Align glucose transporter, permease component (characterized)
to candidate WP_085635594.1 MGEO_RS05030 ABC transporter permease
Query= reanno::Phaeo:GFF3640 (433 letters) >NCBI__GCF_002115805.1:WP_085635594.1 Length = 333 Score = 104 bits (260), Expect = 4e-27 Identities = 105/379 (27%), Positives = 159/379 (41%), Gaps = 93/379 (24%) Query: 44 LTDGRFLTPRNIFNLTIQTVSVAIMATGMVFVIVTRHIDLSVGALLATCSAVMAVVQTDV 103 L++ F+ N+ L Q+ + I+A GM +++ +IDLSVGA+ A C+ V+ Sbjct: 35 LSEKAFMDVDNMLLLFKQSAPIGIIAMGMTIIMINGNIDLSVGAIYAICAIVL------- 87 Query: 104 LPDMFGLGLNHPATWIITVAVGLAIGTLIGAFQGWMVGFLTIPAFIVTLGGFLVWRNVAW 163 L M TW I F G +G + IP VAW Sbjct: 88 LDSM---------TWPI--------------FAG--LGDMVIP--------------VAW 108 Query: 164 YLTDGQTIGPLDSTFLVFGGTSGTLGTTLSWVVGIVATLLALAALWNSRRAKQGHGFPVK 223 L L+ G G L + W G+ A ++ L ++ R Sbjct: 109 VLA------------LLAGVALGALNGLIVWKTGVDAFIVTLGSMLGYR----------- 145 Query: 224 PAWAEAVIAGSIAASILGFVAILNAYQIPARRLKRMMEAQGETMPEGLVVGYGLPISVLI 283 G V + N Q P L + E GL + + Sbjct: 146 -----------------GLVFMYNGEQ-PTSHLNWTLVDFAEAQFLGLHTA-----TWFL 182 Query: 284 LIATAVVMTIIARRTRLGRYIFATGGNPDAAELSGINTRLLTVKIFALMGFLCALSAVVA 343 LI TA + ++ RT GR +A G N +AA +GI + F ++GFL ALSAVV Sbjct: 183 LIVTAAIWFLM-NRTVHGRNAYAIGDNREAAVNAGIRVGPHMMINFMIIGFLAALSAVVF 241 Query: 344 SARLANHSNDIGTLDELRVIAAAVIGGTALSGGFGTIYGAILGALIMQSLQSGMAMVGVD 403 + + + + G L EL VI A V+GGT L+GG G+I G L +Q L+ G+A +G D Sbjct: 242 YSESGSVNPNDGELYELWVITAVVLGGTKLTGGAGSIISTFGGVLAIQLLRKGLAHIGAD 301 Query: 404 APFQNIVVGTVLVAAVWID 422 N+V+G +L+ +++D Sbjct: 302 TETVNLVIGLILIVVLFLD 320 Lambda K H 0.327 0.141 0.419 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: 416 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 433 Length of database: 333 Length adjustment: 30 Effective length of query: 403 Effective length of database: 303 Effective search space: 122109 Effective search space used: 122109 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 (21.7 bits) S2: 50 (23.9 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