Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate H281DRAFT_00981 H281DRAFT_00981 D-galactonate transporter
Query= reanno::Koxy:BWI76_RS23715 (445 letters) >FitnessBrowser__Burk376:H281DRAFT_00981 Length = 450 Score = 321 bits (823), Expect = 3e-92 Identities = 179/436 (41%), Positives = 255/436 (58%), Gaps = 13/436 (2%) Query: 16 RTHKKIYRHLMPLLIVAYIISFIDRTNIGMAKATMSVDIGLSATAFGLGAGLFFLTYAVL 75 RT K++ L+P LIV Y I+++DR N+G A M+ +GLSA+AFG GAG+FF+ Y Sbjct: 6 RTMKRVTVRLVPFLIVCYFIAYLDRVNVGFAALQMNKALGLSASAFGFGAGIFFIAYFFF 65 Query: 76 EIPSNLFLTRIGARRWIARIMITWGIISCGMAFV------TGPTS---FYVMRLLLGAAE 126 E+PSNL L + GARRWIARIM TWG+++ MA++ TG ++ FY +R+LLG AE Sbjct: 66 EVPSNLLLEKFGARRWIARIMFTWGLLAGAMAYIPHIAQYTGLSAAHVFYGLRILLGVAE 125 Query: 127 AGLYPGIIYYLTLWFGREERAKATGLFLLGVCLANIIGAPLGGLLLSLDGMSGWHGWQWM 186 AG +PG+I+ LTLWF R + G F+ + L+ +IG P+ G LLS+DG +G GWQW+ Sbjct: 126 AGFFPGVIFLLTLWFPAAYRGRVVGYFMAAIPLSTVIGGPISGALLSMDGFAGLAGWQWV 185 Query: 187 FFIEGLPAIALAFVVWRRLPDKPADARWLDSHDVQAITAVLEKEAEETRHTPSRFSLKTA 246 + IE LPA+ LAF VW L DKPADA WL + + + A +K+ E R FS+K A Sbjct: 186 YLIEALPALILAFAVWFYLTDKPADATWLAADERDWLVA-RQKQEREHREAVHAFSVKEA 244 Query: 247 LTTRVFLLLVLIYFTHQFSVYGLSYFLPGIIGSWGQLTPLQIGLLTAIPWIAAAAGGILL 306 L R L + LIYF + YGLS+FLP I+ ++G LT LQ G +T++P+I + Sbjct: 245 LLNRRVLAIALIYFGANATNYGLSFFLPQIVKAFG-LTNLQTGFVTSLPYIVGVISMVYW 303 Query: 307 PRFARTEQRSRSMLMAGYLVMATGMAIGAIAGHGV-ALLGFSLAAFMFFAMQSIIFNWLP 365 R + + + + V A G+A A + V ++ S+A F F +I+ Sbjct: 304 GRHSDRKLERKRHVAIALTVAALGIAASAGLDNPVQKMIALSIAGFGIFGCLPVIWTLPA 363 Query: 366 SIMSGHMLAGSFGLLNCLGLCGGFLGPFILGAFEDRTGAATSGLWFAVALLIVGALASLL 425 + +SG AG +N LG GF GP+ +G +D TG +GL +VGA A+LL Sbjct: 364 AFLSGAAAAGGIAAINSLGNLAGFFGPYAMGWIKDSTGGFGAGLLCLAGAGLVGAAAALL 423 Query: 426 IKSSSSSTPASAKQAR 441 + + ASA AR Sbjct: 424 L-HHDPALEASAGTAR 438 Lambda K H 0.328 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: 528 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 450 Length adjustment: 33 Effective length of query: 412 Effective length of database: 417 Effective search space: 171804 Effective search space used: 171804 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