Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate BWI76_RS26320 BWI76_RS26320 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__Koxy:BWI76_RS26320 Length = 436 Score = 288 bits (738), Expect = 2e-82 Identities = 159/402 (39%), Positives = 233/402 (57%), Gaps = 12/402 (2%) Query: 20 KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79 +L+PL+ I Y ++F+DR N+ AK + VD+G+S +A+ LGAG+FF YAL IP+NLI+ Sbjct: 22 RLVPLMFILYFIAFIDRVNVGFAKEAMQVDIGLSNSAFALGAGIFFAAYALFGIPANLIL 81 Query: 80 HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139 +K+GA+ W++ V WG++SA VQ ET F VLR LLG+ EAG +PG++L + +F Sbjct: 82 NKIGAQKWLSITTVLWGVLSALTGLVQTETQFIVLRFLLGLGEAGFYPGILLLASIYFPN 141 Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFAWVVWR 199 + RA G F+LGV A +G P+ AL+ M G LG GW WMF +EG+PAV W Sbjct: 142 KVRASVVGIFVLGVPLALTLGSPISGALLEMHGFLGRPGWFWMFFIEGIPAVIMGIFAWF 201 Query: 200 KLPDRPSKAPWLSAEEARGIEQRIAQETEE----GAGEGGHSLKNWLTPQILLAIFVYFC 255 L D P+KA +L+ EE + + ++ QE + G SLK W LA+ +Y Sbjct: 202 WLDDTPAKARFLNDEEKKALIAQLQQEQRQTETSNVGTALKSLKVW-----HLAL-IYGT 255 Query: 256 HQITIYTVIFFLPS-IISKYGELSTMSVGLLTSLPWIAAALGALLIPRFA-TTPGRCRRL 313 QI++Y ++FFLPS + S G L+ ++PW +A+G IPR A P R + Sbjct: 256 IQISVYGLMFFLPSQVASLMGSTLGFKESLVAAIPWACSAVGVYYIPRLADKMPARRVLI 315 Query: 314 LVTGLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGF 373 V +L ALGL +++ SGPV ++ LSA+ F VQ I + +PA + G ALA +GF Sbjct: 316 SVICMLAAALGLFVSAWSGPVLAIAALSLSAIGFLSVQPIFWTFPAQIVSGSALAASIGF 375 Query: 374 VNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAAL 415 G F+ P + ++ GN GL ++L+ V AL Sbjct: 376 CTTMGAFCSFLAPLIRVEVDAFFGNDSAGLVALSLITVCCAL 417 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: 533 Number of extensions: 29 Number of successful extensions: 4 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: 436 Length adjustment: 32 Effective length of query: 406 Effective length of database: 404 Effective search space: 164024 Effective search space used: 164024 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