Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >MicrobesOnline__882:209225 Length = 354 Score = 160 bits (406), Expect = 4e-44 Identities = 101/310 (32%), Positives = 162/310 (52%), Gaps = 23/310 (7%) Query: 11 KSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISIDGKKINDI 70 ++ +VL ++L A GE + LVGPSG GK+TLLR +AGL++ D GTI ++ Sbjct: 10 RTLAGREVLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTI-----RVTPP 64 Query: 71 EPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQIK-----H 125 + + +VFQ Y L+PH++V EN+ FG + + + A + +RV+ + ++ H Sbjct: 65 QGHGGGVVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAFRLDTDDLAH 124 Query: 126 LLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHNSKS 185 + R P +LS GQRQRVAL RAL V+L DEP +NLD LR +M ++ + Sbjct: 125 MASRYPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRDVVRRFGV 184 Query: 186 TMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFLEGA 245 + VTHD EA +GDR+ V+ G + Q+ P ++Y P + A F+G + L+ Sbjct: 185 ATVTVTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLG--PVTVLDET 242 Query: 246 V-----LEKIPWPEARKADQILGI---RPDAFALNQGPLGTQEVALGDFQIDISE---NL 294 ++ P AD + G+ RP+A A+ G + F + + ++ Sbjct: 243 TRRTLGIDTPPAAATACADTMQGLRLYRPEALAVRPWADGPAVLVSARFTGQVMQLLLDV 302 Query: 295 GGQQMLHGTL 304 GQ++L TL Sbjct: 303 EGQELLVHTL 312 Lambda K H 0.318 0.136 0.383 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: 266 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: 347 Length of database: 354 Length adjustment: 29 Effective length of query: 318 Effective length of database: 325 Effective search space: 103350 Effective search space used: 103350 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 (21.7 bits) S2: 49 (23.5 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