Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate HSERO_RS11250 HSERO_RS11250 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__HerbieS:HSERO_RS11250 Length = 435 Score = 296 bits (758), Expect = 9e-85 Identities = 160/404 (39%), Positives = 235/404 (58%), Gaps = 5/404 (1%) Query: 20 KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79 +L+PLL + Y+ S+LDR N+ AK + DL S YGLGAG+FFL Y + E+PSN+I+ Sbjct: 27 RLLPLLFLCYVASYLDRVNVGFAKLQMLQDLKFSDTVYGLGAGIFFLGYFVFEVPSNMIL 86 Query: 80 HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139 HKVGAR WIARIM+TWG+IS AMA+V FY++R LLG+AEAG FPGV+LYLTYW+ Sbjct: 87 HKVGARLWIARIMITWGIISGAMAYVTTPEMFYIMRFLLGVAEAGFFPGVILYLTYWYPA 146 Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALMR-MDGMLGWHGWQWMFMLEGLPAVAFAWVVW 198 +R + T F+ G+ + +IGGP+ +M M G+ G GWQWMF+LE +P++ +V Sbjct: 147 ARRGKITALFMTGIALSGVIGGPLSGWIMHAMPGVWGHTGWQWMFILEAIPSLILGVMVI 206 Query: 199 RKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQI 258 + DR A WLS EE R +E I+ EE E + ++ L +YFC + Sbjct: 207 LYMKDRIRDADWLSEEEKRLLEANISH--EESQKEHLSLGAMFANGRVWLGALIYFCFVM 264 Query: 259 TIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTGL 318 +Y V F+LP+II G ++VGLLT++P+ AA +LI R A R + Sbjct: 265 GLYGVSFWLPTIIKATGVSDPLNVGLLTAIPYAFAAAAMVLIGRSADARRERRWHVAIPA 324 Query: 319 LTMALGLGIASVSG--PVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNA 376 +GL +++ G ++ L++V + + P + L G A A G+ +N+ Sbjct: 325 FIGCIGLLLSTQYGHNTTLAMASLTLASVGILTTLPLFWSLPTAFLSGTAAAAGIALINS 384 Query: 377 CGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRL 420 G L GFV P ++G ++ +T + G+ V+A LV+ L L L Sbjct: 385 LGNLAGFVSPFLVGWLKDATQSTNAGMYVLAASLVIGGLLTLTL 428 Lambda K H 0.327 0.141 0.438 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: 597 Number of extensions: 23 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: 438 Length of database: 435 Length adjustment: 32 Effective length of query: 406 Effective length of database: 403 Effective search space: 163618 Effective search space used: 163618 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: 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