Align Inositol transport system permease protein (characterized)
to candidate PfGW456L13_3910 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910 Length = 325 Score = 171 bits (433), Expect = 2e-47 Identities = 109/284 (38%), Positives = 155/284 (54%), Gaps = 17/284 (5%) Query: 62 QVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWI 121 Q+ + +LA+G+T V+I GIDLS GSVLAL+A + + V P+ Sbjct: 53 QIPDLMVLAVGMTFVLIIGGIDLSVGSVLALAASTVS--VAILGWGWGVLPA-------- 102 Query: 122 PVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYT- 180 +G+ V LAG I GSI IP FI +LG++ ARG+A Y G + + D++ Sbjct: 103 -ALLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMARGVA-YQMTGSRTAYIGDAFAW 160 Query: 181 ---AIGHGAMP-VIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIV 236 I G P II L++ + L T +G+Y IG N +A R +GIN K + ++V Sbjct: 161 LSNPIAFGISPSFIIALLIIFVAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKVLV 220 Query: 237 YSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGAL 296 +S+ GLLAG+A + +R G EL IAA VIGGTSL GG G + T G L Sbjct: 221 FSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVL 280 Query: 297 ILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRKLKR 340 I+ V+A+G +G + II G +IVVAVV+D YR++R +R Sbjct: 281 IISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTYRSQRASRR 324 Lambda K H 0.325 0.140 0.394 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: 259 Number of extensions: 15 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: 340 Length of database: 325 Length adjustment: 28 Effective length of query: 312 Effective length of database: 297 Effective search space: 92664 Effective search space used: 92664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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