Align Fructose import permease protein FrcC (characterized)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 261 bits (667), Expect = 2e-74 Identities = 142/307 (46%), Positives = 191/307 (62%), Gaps = 6/307 (1%) Query: 51 PLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIM 110 P I L+L+ AF +F SA LILQQV +V ++ QTLVILTAGIDLS G +M Sbjct: 16 PFIALILAC-AFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVM 74 Query: 111 VLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLA 170 L ++M + YG +++ CG+ V L G ING LV ++KLPPFIVTLG I A Sbjct: 75 ALGGIVMTKMAADYGLSAPVAIACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNIAFA 134 Query: 171 SNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAW 230 + LYS +TI DI A + L G F++G +G V+M+ L + W+ L TA Sbjct: 135 ATQLYSGAQTIT--DIPAGMTAL---GNTFQLGQTAIVWGAVLMLALYLVTWFALRETAP 189 Query: 231 GRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANI 290 GR+VYAVG+ PEA +L G+ ++L+ +Y L+GL +A + R G+ P AGQ N+ Sbjct: 190 GRHVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENL 249 Query: 291 ESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVA 350 ++I+AVV+GG SLFGGRG I+G L GALIVGVF GL LMG + L+ G+L+I+AVA Sbjct: 250 DAISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVA 309 Query: 351 IDQWIRK 357 DQ RK Sbjct: 310 TDQLSRK 316 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: 356 Number of extensions: 19 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: 360 Length of database: 319 Length adjustment: 28 Effective length of query: 332 Effective length of database: 291 Effective search space: 96612 Effective search space used: 96612 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