Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 137 bits (345), Expect = 4e-37 Identities = 93/306 (30%), Positives = 149/306 (48%), Gaps = 9/306 (2%) Query: 58 IVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAALTMY 117 +++ C + RF +L +++ A+G +V+ + GID+S + AL Sbjct: 20 LILACAFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVMALGGI 79 Query: 118 GITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQYLYRGLLL 177 +TK + AP A+ G ++ G++NGLLV ++K P IVT+GT + Sbjct: 80 VMTKMAADYGLSAPVAI--ACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNIAFAATQ 137 Query: 178 TFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWLLNRTMMG 237 + G +IP M G G A++ +VL L A +VTW+ L T G Sbjct: 138 LYSGAQTITDIPAGMTALGNTFQL------GQTAIVWGAVLML-ALYLVTWFALRETAPG 190 Query: 238 RAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFDLVGSELD 297 R VYA+G S G + L V+ G+ GIA +L V+ +P LD Sbjct: 191 RHVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENLD 250 Query: 298 VIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAFILLAGTL 357 I+AV+LGG + GG G ++GTL+G ++V + ++ L L+GV S +Q ++ G ++LA Sbjct: 251 AISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVAT 310 Query: 358 FALQRK 363 L RK Sbjct: 311 DQLSRK 316 Lambda K H 0.328 0.141 0.426 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: 273 Number of extensions: 14 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: 364 Length of database: 319 Length adjustment: 28 Effective length of query: 336 Effective length of database: 291 Effective search space: 97776 Effective search space used: 97776 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