Align ABC transporter for L-Histidine, permease component (characterized)
to candidate PP_3559 PP_3559 glycine betaine ABC transporter (permease)
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__Putida:PP_3559 Length = 282 Score = 369 bits (948), Expect = e-107 Identities = 182/275 (66%), Positives = 229/275 (83%) Query: 2 FPESFTFSIADWVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGG 61 FP++ FS AD +N VD LV NYGD R +SD LL +V LE LLR+ PWWL+L +VG Sbjct: 5 FPQTLQFSFADSINRLVDWLVLNYGDHLRSLSDQLLQLLVGLENLLRLLPWWLLLLLVGL 64 Query: 62 IAWHATRKVLATAVIVGLLFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSN 121 +AWHA+R +L +AV+V LL L+G +GLWDKL+QTLAL+LV+T + VL+G+PLGIL A Sbjct: 65 LAWHASRSLLRSAVLVALLALIGMLGLWDKLLQTLALVLVSTGLCVLVGVPLGILLAARP 124 Query: 122 RLRSVLMPLLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVD 181 R +L+P+LD+MQT+P+FVYLIPVLMLFGLGKVPA+FAT+IYA PPL+RLT+LG+ Q+D Sbjct: 125 LARRLLLPVLDVMQTLPAFVYLIPVLMLFGLGKVPAVFATLIYALPPLVRLTELGLSQID 184 Query: 182 GEVMEAINAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDV 241 +++A + GA+RWQ+L + LPLALPSIMAG+NQ+ MMALSMVV+ASMIGARGLGEDV Sbjct: 185 PSLLQAAHGLGASRWQRLRRIALPLALPSIMAGLNQSVMMALSMVVVASMIGARGLGEDV 244 Query: 242 LVGIQTLNVGRGLEAGLAIVILAVVIDRITQAYGR 276 L GIQTLNVG+G+EAGLAIV LA+VIDRI+QAYGR Sbjct: 245 LAGIQTLNVGQGMEAGLAIVALAMVIDRISQAYGR 279 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: 328 Number of extensions: 10 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: 283 Length of database: 282 Length adjustment: 26 Effective length of query: 257 Effective length of database: 256 Effective search space: 65792 Effective search space used: 65792 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: 47 (22.7 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