Align Histidine transport system permease protein HisQ (characterized)
to candidate GFF3833 PGA1_262p02370 putative histidine transport system permease protein HisQ
Query= SwissProt::P52094 (228 letters) >FitnessBrowser__Phaeo:GFF3833 Length = 250 Score = 159 bits (403), Expect = 4e-44 Identities = 83/214 (38%), Positives = 130/214 (60%) Query: 4 GFSGVILQGALVTLELAISSVVLAVIIGLIGAGGKLSQNRLSGLIFEGYTTLIRGVPDLV 63 G+ G +L+G +L++A+ + + +IIGL GA GKL + + YTT+IR VP+LV Sbjct: 23 GWGGNLLRGLANSLQIALGAFGMGLIIGLFGAYGKLYGGPILRDLLAIYTTVIRAVPELV 82 Query: 64 LMLLIFYGLQIALNTVTEAMGVGQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGH 123 L+L+++Y +N V ++G G+++I +VAGI LG + GAY TE RGA AVP G Sbjct: 83 LILILYYVGTDLINKVAGSLGYGRVEISGIVAGIWVLGIVQGAYATEVLRGAIKAVPPGQ 142 Query: 124 IEAATAFGFTRGQVFRRIMFPSMMRYALPGIGNNWQVILKSTALVSLLGLEDVVKATQLA 183 IEAA ++G RR+ P+MM +A PG+ N W + K TAL++++G ++ T+ A Sbjct: 143 IEAARSYGMPPFMTMRRVTIPAMMSFATPGLANLWLIATKDTALLAIVGFAELTLETRQA 202 Query: 184 GKSTWEPFYFAIVCGVIYLVFTTVSNGVLLFLER 217 ST F F + G +YL+ T S+ + ++ER Sbjct: 203 ASSTRAYFTFFLAAGALYLMITLCSSVIFGWIER 236 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: 189 Number of extensions: 9 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: 250 Length adjustment: 23 Effective length of query: 205 Effective length of database: 227 Effective search space: 46535 Effective search space used: 46535 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