Align ABC transporter permease (characterized, see rationale)
to candidate WP_086510094.1 BZY95_RS11665 sugar ABC transporter permease
Query= uniprot:A0A166QFV1 (320 letters) >NCBI__GCF_002151265.1:WP_086510094.1 Length = 325 Score = 458 bits (1178), Expect = e-134 Identities = 218/302 (72%), Positives = 262/302 (86%) Query: 17 RETPVQRRRVRAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYL 76 R T V+R+RVRAAWLFL PML+ LA+VA WPLLRTF+FS TDA+L+D FIG NYL Sbjct: 21 RSTKVRRQRVRAAWLFLAPMLVTLAMVAGWPLLRTFYFSFTDASLSDMSNTLFIGLENYL 80 Query: 77 FHNGSSWSGILVDPQWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALIL 136 ++ W G+L DP WW AV NT+YF+VVSV LEVV G++VAL+LN +F GR LVRA +L Sbjct: 81 VYDDGRWFGVLADPIWWRAVWNTVYFSVVSVSLEVVFGVIVALVLNAEFKGRTLVRAAVL 140 Query: 137 IPWAIPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKT 196 IPWAIPTIVSA++W+WMLNDQFGIINHL+++LG+I +P+AWTADA+ SMWAVI+VDVWKT Sbjct: 141 IPWAIPTIVSAQMWAWMLNDQFGIINHLLMALGIIASPIAWTADANYSMWAVIMVDVWKT 200 Query: 197 VPFVTLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRV 256 PFV LL+LAALQMLP DCYEAA VDGIHP+KVF+RVTLPL+ PAL+VA IFR+LD+LRV Sbjct: 201 TPFVALLVLAALQMLPKDCYEAAEVDGIHPVKVFFRVTLPLITPALMVAVIFRLLDALRV 260 Query: 257 FDVIYVLTSNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLGRRQL 316 FDVIYVLTSNS+STMSMS+YARQ LVEFQDVGYGSAASTLLFL++A+ + YLYLGR+QL Sbjct: 261 FDVIYVLTSNSTSTMSMSIYARQQLVEFQDVGYGSAASTLLFLIIALATIAYLYLGRKQL 320 Query: 317 EV 318 ++ Sbjct: 321 QL 322 Lambda K H 0.329 0.140 0.443 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: 378 Number of extensions: 12 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: 320 Length of database: 325 Length adjustment: 28 Effective length of query: 292 Effective length of database: 297 Effective search space: 86724 Effective search space used: 86724 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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