Align Fructose import permease protein FrcC (characterized)
to candidate AO353_21390 AO353_21390 ABC transporter
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21390 Length = 340 Score = 169 bits (429), Expect = 8e-47 Identities = 111/320 (34%), Positives = 170/320 (53%), Gaps = 28/320 (8%) Query: 52 LIVLVLSLIAFGVILGGKFFSAFTMTLILQ--QVAIVGIVGAAQTLVILTAGIDLSVGAI 109 LI + L FG I+ + F + L+L QV+I+G++ T VI+T GIDLS G++ Sbjct: 30 LIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSV 89 Query: 110 MVLSSVIMGQFTFRYGF-----------PPALSVICGLGVGALCGYINGTLVARMKLPPF 158 + LS++I F P + VI GLGVG L G ING+++A +PPF Sbjct: 90 LALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGAINGSIIAVTGIPPF 149 Query: 159 IVTLGMWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLV 218 I TLGM Y+ + + S A IG+ V++ L+V Sbjct: 150 IATLGMMVSARGLARYYTEGQPVSMLSDSYTA-----------IGHGAMP---VIIFLVV 195 Query: 219 CLLWYV-LNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRI 277 +++++ L T +G+Y YA+G + +AA+ +G+NV R L+ +Y+++GL+ LAG R Sbjct: 196 AVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARA 255 Query: 278 GSVSPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWT 337 + G +++I A VIGG SL GG G I G + GALI+GV + G +G D Sbjct: 256 ATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQ 315 Query: 338 YLLIGLLIIIAVAIDQWIRK 357 ++ GL+I+IAV IDQ+ K Sbjct: 316 DIIKGLIIVIAVVIDQYRNK 335 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: 22 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: 340 Length adjustment: 29 Effective length of query: 331 Effective length of database: 311 Effective search space: 102941 Effective search space used: 102941 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