Align Histidine transport system permease protein HisQ (characterized)
to candidate Pf6N2E2_5661 Arginine/ornithine ABC transporter, permease protein AotQ
Query= SwissProt::P0A2I9 (228 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5661 Length = 229 Score = 230 bits (587), Expect = 1e-65 Identities = 123/229 (53%), Positives = 161/229 (70%), Gaps = 1/229 (0%) Query: 1 MLYGFSGVILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVP 60 ML G+ VIL GA +TLELALSS+ LA+++GL+G +LS R + + Y T+IRG+P Sbjct: 1 MLKGYGAVILDGAWLTLELALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYATVIRGIP 60 Query: 61 DLVLMLLIFYGLQIALNVVTDSLGIDQ-IDIDPMVAGIITLGFIYGAYFTETFRGAFMAV 119 DLVL+LLIFYG Q LN V LG D ID++P+ AGI TLGFI+GAY +ETFRGAFMA+ Sbjct: 61 DLVLILLIFYGGQDLLNRVAPMLGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAI 120 Query: 120 PKGHIEAATAFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKA 179 PKG EA A+G Q F R++ P M+R A+PG NNW V+ KATAL+S++GL+D++ Sbjct: 121 PKGQAEAGMAYGMNGFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFK 180 Query: 180 TQLAGKSTWEPFYFAVVCGLIYLVFTTVSNGVLLLLERRYSVGVKRADL 228 + A +T EPF F + +YLV T+VS L LE+RYSVGV+ ADL Sbjct: 181 AKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAADL 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: 176 Number of extensions: 8 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: 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