Align Fructose import permease protein FrcC (characterized)
to candidate SMc02031 SMc02031 permease
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Smeli:SMc02031 Length = 349 Score = 188 bits (478), Expect = 2e-52 Identities = 117/323 (36%), Positives = 177/323 (54%), Gaps = 22/323 (6%) Query: 49 AVPLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGA 108 A PLI LVL L+A+ F + ++ + +Q A V I+ QT VILT GIDLSV A Sbjct: 30 AGPLIALVL-LMAYLAFATSNFLTLDNLSNVARQSAFVAILAVGQTFVILTGGIDLSVAA 88 Query: 109 IMVLSS----VIMGQ----FTFRYGF-PPALSVICGLGVGALCGYINGTLVARMKLPPFI 159 I LS+ V++ Q F +GF PP ++++ G+ +G G +NG L+++ K+P FI Sbjct: 89 IAALSASITAVLLTQPLVLFGIDFGFVPPPVAILIGILIGMAAGALNGWLISKFKIPDFI 148 Query: 160 VTLGMWQIVLASNFLYSANETIRAQDISANASI---LQFFGQNFRIGNAVFTYGVVVMVL 216 TLG + L + + + +A + L + G G +F V ++ Sbjct: 149 ATLGTMTAFRGAALLVT--DGLPVPSFNAGRQLPESLIWVG-----GGQLFGVPVSALIA 201 Query: 217 LVCLL--WYVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALI 274 L+C WYVL TA GR +YAVG + AA +G++++R I Y +SGL+ A+AG L+ Sbjct: 202 LLCAAAGWYVLRYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAGIILV 261 Query: 275 GRIGSVSPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDP 334 GR+ S + + SI +VVIGG +LFGG G + G + GA I+GV GL L+ P Sbjct: 262 GRLNSANALMADGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNLLDVSP 321 Query: 335 QWTYLLIGLLIIIAVAIDQWIRK 357 W + G++I++ V DQW R+ Sbjct: 322 FWQRIAQGVVIVVVVIFDQWRRR 344 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: 370 Number of extensions: 26 Number of successful extensions: 4 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: 349 Length adjustment: 29 Effective length of query: 331 Effective length of database: 320 Effective search space: 105920 Effective search space used: 105920 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