Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Koxy:BWI76_RS06690 Length = 369 Score = 297 bits (760), Expect = 4e-85 Identities = 161/316 (50%), Positives = 214/316 (67%), Gaps = 18/316 (5%) Query: 20 TVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDI 79 T+ + NL+I DGEF V VGPSGCGKST LRM+AGLE V++G + IGD+ + V P R + Sbjct: 18 TLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEGEVLIGDEVMNDVVPAHRGV 77 Query: 80 AMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGG 139 AMVFQ+YALYPHMTV ENMG+ LK+ +DEI ++V+ A TL L+ L+RKPK LSGG Sbjct: 78 AMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVAKTLQLSHLLDRKPKQLSGG 137 Query: 140 QRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEA 199 QRQRVA+GRAIVRNP+VF+ DEPLSNLDA+LRV+ R IA L +L T VYVTHDQ EA Sbjct: 138 QRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAKLHHELKTTMVYVTHDQVEA 197 Query: 200 LTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHAR 259 +T+ D+I V+ G ++Q+G+P LY P N FVAGFIGSP MN +V G Sbjct: 198 MTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPKMNFLPATVTAWQ--PGQLS 255 Query: 260 IKLSPE---TLAAMTP--EDNGRITIGFRPEALEIIPEGESTDLSIPIKLDF----VEEL 310 +K++ + TL T + +T+G RPE L STD++I ++F VE L Sbjct: 256 VKMAQDHNLTLNITTSPLQPGAAVTLGIRPEHL-------STDVNIGTVVEFQCEVVERL 308 Query: 311 GSDSFLYGKLVGEGDL 326 G++++L+G+ G ++ Sbjct: 309 GNNTYLFGQCYGHDNV 324 Lambda K H 0.316 0.135 0.380 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: 347 Number of extensions: 11 Number of successful extensions: 2 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: 376 Length of database: 369 Length adjustment: 30 Effective length of query: 346 Effective length of database: 339 Effective search space: 117294 Effective search space used: 117294 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 (21.6 bits) S2: 50 (23.9 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