Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_068002943.1 PsAD2_RS04510 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_001623255.1:WP_068002943.1 Length = 363 Score = 286 bits (731), Expect = 8e-82 Identities = 149/296 (50%), Positives = 198/296 (66%), Gaps = 5/296 (1%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 NLE+ + EF V VGPSGCGK+TTLRM+AGLE V+DG I+IGD+ V+ + P+ RD+AMVFQ Sbjct: 23 NLEMEENEFTVFVGPSGCGKTTTLRMIAGLETVSDGEIYIGDRPVSQLEPKARDLAMVFQ 82 Query: 85 NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144 +YALYPHM V +NM FAL++ + + EI+++V A LGLT+FL RKP LSGGQRQRV Sbjct: 83 DYALYPHMNVAKNMSFALRLQRRPRKEIDEKVGLVAEMLGLTKFLHRKPGELSGGQRQRV 142 Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204 AMGRA+ R+ FL DEPLSNLDAKLR Q R ++A +++K+ +YVTHDQ EA+T+GD Sbjct: 143 AMGRALARDAGTFLFDEPLSNLDAKLRCQMRAELAIMRQKVRKNMIYVTHDQIEAMTLGD 202 Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDA---TSGHA-RI 260 RI V+ GY+QQ G P EL+ +PAN FVAGF+GSP MN ++D SG + Sbjct: 203 RIVVMNGGYIQQQGTPEELFKQPANKFVAGFLGSPPMNFLGAKIQDLGGQVFVSGDGFEV 262 Query: 261 KLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFL 316 L E + + +G RP L P + +I +K+ E +G+ S L Sbjct: 263 ALPEERASVALGHSASSVILGIRPSDLHFSPHAPDHE-AIDLKVIVSEYIGAQSVL 317 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: 389 Number of extensions: 15 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: 363 Length adjustment: 30 Effective length of query: 346 Effective length of database: 333 Effective search space: 115218 Effective search space used: 115218 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 24 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