Align ABC transporter for L-Histidine, permease component (characterized)
to candidate GFF2519 PGA1_c25580 putative glycine betaine/L-proline transport system permease protein
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__Phaeo:GFF2519 Length = 343 Score = 225 bits (573), Expect = 1e-63 Identities = 115/244 (47%), Positives = 172/244 (70%), Gaps = 3/244 (1%) Query: 32 ISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATRKVLATAVIVGLLFLVGAVGLWDK 91 ++ L W + PWW+++ ++ W ATRK+ T + + G + D Sbjct: 89 LTQPLSWLLEGALFTFTTIPWWILIPLLVLATWAATRKLGVTIFVAVVFLFFGLIDHLDV 148 Query: 92 LMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMPLLDIMQTMPSFVYLIPVLMLFG 151 +QTL+++ V T +SVL G+P+GI+ +RS+R++ +++P+LD++QT+PSFVYLIP++ LF Sbjct: 149 ALQTLSIIFVCTGLSVLFGVPVGIMMSRSDRMQKIMLPILDMLQTLPSFVYLIPLIFLFS 208 Query: 152 LGKVPAIF--ATVIYAAPPLIRLTDLGIRQVDGEVMEAINAFGANRWQQLFGVQLPLALP 209 + + P ++ A ++YA P+IRLTDLGIR VD +V+EA +AFG Q+L+GVQLPLALP Sbjct: 209 VTE-PKLYGIAIILYAIVPVIRLTDLGIRLVDKDVVEAADAFGMTDRQKLYGVQLPLALP 267 Query: 210 SIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLNVGRGLEAGLAIVILAVVIDR 269 +IMAG+NQT MM+L+MVVIAS++ A GLG VL GI+ L +G GL AG IV+LAVV+DR Sbjct: 268 NIMAGVNQTIMMSLAMVVIASLVSAPGLGVLVLRGIRNLELGVGLVAGFGIVLLAVVLDR 327 Query: 270 ITQA 273 ++A Sbjct: 328 CSKA 331 Lambda K H 0.328 0.142 0.429 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: 324 Number of extensions: 13 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: 283 Length of database: 343 Length adjustment: 27 Effective length of query: 256 Effective length of database: 316 Effective search space: 80896 Effective search space used: 80896 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: 48 (23.1 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