Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate 209035 DVU0105 glutamine ABC transporter, ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >MicrobesOnline__882:209035 Length = 244 Score = 159 bits (403), Expect = 6e-44 Identities = 97/238 (40%), Positives = 140/238 (58%), Gaps = 8/238 (3%) Query: 4 VTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLID 63 + +R++ KSY + R IDL + GE VV +GPSG GKST LR I LE+ITSG +++D Sbjct: 5 IEIRNLHKSYGDHHVLRGIDLTVRTGEVVVVIGPSGSGKSTALRCINRLEEITSGTIIVD 64 Query: 64 NQRVNDLPPKD-----RSVGMVFQSYALYPHMTVAENMAFG-LKLASVDKREIKRRVEAV 117 + D P D GMVFQ + L+PHM+V EN+ G +K+ + ++E + A+ Sbjct: 65 GYDLYD-PKTDINHVRTEAGMVFQQFNLFPHMSVLENVTIGPVKVRRMARQEAQALGLAL 123 Query: 118 AEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIA 177 E + L P LSGGQ+QRVAI R++ +PKV LFDEP S LD L V +E+ Sbjct: 124 LEKVGLADKAHAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPEL-VGEVLEVM 182 Query: 178 RLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLG 235 + R TM+ VTH+ A +AD+++ ++ G+I + G P L+ PKN + FLG Sbjct: 183 KQLAREGMTMVVVTHEMGFAREVADRVIFIDYGKIQEEGPPNELFADPKNPRLREFLG 240 Lambda K H 0.322 0.139 0.405 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: 223 Number of extensions: 15 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: 371 Length of database: 244 Length adjustment: 27 Effective length of query: 344 Effective length of database: 217 Effective search space: 74648 Effective search space used: 74648 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 (21.9 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