Align Inner-membrane translocator (characterized, see rationale)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 147 bits (370), Expect = 5e-40 Identities = 105/300 (35%), Positives = 164/300 (54%), Gaps = 21/300 (7%) Query: 14 SLLLTMFLVGTFQF--DGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIA 71 ++L + LV F + F + R N+L + + I A+GMT VI+ GGID++VG+++A Sbjct: 28 TILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLA 87 Query: 72 LSGVVTSLLITEY------QWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGM 125 + + + ++T W L+A +V +G G + G + + FIVTL GM Sbjct: 88 FASIAAAYVVTAVVGDGPATW--LIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGM 145 Query: 126 FLARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIA---VVMH 182 + RG AT L + I F DA G+G + + ++F ++ A V + Sbjct: 146 TVWRG-ATLLLNDGGPISG-FNDAYRWW-----GSGEILFLPVPVVIFALVAAAGHVALR 198 Query: 183 YTRFGTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAI 242 YTR+G VYA+GGN +A L G+++ T S+YAI LA L+G + + S A+ Sbjct: 199 YTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGT 258 Query: 243 GVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLL 302 G EL IA+VVIGG LTGGSG V GTVLG +L+GV+ + ++S+ ++VIGL++ Sbjct: 259 GYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVM-LHVTSYVQQVVIGLII 317 Lambda K H 0.330 0.145 0.424 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: 398 Number of extensions: 36 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 320 Length of database: 332 Length adjustment: 28 Effective length of query: 292 Effective length of database: 304 Effective search space: 88768 Effective search space used: 88768 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 (21.8 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