Align Glutamate/aspartate import permease protein GltJ (characterized)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= SwissProt::P0AER3 (246 letters) >FitnessBrowser__psRCH2:GFF3103 Length = 394 Score = 96.7 bits (239), Expect = 6e-25 Identities = 65/176 (36%), Positives = 98/176 (55%), Gaps = 15/176 (8%) Query: 71 LFRNVPLIVQF-----FTWYLVIPELLPEKI-GMWFKAELDPNIQFFLSSMLCLGLFTAA 124 LF +P ++ F FTW +PEL I G W I +S ++ L ++TAA Sbjct: 224 LFLAIPWLMTFIAGAPFTWE--VPELQRFNIRGGWVV------IPELVSIVVALSVYTAA 275 Query: 125 RVCEQVRAAIQSLPRGQKNAALAMGLTLPQAYRYVLLPNAYRVIVPPMTSEMMNLVKNSA 184 + E VR+ IQS+ GQ AA ++GL Q R V++P A RVIVPP+TS+ +NL KNS+ Sbjct: 276 FIGETVRSGIQSVSHGQTEAAASLGLRPGQVLRLVIVPQALRVIVPPLTSQYLNLAKNSS 335 Query: 185 IASTIGLVDMAAQ-AGKLLDYSAHAWESFTAITLAYVLINAFIMLVMTLVERKVRL 239 +A+ IG DM + AG +L+ + A E+ Y+ I+ I L+M +++ L Sbjct: 336 LAAAIGYPDMVSLFAGTVLNQTGQAIETMAITMSVYLAISISISLLMNWYNKRIAL 391 Score = 49.3 bits (116), Expect = 1e-10 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 1/73 (1%) Query: 20 TYLGWIWSGFQVTIALSICAWIIAFLVGSFFGILRTVPNRFLSGLGTLYVELFRNV-PLI 78 TY W G T+ +S+ +A ++G G+ R N + L TLY+E+FRN+ PL+ Sbjct: 80 TYGRVFWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIEIFRNIPPLL 139 Query: 79 VQFFTWYLVIPEL 91 + FF ++ VI L Sbjct: 140 LIFFVYFAVISPL 152 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: 265 Number of extensions: 20 Number of successful extensions: 2 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: 246 Length of database: 394 Length adjustment: 27 Effective length of query: 219 Effective length of database: 367 Effective search space: 80373 Effective search space used: 80373 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