Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 218 bits (554), Expect = 2e-61 Identities = 120/279 (43%), Positives = 175/279 (62%), Gaps = 6/279 (2%) Query: 62 QVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWI 121 QVS+ +++G+T VI+T GIDLS GS+LAL + ASL + + + P+ Sbjct: 39 QVSVNICISVGMTLVILTAGIDLSVGSILALCGAVTASLIKNGIAVEGLNLHIGFAPLGA 98 Query: 122 PVIAGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTA 181 VI G+G+G G NG I +PPF+ATL M+ ARGL +T G P++ L + + Sbjct: 99 -VILGVGLGFGLGWFNGWTITRFKVPPFVATLAMLTIARGLTMLWTGGFPINGLGEDFAF 157 Query: 182 IGHG-----AMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIV 236 +G G MPV I V+ + + + TK+G+Y YAIGGN +AAR SGIN+ R + V Sbjct: 158 LGTGWFLGIPMPVWITAVIVALAVLLTKKTKFGRYVYAIGGNERAARLSGINISRVKMTV 217 Query: 237 YSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGAL 296 Y+IAG LA + G++ ++R + Q G+SYELDAIAA VIGGTSL+GG G I G V+G + Sbjct: 218 YAIAGGLAAVGGMIVTSRLDSAQPNAGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGI 277 Query: 297 ILGVMASGFTFVGVDAYIQDIIKGLIIVIAVVIDQYRNK 335 I+GV+ +G + V + Q ++KG +I++AVVID+ +K Sbjct: 278 IIGVLNNGLVLLNVSPFWQQVVKGAVILLAVVIDKANSK 316 Lambda K H 0.326 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: 276 Number of extensions: 7 Number of successful extensions: 3 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: 318 Length adjustment: 28 Effective length of query: 312 Effective length of database: 290 Effective search space: 90480 Effective search space used: 90480 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