Align ABC transporter permease (characterized, see rationale)
to candidate SM_b21459 SM_b21459 sugar uptake ABC transporter permease
Query= uniprot:A0A166QFV1 (320 letters) >FitnessBrowser__Smeli:SM_b21459 Length = 297 Score = 313 bits (803), Expect = 2e-90 Identities = 153/293 (52%), Positives = 211/293 (72%), Gaps = 8/293 (2%) Query: 21 VQRRRVRAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYLFHNG 80 ++R++ R AW+FL P+LL L VA WPL R+ +FS TDA L F+G N++ Sbjct: 7 MERQQRRTAWIFLLPLLLTLMAVAIWPLARSIFFSFTDAYLDAPSDYGFVGIENFV---- 62 Query: 81 SSWSGILVDPQWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWA 140 + DP +W AVRNTL FT+VSVGLE +LGL +ALLL+ F GR +VRA ILIPWA Sbjct: 63 ----EVAEDPVFWGAVRNTLVFTLVSVGLETLLGLAIALLLHRAFLGRGIVRAAILIPWA 118 Query: 141 IPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFV 200 +P +VSA+IW WMLNDQFG+IN L+++LGL++ +AWTAD L + VI +DVW T PF+ Sbjct: 119 MPMVVSARIWEWMLNDQFGLINKLLVALGLVEKGVAWTADPSLILGTVIFIDVWVTTPFM 178 Query: 201 TLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVI 260 LL+LA LQ++P + YEAA V G+ K FW +TLPL PA+ VA +FR LD+LR+FD+ Sbjct: 179 VLLILAGLQLIPEEIYEAADVSGVPQWKRFWSITLPLATPAIGVAILFRTLDALRMFDLS 238 Query: 261 YVLTSNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLGR 313 YVL +N+ +TM+MS+YAR L+ FQD+G G+AAST +F+++ +IA++ + L R Sbjct: 239 YVLAANNENTMTMSIYARDQLISFQDLGLGAAASTWVFMIIGLIAIVIVGLLR 291 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: 291 Number of extensions: 14 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: 320 Length of database: 297 Length adjustment: 27 Effective length of query: 293 Effective length of database: 270 Effective search space: 79110 Effective search space used: 79110 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 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