Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate Pf1N1B4_1712 Glutamate transport membrane-spanning protein
Query= SwissProt::P0AER3 (246 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1712 Length = 219 Score = 107 bits (267), Expect = 2e-28 Identities = 66/209 (31%), Positives = 118/209 (56%), Gaps = 12/209 (5%) Query: 28 GFQVTIALSICAWIIAFLVGSFFGILRTVPNRFLSGLGTLYVELFRNVPLIVQFFTWYLV 87 G T+++S + +I+ + G +G+LRT+ + +L+G +Y+ELFR +P++V W + Sbjct: 19 GAAQTLSISFLSIVISTVGGVLYGVLRTLNSEWLNGFLRVYLELFRAIPVLV----WLYL 74 Query: 88 IPELLPEKIGMWFKAELDPNIQFFLSSMLCLGLFTAARVCEQVRAAIQSLPRGQKNAALA 147 + LP G+ +I F ++L L L+ A+ V E VR A+ SLPRGQ+ A L+ Sbjct: 75 LFFGLPIFFGL--------SIPSFWCAVLVLSLWGASEVGEVVRGALHSLPRGQREAGLS 126 Query: 148 MGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNLVKNSAIASTIGLVDMAAQAGKLLDYSAH 207 +GL PQ Y YVLLP A + + PP + ++K S++A IG+VD+ ++++ + Sbjct: 127 IGLDGPQLYGYVLLPQALKRMTPPTINVYTRIIKTSSLAVLIGVVDVIKVGQQIIERTYE 186 Query: 208 AWESFTAITLAYVLINAFIMLVMTLVERK 236 + + A+ L + I + ++ER+ Sbjct: 187 SVLIYGALFLFFFFICYPLSAASRVLERR 215 Lambda K H 0.328 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: 151 Number of extensions: 9 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: 246 Length of database: 219 Length adjustment: 23 Effective length of query: 223 Effective length of database: 196 Effective search space: 43708 Effective search space used: 43708 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: 46 (22.3 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