Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >MicrobesOnline__882:209225 Length = 354 Score = 154 bits (388), Expect = 5e-42 Identities = 117/336 (34%), Positives = 161/336 (47%), Gaps = 30/336 (8%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 NL A GE + LVGPSG GK+T LR +AGL+ +G I VT + +VFQ Sbjct: 22 NLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTI-----RVTPPQGHGGGVVLVFQ 76 Query: 85 NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAA-----TLGLTEFLERKPKALSGG 139 +Y L+PH++V EN+ F + G + +RV T L R P LS G Sbjct: 77 DYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAFRLDTDDLAHMASRYPAQLSAG 136 Query: 140 QRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEA 199 QRQRVA+ RA+V +P V L+DEP +NLD LR + + + R+ GV TV VTHD EA Sbjct: 137 QRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRDVVRRFGVATVTVTHDLEEA 196 Query: 200 LTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHAR 259 +GDR+ V+ G L Q+ P ++Y PA+ A F LG +V D + T Sbjct: 197 FAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARF-------LGPVTVLD-ETTRRTLG 248 Query: 260 IKLSPETLAAMTPEDNG-RITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFLYG 318 I P A G R+ +RPEAL + P + P L G L Sbjct: 249 IDTPPAAATACADTMQGLRL---YRPEALAVRPWADG-----PAVLVSARFTGQVMQLLL 300 Query: 319 KLVGEGDLGSSSEDVPESGQ---IVVRAAPNAAPAP 351 + G+ L + +D P +G + +R P AP Sbjct: 301 DVEGQELLVHTLDDAPPTGTRLCVSLREIPGMTSAP 336 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: 308 Number of extensions: 20 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: 376 Length of database: 354 Length adjustment: 30 Effective length of query: 346 Effective length of database: 324 Effective search space: 112104 Effective search space used: 112104 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