Align Histidine transport system permease protein HisQ (characterized)
to candidate RR42_RS29650 RR42_RS29650 histidine ABC transporter permease
Query= SwissProt::P0A2I9 (228 letters) >FitnessBrowser__Cup4G11:RR42_RS29650 Length = 229 Score = 275 bits (702), Expect = 7e-79 Identities = 136/227 (59%), Positives = 175/227 (77%) Query: 2 LYGFSGVILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVPD 61 LYGF ++L G I T+EL+L S+ A+++GL+GA AKLS NR + YTTLIR VPD Sbjct: 3 LYGFGPLLLAGTIRTIELSLLSLATAIVLGLLGATAKLSFNRPLRELGRCYTTLIRSVPD 62 Query: 62 LVLMLLIFYGLQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPK 121 LVLMLL+FY +QI +N +TD++G+ Q DIDP VAG++TLGFIYGAYFTETFRGAF++VP+ Sbjct: 63 LVLMLLLFYSIQIGINNLTDAVGLPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLSVPR 122 Query: 122 GHIEAATAFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKATQ 181 G +EA A+G FRRI+FP MMR+A+PGIGNNWQV++KATALVS++GL D+VKA Q Sbjct: 123 GQLEAGAAYGMNGTLVFRRILFPQMMRFAIPGIGNNWQVLVKATALVSIIGLADIVKAAQ 182 Query: 182 LAGKSTWEPFYFAVVCGLIYLVFTTVSNGVLLLLERRYSVGVKRADL 228 AGKST++ F+F + IYLV TT SN VL L + YS GV+ A+L Sbjct: 183 DAGKSTFKMFFFILCAAFIYLVITTFSNLVLAWLAKHYSSGVRHAEL 229 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: 215 Number of extensions: 11 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: 229 Length adjustment: 23 Effective length of query: 205 Effective length of database: 206 Effective search space: 42230 Effective search space used: 42230 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