Align Histidine transport system permease protein HisQ (characterized)
to candidate GFF2619 PGA1_c26600 amino acid ABC transporter, permease protein
Query= SwissProt::P0A2I9 (228 letters) >FitnessBrowser__Phaeo:GFF2619 Length = 273 Score = 104 bits (259), Expect = 2e-27 Identities = 77/227 (33%), Positives = 123/227 (54%), Gaps = 13/227 (5%) Query: 9 ILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVPDLVLMLLI 68 +++G +T+ + L S LA L+GL A A S+ V Y ++RG+P +VL+L + Sbjct: 49 LMRGVQLTIFVTLISFFLASLLGLGLALAAGSRWLVIRQGARFYIEVVRGIPIIVLLLYV 108 Query: 69 FYGLQIALNVVTDSLGIDQIDIDPMVA--------GIITLGFIYGAYFTETFRGAFMAVP 120 + L AL + + LG D I +DP+ II L Y A+ +E FR +V Sbjct: 109 AFVLAPALVELRNWLG-DHIGLDPIRTRNFPLLWRAIIALMIAYSAFISEVFRAGLQSVD 167 Query: 121 KGHIEAATAFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKAT 180 +G IEAA + G + FR I+FP +R LP +GN++ ++K ++LVS+LG+ DV + Sbjct: 168 EGQIEAAKSLGLSRWHRFRFIVFPQAIRTILPPLGNDFVALVKDSSLVSVLGVADVTQLG 227 Query: 181 QLAGKSTWEPFYFAVVCGLIYLVFTTVSNGVLLLLERRYSVGVKRAD 227 +L + F V LIYL T++ G+ LLL RR+ ++R + Sbjct: 228 KLTAVGNFRYFETYNVVALIYL---TLTIGLSLLL-RRFEKHLRRRE 270 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: 137 Number of extensions: 7 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: 228 Length of database: 273 Length adjustment: 24 Effective length of query: 204 Effective length of database: 249 Effective search space: 50796 Effective search space used: 50796 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