Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF2490 PS417_12700 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__WCS417:GFF2490 Length = 367 Score = 300 bits (768), Expect = 4e-86 Identities = 161/322 (50%), Positives = 212/322 (65%), Gaps = 12/322 (3%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA + K+ + G +K +LE+ D EF+V VGPSGCGKST LR++AGLE V++G Sbjct: 1 MANLKIKNLQKGFEGFS--IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEG 58 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 I + +D+T V P RD+AMVFQ YALYPHM+V +NM FAL +AG + + +V EAA Sbjct: 59 TIELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAA 118 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 L L LERKPK LSGGQRQRVA+GRAIVRNP++FL DEPLSNLDA LRVQ R ++A Sbjct: 119 RILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELAR 178 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L ++L T +YVTHDQ EA+T+ D++ VL G ++QVG+P ELY +PAN+FVAGF+G+P Sbjct: 179 LHKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPK 238 Query: 241 MNLGTFSVKDGDATSGHARIKLSPET-----LAAMTPEDNGRITIGFRPEALEIIPEGES 295 M G K S ++L T L+ T +T+G RPE LEI G++ Sbjct: 239 M--GFLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQT 296 Query: 296 TDLSIPIKLDFVEELGSDSFLY 317 T + + D E LGSD+F + Sbjct: 297 T---LTVTADVGERLGSDTFCH 315 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: 384 Number of extensions: 10 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: 367 Length adjustment: 30 Effective length of query: 346 Effective length of database: 337 Effective search space: 116602 Effective search space used: 116602 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: 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