Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate Synpcc7942_0948 Synpcc7942_0948 permease protein of sugar ABC transporter
Query= reanno::Phaeo:GFF1303 (276 letters) >FitnessBrowser__SynE:Synpcc7942_0948 Length = 275 Score = 127 bits (319), Expect = 3e-34 Identities = 82/273 (30%), Positives = 147/273 (53%), Gaps = 22/273 (8%) Query: 17 AWAVGLLIFFPILWTILTSFKTEAQAISDPPVFLFFDWTLENYSVV-QERSDYMRFLWNS 75 A A+ L PILW +LTS K A + P ++ WT+E+Y + Q+ + R+L NS Sbjct: 11 ALALSLFSLAPILWQLLTSIKVNADIAAIPTIYWPRQWTVEHYQALWQQTPAFGRYLLNS 70 Query: 76 VIIAGGSTILGIIIAVPAAWSMAFVPSKRTKDILLWMLSTKMLPAVGVLYPIYILFIKMG 135 +++ +T+ ++I P A+++A R +D +L +L + L+P +LF G Sbjct: 71 AVVSAIATLAALLIGTPCAYAIA-----RRRDRSSQVLVGSLL--LVTLFPYVLLF--QG 121 Query: 136 LLD---------NRFGLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGATLKEEIL 186 LL+ N LVV +NLP+++ +L ++F+++P E+ EAA++DG +L + + Sbjct: 122 LLEVVRWLQWGNNYAALVVPYTALNLPLVILLLRSFFEQLPPELEEAAQIDGLSLGQRLW 181 Query: 187 YVLTPMAIPGIASTLLLNIILAWNE---AFWTLNLTAAKAAPLTAFIASYSSPEGLFYAK 243 +L P+ P + + +L I +WNE A ++ A K P+ S + Y Sbjct: 182 LILVPLTAPALVTAGILAFIFSWNEYVLALSFISQQALKTVPIAVAEIGGISIFDVPYGD 241 Query: 244 LSAASTMAIAPILILGWFSQKQLVSGLTFGAVK 276 ++AA+ +A P++ L +Q++++ GLT GAVK Sbjct: 242 IAAATVVATLPLIGLVLVAQRRILEGLTAGAVK 274 Lambda K H 0.327 0.139 0.428 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: 252 Number of extensions: 17 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: 276 Length of database: 275 Length adjustment: 25 Effective length of query: 251 Effective length of database: 250 Effective search space: 62750 Effective search space used: 62750 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 (21.7 bits) S2: 47 (22.7 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