: 61 DGTSIADPKTDLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120 DG + DPKTD+ +R+ GMVFQ F LFPH+++ EN+TI +KV +++EA GL L Sbjct: 64 DGYDLYDPKTDINHVRTEAGMVFQQFNLFPHMSVLENVTIGPVKVRRMARQEAQALGLAL 123 Query: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180 LE+VGL+ AH +P QLSGGQ+QRVAIAR+LAM P V+LFDEPTSALDPE+V EVL+VM Sbjct: 124 LEKVGLADKAHAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPELVGEVLEVMK 183 Query: 181 QLANEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARSDRAQHFLDK 240 QLA EGMTM+ VTHEMGFAR+VADRVIF+D GKI E+ E F D ++ R + FL K Sbjct: 184 QLAREGMTMVVVTHEMGFAREVADRVIFIDYGKIQEEGPPNELFAD--PKNPRLREFLGK 241 Query: 241 IL 242 ++ Sbjct: 242 VI 243 Lambda K H 0.321 0.136 0.394 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: 3 Number of successful extensions: 1 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: 244 Length of database: 244 Length adjustment: 24 Effective length of query: 220 Effective length of database: 220 Effective search space: 48400 Effective search space used: 48400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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