Align Histidine transport system permease protein HisQ (characterized)
to candidate AO356_23510 AO356_23510 amino acid ABC transporter permease
Query= SwissProt::P52094 (228 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23510 Length = 229 Score = 215 bits (547), Expect = 6e-61 Identities = 115/225 (51%), Positives = 150/225 (66%) Query: 2 LYGFSGVILQGALVTLELAISSVVLAVIIGLIGAGGKLSQNRLSGLIFEGYTTLIRGVPD 61 L G+ +I QGA +T+++A + +A+++GL+GA KLS L+ YTTL+R VPD Sbjct: 3 LEGYGYLIFQGAWLTVQVATWAACVALVLGLLGALAKLSPLAPLRLVATLYTTLVRSVPD 62 Query: 62 LVLMLLIFYGLQIALNTVTEAMGVGQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPK 121 LVLMLLI+Y QI LN V EA G + ++P I TLGFIYGAY ETFRGAF A+ Sbjct: 63 LVLMLLIYYSAQIGLNQVAEAFGRESLQLNPYGTAIGTLGFIYGAYCAETFRGAFQAIAF 122 Query: 122 GHIEAATAFGFTRGQVFRRIMFPSMMRYALPGIGNNWQVILKSTALVSLLGLEDVVKATQ 181 G +EAA A+G + QV RRI P MMR+ALPGIGN WQV+LKS L+SLLGL D+V+ + Sbjct: 123 GQLEAARAYGMSHWQVLRRIRLPQMMRFALPGIGNIWQVLLKSAGLISLLGLNDMVQVAK 182 Query: 182 LAGKSTWEPFYFAIVCGVIYLVFTTVSNGVLLFLERRYSVGVKRA 226 AG +T +F +V I+L F +S+ VL LERRYSV R+ Sbjct: 183 QAGNATSRQMFFYLVIAAIFLAFAILSSLVLKHLERRYSVEPPRS 227 Lambda K H 0.328 0.145 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: 191 Number of extensions: 3 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