Align Histidine transport system permease protein HisQ (characterized)
to candidate SMa0493 SMa0493 ABC transporter permease
Query= SwissProt::P52094 (228 letters) >FitnessBrowser__Smeli:SMa0493 Length = 232 Score = 157 bits (396), Expect = 2e-43 Identities = 85/217 (39%), Positives = 125/217 (57%), Gaps = 2/217 (0%) Query: 2 LYGFSGVILQGALVTLELAISSVVLAVIIGLIGAGGKLSQNRLSGLIFEGYTTLIRGVPD 61 L G+ L ++ ++ + S++L VI GL+GA KLS NRL+ + YT RG P+ Sbjct: 4 LNGWWDDYLLASVTVAKVFVCSLILMVIFGLLGASAKLSSNRLANAVGNAYTVFFRGTPE 63 Query: 62 LVLMLLIFYGLQIALNTVTEAM--GVGQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAV 119 ++++LL+++G ++L T+ V +DI P AG I + + G+Y TETFRGAF V Sbjct: 64 ILVILLLYFGSAVSLTTIARVFDPSVAFVDIPPFWAGSIAIALVVGSYATETFRGAFNGV 123 Query: 120 PKGHIEAATAFGFTRGQVFRRIMFPSMMRYALPGIGNNWQVILKSTALVSLLGLEDVVKA 179 G IEAA A G Q F I P M R ALP GN+ ++K TAL+S++GL + + Sbjct: 124 KSGSIEAARALGMNGLQTFFYIRIPEMWRIALPPFGNHMLSLIKDTALISIIGLNETLFV 183 Query: 180 TQLAGKSTWEPFYFAIVCGVIYLVFTTVSNGVLLFLE 216 + A +T +PF IV G+IYL F+T +L LE Sbjct: 184 AKQAASTTGKPFTMYIVVGLIYLGFSTAITISVLLLE 220 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: 155 Number of extensions: 10 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: 232 Length adjustment: 23 Effective length of query: 205 Effective length of database: 209 Effective search space: 42845 Effective search space used: 42845 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