Align Fructose import binding protein FrcB (characterized)
to candidate WP_160475710.1 RSPH17029_RS13370 sugar ABC transporter substrate-binding protein
Query= SwissProt::Q9F9B2 (341 letters) >NCBI__GCF_000015985.1:WP_160475710.1 Length = 332 Score = 499 bits (1286), Expect = e-146 Identities = 249/331 (75%), Positives = 287/331 (86%), Gaps = 1/331 (0%) Query: 11 GALAMGVAFASPSQAAEVSACLITKTDTNPFFVKMKEGAAAKAKELGVTLKSYAGKIDGD 70 GA A+ ++ A P+ A +++ACLITKTDTNPFFVKMKEGA AKA+ELG+TLKSYAG+IDGD Sbjct: 3 GAAALALS-ALPALAQDMTACLITKTDTNPFFVKMKEGATAKAQELGITLKSYAGRIDGD 61 Query: 71 SESQVAAIETCIADGAKGILIAASDTQGIVPQVQKARDAGLLVIALDTPLEPLDAADATF 130 SESQVAAIETCIADGAKGILI ASDT+GIVP VQKARDAGLLVIALDTPL+P+DAAD TF Sbjct: 62 SESQVAAIETCIADGAKGILITASDTKGIVPSVQKARDAGLLVIALDTPLDPIDAADGTF 121 Query: 131 ATDNLLAGKLIGQWAAATLGDAAKEAKVAFLDLTPSQPSVDVLRDQGFMIGFGIDPKDPN 190 ATDN LAG+LIG+WA A +GDAA +A++A L+L SQPSVDVLR+QGF+ GFG++ D Sbjct: 122 ATDNFLAGELIGKWAKARMGDAAGDARIALLNLDVSQPSVDVLRNQGFLQGFGVELGDKT 181 Query: 191 KIGDEDDPRIVGHDITNGNEEGGRTAMENLLQKDPTINVVHTINEPAAAGAYEALKSVGR 250 + GDEDDPRIVG ++T GNEEGGR AME+LL +DPTIN+VHTINEPAAAGAYEALKS+GR Sbjct: 182 RWGDEDDPRIVGQEVTQGNEEGGRRAMESLLAQDPTINLVHTINEPAAAGAYEALKSIGR 241 Query: 251 EKDVLIVSVDGGCPGVKNVAEGVIGATSQQYPLMMAALGIEAIKKFADTGEKPTPTEGKD 310 E DVLIVSVDGGCPGV+NV +GVIGATSQQYPL MAALG+EAI FA G KP +EGKD Sbjct: 242 EADVLIVSVDGGCPGVQNVKDGVIGATSQQYPLQMAALGVEAIAAFAKDGTKPATSEGKD 301 Query: 311 FVDTGVSLVADKPVSGVESIDTKTGMEKCWG 341 F DTGV+LV D+PV GVESID+ G E CWG Sbjct: 302 FTDTGVALVTDQPVEGVESIDSAKGAELCWG 332 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: 510 Number of extensions: 25 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: 341 Length of database: 332 Length adjustment: 28 Effective length of query: 313 Effective length of database: 304 Effective search space: 95152 Effective search space used: 95152 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 Apr 10 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