Align Fructose import binding protein FruE (characterized)
to candidate WP_106712861.1 CU102_RS19525 ABC transporter substrate-binding protein
Query= SwissProt::Q8G848 (327 letters) >NCBI__GCF_003010955.1:WP_106712861.1 Length = 318 Score = 122 bits (307), Expect = 9e-33 Identities = 96/305 (31%), Positives = 150/305 (49%), Gaps = 14/305 (4%) Query: 17 LVSVAACGSSNAGGSSDSGKKTVGFVAVGPEGGFRTANEKDIQKAFEDAGFDLTYSPTQN 76 L S A + A +SD TVGF +G E G+R A + + DL + Q Sbjct: 6 LASTVAMSFAGAASASDL---TVGFSQIGSESGWRAAETSVSKIEAKKRSIDLKIADAQQ 62 Query: 77 NDQQKQIQAFNKFVNDEVDAIILSSTEDSGWDDSLKKAAEAEIPVFTVDRNVDVKDAEAK 136 Q+ QI+A FV VDAI ++ +GWD L +A EAEIPV +DR ++ + + Sbjct: 63 K-QENQIKAIRGFVAQGVDAIFVAPVVATGWDTVLAEAKEAEIPVILLDRTIETANND-- 119 Query: 137 KAIVAHIGPSNVWCGEQAAEFVNKNFP-DGANGFILEGPAGLSVVKDRGTGW--GNKVAS 193 + + V G+ A +++ K N L+G G S +R G+ G AS Sbjct: 120 -LYLTAVTSDTVHEGKVAGDWLVKTTAGKPCNVVELQGTVGSSPAINRKKGFEEGIASAS 178 Query: 194 NVKVLESQSANWSTDEAKTVTAGLLD-KYKSDNPQFIFAQNDEMGLGAAQAVDAAGLK-G 251 N+K+ SQ+ +++ + K V G L + N ++A ND+M +GA QA+ AGLK G Sbjct: 179 NIKITRSQTGDFTRAKGKEVMEGFLKAENGGKNICALYAHNDDMAVGAIQAIKEAGLKPG 238 Query: 252 K-VKIITIDGTKNALQALVDGDLSYVIEYNPIFGKETAQAVKDYLD-GKTVEKDIEIESK 309 K + +++ID + +A+ +G+ + +E P A+K Y D GK K I+ ESK Sbjct: 239 KDILVVSIDAVPDIFKAMSEGEANATVELTPNMAGPAFDALKAYKDSGKAPPKWIQTESK 298 Query: 310 TFDAA 314 + A Sbjct: 299 LYTQA 303 Lambda K H 0.310 0.128 0.360 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: 234 Number of extensions: 14 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 327 Length of database: 318 Length adjustment: 28 Effective length of query: 299 Effective length of database: 290 Effective search space: 86710 Effective search space used: 86710 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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