Align Histidine transport system permease protein HisQ (characterized)
to candidate BWI76_RS19235 BWI76_RS19235 polar amino acid ABC transporter inner membrane subunit
Query= SwissProt::P0A2I9 (228 letters) >FitnessBrowser__Koxy:BWI76_RS19235 Length = 230 Score = 194 bits (492), Expect = 2e-54 Identities = 92/221 (41%), Positives = 153/221 (69%) Query: 1 MLYGFSGVILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVP 60 M+ + ++L+GA ++L + LSS+++A+L+GL+ + KL L YTTL+RG+P Sbjct: 1 MVADYLPLLLRGAALSLCVMLSSLLVALLLGLINSLIKLFGPPWLRLFSTAYTTLVRGIP 60 Query: 61 DLVLMLLIFYGLQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVP 120 +LV+MLL+F+G ++ +N++ +G+ + + ++G++ +GF++GAY+TETFRGAF+ V Sbjct: 61 ELVIMLLLFFGGEMLVNLLLGLVGLGPVRFNTFISGVLAIGFVFGAYYTETFRGAFLTVD 120 Query: 121 KGHIEAATAFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKAT 180 G EAA A+G FRR+M P M+ +A+PGI NNW ++KA+ALVS+LGLED+V Sbjct: 121 SGQTEAAQAYGMRPWTVFRRVMLPQMLSFAIPGINNNWLGLMKASALVSILGLEDMVWLA 180 Query: 181 QLAGKSTWEPFYFAVVCGLIYLVFTTVSNGVLLLLERRYSV 221 + AG++T +PF F + LIY+V T +S+ + L +RY++ Sbjct: 181 EQAGRATQKPFLFYFLVSLIYMVITALSSWLFSRLAKRYAL 221 Lambda K H 0.328 0.144 0.422 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: 186 Number of extensions: 8 Number of successful extensions: 1 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: 228 Length of database: 230 Length adjustment: 23 Effective length of query: 205 Effective length of database: 207 Effective search space: 42435 Effective search space used: 42435 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: 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