Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate 209035 DVU0105 glutamine ABC transporter, ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >MicrobesOnline__882:209035 Length = 244 Score = 163 bits (412), Expect = 5e-45 Identities = 97/245 (39%), Positives = 147/245 (60%), Gaps = 22/245 (8%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELD 63 ++I+NL K + +++GIDL V E VV +GPSG GKST LR I LEE+T+GTI +D Sbjct: 5 IEIRNLHKSYGDHHVLRGIDLTVRTGEVVVVIGPSGSGKSTALRCINRLEEITSGTIIVD 64 Query: 64 GRDI----TEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAAR 119 G D+ T+++ + + MVFQ + L+PHMSV +N++ + +V + + A+ Sbjct: 65 GYDLYDPKTDINHVRTEAGMVFQQFNLFPHMSVLENVT-------IGPVKVRRMARQEAQ 117 Query: 120 ILELGPMLER---------KPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRV 170 L L +LE+ P QLSGGQ+QRVAI R++ PK+ LFDEP S LD L Sbjct: 118 ALGLA-LLEKVGLADKAHAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPELVG 176 Query: 171 QMRLELARLHKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFV 230 ++ + +L +E TM+ VTH+ A +AD+V+ ++ G+I++ G P EL+ P N + Sbjct: 177 EVLEVMKQLARE-GMTMVVVTHEMGFAREVADRVIFIDYGKIQEEGPPNELFADPKNPRL 235 Query: 231 AGFLG 235 FLG Sbjct: 236 REFLG 240 Lambda K H 0.321 0.137 0.390 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: 220 Number of extensions: 11 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: 367 Length of database: 244 Length adjustment: 27 Effective length of query: 340 Effective length of database: 217 Effective search space: 73780 Effective search space used: 73780 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: 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