Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 214 bits (545), Expect = 3e-60 Identities = 123/286 (43%), Positives = 175/286 (61%), Gaps = 14/286 (4%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80 V+ +L I GEF L+G SGCGK+T LRMLAG E T G I I +DVT V P +R + Sbjct: 38 VEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILIDGQDVTEVPPYERPVN 97 Query: 81 MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140 M+FQ+YAL+PHM+V +N+ F LK G ++ I +V A + + F RKP LSGGQ Sbjct: 98 MMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQMGRFSGRKPHQLSGGQ 157 Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200 RQRVA+ R + + P+V L+DEPL+ LD KLR T+ ++ +Q ++G+T V VTHDQ EA+ Sbjct: 158 RQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDRVGITFVMVTHDQGEAM 217 Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260 TM RI V+ G ++QVG+P ++Y+ P FVA FIG A N+ SV+ G+ A Sbjct: 218 TMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIG--AANMFQGSVRGGEGALAIACP 275 Query: 261 KLSPE-------TLAAMTPEDNGRITIGFRPEALEIIPEGESTDLS 299 +L + +AA TP +T+ RPE + I + ++ L+ Sbjct: 276 ELEHDLSVTEAGAVAAGTP-----VTVMVRPEKVMIARDKPASGLN 316 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: 340 Number of extensions: 16 Number of successful extensions: 1 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: 379 Length adjustment: 30 Effective length of query: 346 Effective length of database: 349 Effective search space: 120754 Effective search space used: 120754 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