Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF2518 PGA1_c25570 putative glycine betaine transport system, substrate binding protein
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__Phaeo:GFF2518 Length = 320 Score = 164 bits (415), Expect = 3e-45 Identities = 106/335 (31%), Positives = 156/335 (46%), Gaps = 24/335 (7%) Query: 15 AGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQVDSIPGNSV 74 A + A+ A A CGD VT +DW S +T V K ++ +GY C V ++P ++ Sbjct: 7 ASVCALGMAAPAWAEDCGD---VTITQMDWASANVVTSVAKFLMEQGYGCSVTTVPSSTP 63 Query: 75 TLEQATANNDV-QIFAEEWLGRSDVWNKAVEEKKVIAVGKTFV-GASEGWFVPDYVVHGD 132 T + A I E W+ + + V E K++ + G EGW+VP YVV Sbjct: 64 TALTSVAETGTPDILTELWVNTAPAYADLVAEGKLVELADVLSDGGIEGWWVPQYVVDAH 123 Query: 133 PARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGVSTAKLEAYKL 192 P +A L+ + L +PK+ GRF NCP GW C V+ + + Sbjct: 124 P------EAATLEGI--LANPKLVG----------GRFDNCPDGWGCRTVNDNMNQVIDM 165 Query: 193 -GETYVNFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEEPAYNEACWK 251 G+ F G+G L AI +AY +P F +YW+PTA+LGKF ++ ++ Y+ Sbjct: 166 EGKGIEVFDHGSGETLATAIAAAYADEKPWFGFYWAPTAVLGKFPMVLVDLGKYDADTHT 225 Query: 252 ELSSANGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNASLAYMADNK 311 SS +PS V + F PEI E++ +F D++N LA+M DN Sbjct: 226 CNSSKECASPGVSPYPSAAVKTAATADFQQREPEIAELMSNISFTNDQMNGVLAWMEDNN 285 Query: 312 VDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGLK 346 A A FL D W W++DEA K+ A LK Sbjct: 286 ASAEEGAVYFLTNNKDQWGGWLNDEAHEKLSAILK 320 Lambda K H 0.314 0.130 0.391 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: 315 Number of extensions: 18 Number of successful extensions: 5 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: 346 Length of database: 320 Length adjustment: 28 Effective length of query: 318 Effective length of database: 292 Effective search space: 92856 Effective search space used: 92856 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 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