Align 2-deoxy-D-ribonate transporter (characterized)
to candidate HSERO_RS21145 HSERO_RS21145 MFS transporter
Query= reanno::Burk376:H281DRAFT_00642 (448 letters) >FitnessBrowser__HerbieS:HSERO_RS21145 Length = 437 Score = 269 bits (688), Expect = 1e-76 Identities = 152/408 (37%), Positives = 225/408 (55%), Gaps = 14/408 (3%) Query: 19 RKAMARLIPLMCAIYFMSFLDRTNVALAKLQLAADVGISAAAYGFGSGIFFLGYALLEVP 78 +K R++P + Y +++LDR NV AKLQ++ D+G S +G G+G+FF+GY L EVP Sbjct: 23 KKVFWRIMPFLMLCYVIAYLDRVNVGFAKLQMSQDLGFSETVFGLGAGLFFIGYFLFEVP 82 Query: 79 SNLAAHKVGPRRWIARIAVTWGILSTAMMFVQGTSSFYVLRVLLGIAEAGLFPALMYMVT 138 SN+ HKVG R WIARI +TWGILS A MFVQ + FY+LR LLG+AEAG +P ++ +T Sbjct: 83 SNILMHKVGARIWIARIMITWGILSAAFMFVQNATQFYILRFLLGLAEAGFYPGIILYLT 142 Query: 139 LWFAPHDRPVVVGWIYIAPALALMLGNPLGGALMQLDGF---GGLHGWQWMFMLEGIPSV 195 WF H R V+ +A +LGNPL G +M D F GGL GWQWMF++E IP+V Sbjct: 143 YWFPSHRRAKVIAVFMSGIPVAGILGNPLSGWIM--DAFHQNGGLEGWQWMFLIEAIPAV 200 Query: 196 IVGIVLFFKMPERPRDARWLSAAERDVLETHAVIDGHGRADYSSANWIAALKRPTTVLIG 255 ++G+ + + A+WL+ E+ L+ A IDG + S + A +K L+ Sbjct: 201 LIGVATVLYLDNDVKSAKWLNDEEKASLQ--ADIDGDAKGKESKHGFGAIVKDARVWLMC 258 Query: 256 LIYFLNQVAFVGLYFFTPAIIHQMHVDSSLVVGFLSASVGLGFLLGVLVLPRIHRRTDRD 315 LIYF + GL + P ++ V +L +G LSA + F ++ + I R DR Sbjct: 259 LIYFSFVMGQYGLTLWMPTLVKATGVKGNLEIGLLSA---IPFGCAIIAMNLIGRSADRM 315 Query: 316 CVFLGILTAGLILGACAY----LAVTNPAARIALLTVTAFFAGGVLPSYWAIAMKRLQGI 371 L ++G + L N A IA L++ A P +W++ L G Sbjct: 316 RERRWHLVIPALMGGVGFVGAALFADNTAVSIASLSLAAAGVLTCAPLFWSLPTAFLSGA 375 Query: 372 QAAAGLAFVNTIGLIGGFVGPYLFGIAETSSGRSDAGFTVILIAGVLG 419 AA G+A +N++G + GFV PYL G + + + G ++ + V+G Sbjct: 376 AAAVGIAAINSVGNLAGFVSPYLIGYLKDLTHNNATGMYMLAVMLVVG 423 Lambda K H 0.329 0.142 0.436 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: 583 Number of extensions: 30 Number of successful extensions: 5 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: 448 Length of database: 437 Length adjustment: 32 Effective length of query: 416 Effective length of database: 405 Effective search space: 168480 Effective search space used: 168480 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 (21.8 bits) S2: 51 (24.3 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