Align Fructose import binding protein FrcB (characterized)
to candidate 3606963 Dshi_0390 periplasmic binding protein/LacI transcriptional regulator (RefSeq)
Query= SwissProt::Q9F9B2 (341 letters) >FitnessBrowser__Dino:3606963 Length = 337 Score = 472 bits (1214), Expect = e-138 Identities = 239/341 (70%), Positives = 273/341 (80%), Gaps = 4/341 (1%) Query: 1 MKKTVLSAAFGALAMGVAFASPSQAAEVSACLITKTDTNPFFVKMKEGAAAKAKELGVTL 60 MK +L A M A + A SACLITKTDTNPFFVKM+EGA AKA+ELGV L Sbjct: 1 MKNLMLGTALACATMSGA----ALADTTSACLITKTDTNPFFVKMREGAVAKAEELGVEL 56 Query: 61 KSYAGKIDGDSESQVAAIETCIADGAKGILIAASDTQGIVPQVQKARDAGLLVIALDTPL 120 K++AGK DGD E+QV AIETCI DGAKGILI ASDT I VQ+ARDAGL+VIALDTPL Sbjct: 57 KTFAGKFDGDHETQVQAIETCILDGAKGILITASDTSSITGAVQQARDAGLVVIALDTPL 116 Query: 121 EPLDAADATFATDNLLAGKLIGQWAAATLGDAAKEAKVAFLDLTPSQPSVDVLRDQGFMI 180 P DAADATFATDN +AG LIGQWA A +GDAA +AK+A L++ SQP+V VLR+QGF+ Sbjct: 117 TPADAADATFATDNYVAGLLIGQWARAQMGDAAADAKIAMLNIQVSQPTVGVLRNQGFLE 176 Query: 181 GFGIDPKDPNKIGDEDDPRIVGHDITNGNEEGGRTAMENLLQKDPTINVVHTINEPAAAG 240 GFGID DPN+ GDE DPRIVG D+T G+EEGGR AMEN+L DP +NVV+TINEPAAAG Sbjct: 177 GFGIDIGDPNRWGDETDPRIVGQDVTQGSEEGGRAAMENILAADPMVNVVYTINEPAAAG 236 Query: 241 AYEALKSVGREKDVLIVSVDGGCPGVKNVAEGVIGATSQQYPLMMAALGIEAIKKFADTG 300 AYEALK++GRE DVLIVSVDGGCPGV+NVA+GVIGATSQQYPL+MA+LGIEAIK +A+TG Sbjct: 237 AYEALKAIGRENDVLIVSVDGGCPGVQNVADGVIGATSQQYPLLMASLGIEAIKTWAETG 296 Query: 301 EKPTPTEGKDFVDTGVSLVADKPVSGVESIDTKTGMEKCWG 341 EKP PT GKDF DTGV+LV D P GVESI + G CWG Sbjct: 297 EKPAPTPGKDFFDTGVALVTDTPADGVESISVEEGRNLCWG 337 Lambda K H 0.313 0.132 0.372 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: 487 Number of extensions: 16 Number of successful extensions: 1 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: 341 Length of database: 337 Length adjustment: 28 Effective length of query: 313 Effective length of database: 309 Effective search space: 96717 Effective search space used: 96717 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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