Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate WP_011385542.1 AMB_RS16025 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >NCBI__GCF_000009985.1:WP_011385542.1 Length = 437 Score = 307 bits (787), Expect = 4e-88 Identities = 161/418 (38%), Positives = 243/418 (58%), Gaps = 3/418 (0%) Query: 20 KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79 +++P +++ Y ++++DR NI A ++ DLG +++ +G GAG+FF Y L E+PSNLI+ Sbjct: 16 RIVPFIMLLYFIAYIDRVNIGFASLTMNKDLGFTSSVFGFGAGIFFFGYFLFEVPSNLIL 75 Query: 80 HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139 KVGAR WI R+M+TWGLIS AMAFVQG TSFYVLR LLG AEAG FPG++LYL+YWF Sbjct: 76 EKVGARLWITRVMITWGLISGAMAFVQGSTSFYVLRFLLGAAEAGFFPGIILYLSYWFPA 135 Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWR 199 RA T F+ + +G P+ AAL+ + G++G GWQWMF++E LPA+ VV+ Sbjct: 136 RHRAGVTALFMAAAPISTALGSPISAALLELHGVMGLAGWQWMFIIEALPALILGVVVFF 195 Query: 200 KLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLT-PQILLAIFVYFCHQI 258 + DRP KA W+ +E + + +E +G HS+ L P++L +YF Sbjct: 196 YMTDRPEKATWMPEDERAWLINAMNEEAASKSGHAKHSIWRGLADPRVLALALIYFGTSA 255 Query: 259 TIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLVTGL 318 +YT+ + P II + G +S+M+VG L +P A+ + +L R + +V Sbjct: 256 GLYTLGIWAPQIIKQLG-VSSMTVGWLNMIPPTASVIAMVLWARHSDRTSERTWHVVGAC 314 Query: 319 LTMALGLGIASVSGPVFS-LLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFVNAC 377 L + GL A + VF+ +L L + + ++ P L G A A G+ +N+ Sbjct: 315 LVASAGLVFAGNADGVFTVILALTLVNIGISAAKPPLWSMPTMFLSGSAAAAGIATINSI 374 Query: 378 GLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRMGHEPERGAQASEA 435 G LGGF GP+++G I+ TG+ M GL +A +L ++A+ L L A A+ A Sbjct: 375 GNLGGFAGPAMIGWIKDLTGSFMGGLYFVAALLAISAVTTLLLARSQRKSAAASAAAA 432 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: 547 Number of extensions: 27 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: 438 Length of database: 437 Length adjustment: 32 Effective length of query: 406 Effective length of database: 405 Effective search space: 164430 Effective search space used: 164430 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