Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= BRENDA::P68187 (371 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 209 bits (533), Expect = 7e-59 Identities = 127/328 (38%), Positives = 191/328 (58%), Gaps = 20/328 (6%) Query: 1 MASVQLQNVTKAWGEVVVSK--DINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSG 58 M+ +Q NVTK + +NL+I EGE + +GPSGCGK+T LRM+AG E T+G Sbjct: 1 MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60 Query: 59 DLFIGEKRMNDT----PPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRV 114 + IG++ + D PP +RG+GMVFQ YAL+PHL++ +N++FGL K +R Sbjct: 61 KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLNRW--KNRDKKKRA 118 Query: 115 NQVAEVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRI 174 +V E++ L R P LSGGQ+QRVA+ R L P V L+DEP SNLDA LR +MR Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178 Query: 175 EISRLHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFI 234 +++ + ++ T I VTHDQ +A ++D++VV++ G + Q+ P E+Y PA+ FVA F+ Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238 Query: 235 GSPKMNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSD 294 G K N + + D VE + +V LP E+ +V N+ + IRPE ++ Sbjct: 239 G--KTNLISGTLCP---DLKHVETHI---GRVCLPQETD--KVIENVMVSIRPEGCRLAE 288 Query: 295 IADVILEGEVQVVEQLGNETQIHIQIPS 322 G V+ V G ++H+++ S Sbjct: 289 KGR--YAGLVERVTYSGEYQEVHVRLQS 314 Lambda K H 0.320 0.137 0.393 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: 319 Number of extensions: 12 Number of successful extensions: 3 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: 351 Length adjustment: 29 Effective length of query: 342 Effective length of database: 322 Effective search space: 110124 Effective search space used: 110124 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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