Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= TCDB::B8H230 (332 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 171 bits (432), Expect = 3e-47 Identities = 106/318 (33%), Positives = 176/318 (55%), Gaps = 11/318 (3%) Query: 18 DLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGG 77 D+ K ++ L + F AN +FLT N N++ +I G++A+G+TFV++ G Sbjct: 8 DIGKLLAKQGILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGN 67 Query: 78 IDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTL-IGLAGGYVQGKAVTWLHVP 136 +D++VGS+++F++I + + GP + A+ TL +G G++ G +L + Sbjct: 68 LDLSVGSMMSFSTIVVLDLHDKL---GPTLAIPAMFAMTLCLGALIGFLVG----YLKLN 120 Query: 137 AFIVTLGGMTVWRGATLLLNDGGPISGFNDAYRWW---GSGEILFLPVPVVIFALVAAAG 193 + IVTLG ++ G TL + G + + W+ G G IL + P++IF +AA Sbjct: 121 SLIVTLGMLSAIHGLTLTYSGGKNMDIADKEGTWFAIFGQGNILGIQTPILIFIALAALL 180 Query: 194 HVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAE 253 + L T +GR+VYAVGGN AA SG+ + Y + +G + ++R ++ Sbjct: 181 GIILAKTPFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQ 240 Query: 254 AVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVI 313 G G EL V+A+V++GGASL GGSG + TV+G L++G + NGL+++ + VQ VV Sbjct: 241 NTVGQGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVT 300 Query: 314 GLIIVAAVAFDHYARTHK 331 +II+ AV D A+ K Sbjct: 301 WIIIILAVWLDIAAKRGK 318 Lambda K H 0.325 0.140 0.413 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: 225 Number of extensions: 11 Number of successful extensions: 4 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: 332 Length of database: 324 Length adjustment: 28 Effective length of query: 304 Effective length of database: 296 Effective search space: 89984 Effective search space used: 89984 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