Align Inner-membrane translocator (characterized, see rationale)
to candidate Pf1N1B4_4287 Inositol transport system permease protein
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4287 Length = 340 Score = 159 bits (403), Expect = 7e-44 Identities = 108/300 (36%), Positives = 175/300 (58%), Gaps = 30/300 (10%) Query: 32 SGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGVVTSLL----------- 80 S R+V +L+ + L+ A+G+T VII+ GIDLS G+V+ALS ++ + L Sbjct: 53 SQRLVLMILQVSIIGLL-AIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVF 111 Query: 81 --ITEYQ-WHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLATTLSE 137 +T+ W P+ +V L +G L GA+ G+II + + PFI TL M ARGLA +E Sbjct: 112 PSLTDLPVWIPV---IVGLGVGLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTE 168 Query: 138 -ESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTNVYAIGGN 196 + +++ Y A+ G+GA+ + +IF++ VI + + YT++G YAIGGN Sbjct: 169 GQPVSMLSDSYTAI--------GHGAMPV--IIFLVVAVIFHIALRYTKYGKYTYAIGGN 218 Query: 197 QHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAAVVIGG 256 +A GI++ + + +Y+I+ LA LAG+V + +G A + ELDAIAA VIGG Sbjct: 219 MQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGG 278 Query: 257 TLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILLQKLLNGRK 316 T L GG G + GTV+G +++GV+ + TF G + ++ I+ GL++ +++ + N RK Sbjct: 279 TSLAGGVGRITGTVIGALILGVMASGFTFVG-VDAYIQDIIKGLIIVVAVVIDQYRNKRK 337 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: 340 Number of extensions: 26 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: 320 Length of database: 340 Length adjustment: 28 Effective length of query: 292 Effective length of database: 312 Effective search space: 91104 Effective search space used: 91104 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: 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