Align Periplasmic binding protein/LacI transcriptional regulator, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate BWI76_RS07665 BWI76_RS07665 ABC transporter substrate-binding protein
Query= TCDB::Q9X053 (323 letters) >FitnessBrowser__Koxy:BWI76_RS07665 Length = 311 Score = 177 bits (449), Expect = 3e-49 Identities = 107/313 (34%), Positives = 173/313 (55%), Gaps = 10/313 (3%) Query: 10 VLVGLLLVSFTGLAQEQQKPKGKMAIVISTLNNPWFVVLAETAKQRAEQLGYEATIFDSQ 69 +L L +F+ AQ +K G + I++++L+NP++ A+ A ++A++LGY+ TI Sbjct: 7 LLTAATLTAFSFAAQAAEK--GTIMIMVNSLDNPYYASEAKGASEKAKELGYQTTILSHG 64 Query: 70 NDTAKESAHFDAIIAAGYDAIIFNPTDADGSIANVKRAKEAGIPVFCVDRGINARGLAVA 129 D K++ D I II + D+ S+A +++AK+AGIPV ++R I +A+ Sbjct: 65 EDVKKQNELIDTAIGKKVQGIILDNADSTASVAAIEKAKKAGIPVVLINREIPVDDIALE 124 Query: 130 QIYSDNYYGGVLMGEYFVKFLKEKYPDAKEIPYAELLGILSAQPTWDRSNGFHSVVDQYP 189 QI +N+ G + FV+ + EK YAEL L+ RS FH V+DQYP Sbjct: 125 QITHNNFQAGSEVANVFVEKMAEKGK------YAELTCNLADNNCVTRSKSFHQVIDQYP 178 Query: 190 EFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEAAGRTDIYIF 249 + VA+Q A+ ++ + ILQAHP++K + CGN +ALGA+ A +AA R D+ + Sbjct: 179 DMVSVAKQDAKGTLIDGKRIMDSILQAHPDVKGVICGNGPVALGAIAALKAANRNDVVVV 238 Query: 250 GFDGAEDVINAIKEGKQIVATIMQFPKLMARLAVEWADQYL-RGERSFPEIVPVTVELVT 308 G DG+ D +A+K G + AT+M + +A V D YL +GE+ + V L+T Sbjct: 239 GIDGSNDERDAVKAG-TLQATVMLQAQAIAAQGVTDLDNYLQKGEKPAKQRVMFRGILIT 297 Query: 309 RENIDKYTAYGRK 321 ++N DK + K Sbjct: 298 QDNADKVQDFNIK 310 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: 229 Number of extensions: 13 Number of successful extensions: 2 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: 311 Length adjustment: 27 Effective length of query: 296 Effective length of database: 284 Effective search space: 84064 Effective search space used: 84064 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