Align Inositol transport system permease protein (characterized)
to candidate AO356_00960 AO356_00960 ABC transporter permease
Query= reanno::Phaeo:GFF716 (373 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00960 Length = 325 Score = 142 bits (359), Expect = 1e-38 Identities = 103/336 (30%), Positives = 153/336 (45%), Gaps = 43/336 (12%) Query: 31 GIIGTITVFAMFLIFAGDSGMFNSQGVMNW--SQISAQFMIIAVGACLLMIAGEFDLSVG 88 G+ G + AM +F+ S F S + +QI M++AVG ++I G DLSVG Sbjct: 22 GLAGAL--LAMVALFSTLSSHFLSYDTFSTLANQIP-DLMVLAVGMTFILIIGGIDLSVG 78 Query: 89 SMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGFIVVRTGLPSFIVTLAFLFI 148 S++ A +++ + GW VW + L+ A+A G + G I V +PSFIV+L L + Sbjct: 79 SVLALAASTVSVAVLGWGWSVWPSALLGMAVAALAGTVTGSITVAWRIPSFIVSLGVLEM 138 Query: 149 LRGFAIYLPQTIERKTIIGGVADAAEGDWLAALFGGKILTGLFQWFGDNGWIAVFERGTR 208 RG A + T R IG F W + Sbjct: 139 ARGLAYQM--TGSRTAYIGDS---------------------FAWLSN------------ 163 Query: 209 KGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGGDAEAARNSGVPVNRVKILM 268 P+ G+ + A+L++ I +LT+T FG ++ G + EA R +G+ KIL+ Sbjct: 164 ---PIAFGISPSFIIALLVIFIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILV 220 Query: 269 FMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIGGALLTGGYGSVLGAALGAL 328 F A V A Q+ A + G E + I AVVIGG L GG GSV+ G L Sbjct: 221 FSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVL 280 Query: 329 IFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNTY 364 I V+ GL G R+ G +++ AV+L+TY Sbjct: 281 IISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTY 316 Lambda K H 0.330 0.145 0.443 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: 377 Number of extensions: 22 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 373 Length of database: 325 Length adjustment: 29 Effective length of query: 344 Effective length of database: 296 Effective search space: 101824 Effective search space used: 101824 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