Align Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate Echvi_1284 Echvi_1284 ABC-type sugar transport system, periplasmic component
Query= TCDB::Q9X053 (323 letters) >FitnessBrowser__Cola:Echvi_1284 Length = 316 Score = 339 bits (870), Expect = 5e-98 Identities = 173/317 (54%), Positives = 232/317 (73%), Gaps = 9/317 (2%) Query: 7 VVLVLVGLLLVSFTGLAQEQQKPKGKMAIVISTLNNPWFVVLAETAKQRAEQLGYEATIF 66 +++ + LLL+ + + KGK+A+++STLNNPWFVVLAETA + AE LGYE +IF Sbjct: 8 ILIWCLPLLLLVGACESNSATETKGKVAVIVSTLNNPWFVVLAETAAKEAESLGYEVSIF 67 Query: 67 DSQNDTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRAKEAGIPVFCVDRGINARGL 126 DSQN+TA E+ HF+ I AGY AI+FNPTDA+GS++NV +A EAGI VFC+DR +N+ L Sbjct: 68 DSQNNTALENNHFENAITAGYQAILFNPTDAEGSVSNVTKASEAGIAVFCMDREVNS-SL 126 Query: 127 AVAQIYSDNYYGGVLMGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNGFHSVVD 186 +QI SDNY G V +G+YFV L K Y E+LG++ TW+RS GFHSVV Sbjct: 127 PTSQILSDNYAGCVSLGKYFVDQLD------KSGNYVEILGLVGDNNTWNRSKGFHSVVG 180 Query: 187 QYPEFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEAAG-RTD 245 YP+ KMVAQQSA+FDR+ A +V E ILQ H +I A++CGNDAMA+GA +A +AAG Sbjct: 181 HYPDLKMVAQQSADFDRNKAMEVMESILQVHRDIDAVFCGNDAMAMGAYQALKAAGLENQ 240 Query: 246 IYIFGFDGAEDVINAIKEGKQIVATIMQFPKLMARLAVEWADQYLRGERSFPEIVPVTVE 305 + +FGFDGA DV++A+K+G+ I AT MQFPK+MA+ A + AD+Y++GER F + +PV VE Sbjct: 241 VMVFGFDGAADVVDAVKDGR-IAATAMQFPKVMAKTAAQLADKYIQGERDFVKKLPVDVE 299 Query: 306 LVTRENIDKYTAYGRKE 322 LVT N++ Y AYG+KE Sbjct: 300 LVTLANVEHYAAYGKKE 316 Lambda K H 0.319 0.135 0.393 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: 269 Number of extensions: 8 Number of successful extensions: 5 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: 323 Length of database: 316 Length adjustment: 28 Effective length of query: 295 Effective length of database: 288 Effective search space: 84960 Effective search space used: 84960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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