Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate 17811 b3751 D-ribose transporter subunit (NCBI)
Query= uniprot:A0KWY4 (313 letters) >FitnessBrowser__Keio:17811 Length = 296 Score = 129 bits (325), Expect = 7e-35 Identities = 90/286 (31%), Positives = 143/286 (50%), Gaps = 11/286 (3%) Query: 6 IITALGLWA-VSATCAYATTVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQQKQ 64 +++A+ L A VSA T+ + + S + + EA + G +L D+Q Sbjct: 9 LVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNP 68 Query: 65 ENQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSLFLTR 124 ++ V+ +G ++I P +K A +A IPV+ +DR + ++ Sbjct: 69 AKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGE---VVSH 125 Query: 125 IASDFSEEGRKIGQWLMDKTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRS 184 IASD G+ G ++ K + ELQG G +AA +R GF Q +A + ++ S Sbjct: 126 IASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAH-KFNVLAS 184 Query: 185 QTGEFTRAKGKEVMEGFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVSV 244 Q +F R KG VM+ L A + AV++ NDEMALGA++A++ AG D+++V Sbjct: 185 QPADFDRIKGLNVMQNLLTAH--PDVQAVFAQNDEMALGALRALQTAG---KSDVMVVGF 239 Query: 245 DGVPDYFKAMADGDVNATV-ELSPYLGGPAFDAIDAYLKGNKDQAK 289 DG PD KA+ DG + AT+ +L +G + D LKG K QAK Sbjct: 240 DGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAK 285 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: 205 Number of extensions: 12 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: 313 Length of database: 296 Length adjustment: 27 Effective length of query: 286 Effective length of database: 269 Effective search space: 76934 Effective search space used: 76934 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