Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate 18252 b4227 predicted sugar transporter subunit: periplasmic-binding component of ABC superfamily (NCBI)
Query= uniprot:A0KWY4 (313 letters) >FitnessBrowser__Keio:18252 Length = 318 Score = 357 bits (917), Expect = e-103 Identities = 180/308 (58%), Positives = 231/308 (75%), Gaps = 2/308 (0%) Query: 6 IITALGLWAVSATCAYATTVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQQKQE 65 I++A+ S A TVGFSQVGSESGWR + + K+EA++RGI LK AD QQKQE Sbjct: 7 IVSAVSAAMSSMALAAPLTVGFSQVGSESGWRAAETNVAKSEAEKRGITLKIADGQQKQE 66 Query: 66 NQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSLFLTRI 125 NQIKAVRSF+AQGVDAI IAPVV TGW+PVLKEAK A+IPV ++DR+I V D SL++T + Sbjct: 67 NQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSIDVKDKSLYMTTV 126 Query: 126 ASDFSEEGRKIGQWLMDKTQGN-CDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRS 184 +D EG+ IG WL+ + G C++ ELQGTVGA+ AIDR GF + I N PN KI+RS Sbjct: 127 TADNILEGKLIGDWLVKEVNGKPCNVVELQGTVGASVAIDRKKGFAEAIKNAPNIKIIRS 186 Query: 185 QTGEFTRAKGKEVMEGFLKAQ-NGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVS 243 Q+G+FTR+KGKEVME F+KA+ NG+ +C V++HND+M +GA+QAIKEAGLKPGKDIL S Sbjct: 187 QSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIKEAGLKPGKDILTGS 246 Query: 244 VDGVPDYFKAMADGDVNATVELSPYLGGPAFDAIDAYLKGNKDQAKLISTTGDVFTQETA 303 +DGVPD +KAM DG+ NA+VEL+P + GPAFDA++ Y K KL T ++ +TA Sbjct: 247 IDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKDGTMPEKLTLTKSTLYLPDTA 306 Query: 304 AAEYEKRR 311 E EK++ Sbjct: 307 KEELEKKK 314 Lambda K H 0.316 0.131 0.376 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: 341 Number of extensions: 8 Number of successful extensions: 3 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: 313 Length of database: 318 Length adjustment: 27 Effective length of query: 286 Effective length of database: 291 Effective search space: 83226 Effective search space used: 83226 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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