Align 2-deoxy-D-ribonate transporter (characterized)
to candidate AO353_26910 AO353_26910 MFS transporter permease
Query= reanno::Burk376:H281DRAFT_00642 (448 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26910 Length = 436 Score = 271 bits (693), Expect = 3e-77 Identities = 156/422 (36%), Positives = 230/422 (54%), Gaps = 13/422 (3%) Query: 19 RKAMARLIPLMCAIYFMSFLDRTNVALAKLQLAADVGISAAAYGFGSGIFFLGYALLEVP 78 ++ RLIP + Y ++LDR NV AKLQ+ + S YG G+GIFF+GY L VP Sbjct: 20 KRVTLRLIPFIFVCYLFNYLDRVNVGFAKLQMLDALKFSETVYGLGAGIFFIGYVLCGVP 79 Query: 79 SNLAAHKVGPRRWIARIAVTWGILSTAMMFVQGTSSFYVLRVLLGIAEAGLFPALMYMVT 138 SNLA + GPRRWIA + VTWG+LST ++FV + FY LR+ G AEAG FP ++ ++ Sbjct: 80 SNLALTRFGPRRWIALMMVTWGMLSTCLLFVTTPTGFYTLRLFTGAAEAGFFPGVVLYLS 139 Query: 139 LWFAPHDRPVVVGWIYIAPALALMLGNPLGGALMQ--LDGFGGLHGWQWMFMLEGIPSVI 196 WF R ++ A ++ +LG+P G ++ G GGL GWQWMF+L+GIP++ Sbjct: 140 QWFPTFRRGRIMALFMSAIPVSGLLGSPFSGWILNHFAAGQGGLAGWQWMFLLQGIPTIT 199 Query: 197 VGIVLFFKMPERPRDARWLSAAERDVLETHAVIDGHGRADYSSANWIAALKRPTTVLIGL 256 +G + FF + + A+WL ER VLE ID + ++ + +A K P GL Sbjct: 200 LGALAFFLLSDNFASAKWLKPEERAVLEADQAIDWASKPKTATDSLLAVFKNPAIWAFGL 259 Query: 257 IYFLNQVAFVGLYFFTPAIIHQMHVDSSLVVGFLSASVGLGFLLGVLVLPRIHRRTDRDC 316 IYF Q + F+ P+II + +LV+G+LSA + +LL + + + R D Sbjct: 260 IYFCIQSGVYAINFWLPSIIKNLGFADNLVIGWLSA---IPYLLAAVFMLMVGRSADLHK 316 Query: 317 VFLGILTAGLILGACAYLA----VTNPAARIALLTVTAFFAGGVLPSYWAIAMKRLQGIQ 372 L +++GA L NPA I LT+ A LP +W + L Sbjct: 317 ERRWHLVVPMLMGAVGLLIAVNFAANPAIAILGLTIATMGALTGLPMFWPVPTAMLSAGA 376 Query: 373 AAAGLAFVNTIGLIGGFVGPYLFGIAETSSGRSDAGFTVILIAGVL--GLALVPVLARAM 430 AA GLA +N++G + GF+ PYL G + S+G +DA + L+AGV+ G L + R + Sbjct: 377 AAGGLALINSMGQMAGFLSPYLVGWVKDSTGSTDA--ALYLLAGVIVCGSLLALRMTRTL 434 Query: 431 RS 432 R+ Sbjct: 435 RA 436 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: 584 Number of extensions: 31 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: 448 Length of database: 436 Length adjustment: 32 Effective length of query: 416 Effective length of database: 404 Effective search space: 168064 Effective search space used: 168064 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