Align Fructose import permease protein FrcC (characterized)
to candidate RR42_RS32895 RR42_RS32895 ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Cup4G11:RR42_RS32895 Length = 318 Score = 136 bits (343), Expect = 7e-37 Identities = 96/309 (31%), Positives = 151/309 (48%), Gaps = 16/309 (5%) Query: 50 VPLIVLVLSLIAFGV-ILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGA 108 VP V VL L++ G + G F S + I Q I+ ++ TL+I+T G+DLS+GA Sbjct: 18 VPGSVWVLLLLSLGFSVTGPGFLSVENLLNIGAQSTILLLIALPMTLIIMTEGLDLSMGA 77 Query: 109 IMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIV 168 ++ L V++ P L++ L G G +NG LV+ +++PPF+ TLG + Sbjct: 78 VLTLCGVVLAMVMVATESLP-LALGAALLTGLAFGLLNGALVSWLEIPPFVATLGT--LG 134 Query: 169 LASNFLYSANETIRAQDISANASIL---QFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVL 225 +A A + I ++ Q G I A YG L ++L Sbjct: 135 VAQGLALVATDGQSVTGIGEAIPLIYAGQLLGVPLPIWIAAVFYG---------LFHWLL 185 Query: 226 NRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAG 285 T +G YV+A+G + EA K +GV + LI++Y L GL+ +A L R+ + PTA Sbjct: 186 YHTRFGAYVFALGGNREALKFSGVRINVYLIAVYALGGLMAGVAALLLTARMNAGHPTAA 245 Query: 286 QFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLI 345 ++I AV +GG + G G + G + G L VGV GL L+G IGLL+ Sbjct: 246 IGLEFDAIAAVAVGGTTFDRGNGWLPGTVLGVLAVGVLRNGLNLVGVPSSVQVAAIGLLV 305 Query: 346 IIAVAIDQW 354 ++ + I+ + Sbjct: 306 LVVLLIESF 314 Lambda K H 0.327 0.141 0.420 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: 331 Number of extensions: 17 Number of successful extensions: 3 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: 360 Length of database: 318 Length adjustment: 28 Effective length of query: 332 Effective length of database: 290 Effective search space: 96280 Effective search space used: 96280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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