Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate RR42_RS04270 RR42_RS04270 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__Cup4G11:RR42_RS04270 Length = 434 Score = 306 bits (785), Expect = 6e-88 Identities = 166/401 (41%), Positives = 242/401 (60%), Gaps = 9/401 (2%) Query: 19 VKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLI 78 ++L+P L++ Y++++LDR N+ AK + DL S YGLGAG+FF+ Y L E+PSN+I Sbjct: 25 LRLVPFLLLCYVVAYLDRVNVGFAKLQMLGDLKFSETIYGLGAGIFFIGYFLFEVPSNVI 84 Query: 79 MHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFN 138 +HKVGAR WIARIM+TWG+ISAAM FV T FYVLR LLGIAEAG FPG++LYLTYW+ Sbjct: 85 LHKVGARIWIARIMITWGVISAAMMFVTTPTMFYVLRFLLGIAEAGFFPGIILYLTYWYP 144 Query: 139 REQRARATGYFLLGVCFANIIGGPVGAALMR-MDGMLGWHGWQWMFMLEGLPAVAFAWVV 197 +R R T +F+ + + +IGGP+ +M+ DG GW GWQWMF+LEG+P+V VV Sbjct: 145 SHRRGRTTTFFMTAIALSGVIGGPLSGWMMQSFDGRNGWSGWQWMFLLEGIPSVLVGLVV 204 Query: 198 WRKLPDRPSKAPWLSAEEARGIEQRIAQET--EEGAGEGGHSLKNWLTPQILLAIFVYFC 255 L DR A WLS EE +++ IA E +E A G K +P++ L +YF Sbjct: 205 LAYLDDRIVHAKWLSNEEKALLQRNIAAEDMHKEDAPIG----KVLSSPRVWLMSAIYFS 260 Query: 256 HQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFA-TTPGRCRRLL 314 + +Y V F+LP+II + G S + +GLLT++P+ A G +L+ A T R + Sbjct: 261 FVMGLYGVSFWLPTIIKQTGVKSPLDIGLLTAIPYGCAVAGMVLVAYSADRTRERRWHIA 320 Query: 315 VTGLL-TMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGF 373 + LL + L L + + V +LLG L+ + + + P + L G A G+ Sbjct: 321 IPALLGAVGLVLSVQWHNNTVLALLGLTLATIGILTTLPLFWSLPTAFLAGTGAAAGIAL 380 Query: 374 VNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAA 414 +N+ G L GF+ P +G ++ T + +G+ ++A LV A Sbjct: 381 INSLGNLAGFISPYAVGWLKDMTQSTDSGMYLLAACLVAGA 421 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: 581 Number of extensions: 22 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: 434 Length adjustment: 32 Effective length of query: 406 Effective length of database: 402 Effective search space: 163212 Effective search space used: 163212 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