Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PfGW456L13_4546 Permeases of the major facilitator superfamily
Query= reanno::Koxy:BWI76_RS23715 (445 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4546 Length = 443 Score = 278 bits (710), Expect = 3e-79 Identities = 162/424 (38%), Positives = 231/424 (54%), Gaps = 16/424 (3%) Query: 8 AVNGTQLQRTHKKIYRHLMPLLIVAYIISFIDRTNIGMAKATMSVDIGLSATAFGLGAGL 67 AV+ + + K+ LMPL++V Y+ +F DR NI AK + D+ LS TA+GLGAGL Sbjct: 13 AVSHDEEKALVSKVAWRLMPLIMVCYLFAFFDRINISFAKFQLQADLSLSDTAYGLGAGL 72 Query: 68 FFLTYAVLEIPSNLFLTRIGARRWIARIMITWGIISCGMAFVTGPTSFYVMRLLLGAAEA 127 F + Y + E+PSN+ L ++GARRWIARIM++WG+ + M FV FYV+R ++GA EA Sbjct: 73 FVVGYVIFEVPSNMMLYKVGARRWIARIMMSWGLATAAMVFVNSEWQFYVLRFVIGAMEA 132 Query: 128 GLYPGIIYYLTLWFGREERAKATGLFLLGVCLANIIGAPLGGLLLS-LDGMSGWHGWQWM 186 G PG++YYLTLWF + R + T + L A ++GAP GL+L LDG+ GW W+ Sbjct: 133 GFAPGVLYYLTLWFPQHYRGRITSMLFLASAFAGLVGAPFSGLVLQHLDGVLQMRGWHWL 192 Query: 187 FFIEGLPAIALAFVVWRRLPDKPADARWLDSHDVQAITAVLEKEAEETRHTPSRFSLKTA 246 F + G+P I L +V L D+ DA WL + T + + A+ H S SL A Sbjct: 193 FLLGGVPCIGLGLLVLTLLKDRIEDAHWLTPSEK---TLLASRIAQHEPH-KSGGSLLAA 248 Query: 247 LTTRVFLLLVLIYFTHQFSVYGLSYFLPGIIGSWGQLTPLQIGLLTAIPWIAAAAGGILL 306 L FL L LIYF Q + YGL+++ P +I S G +P+ IGLLTAIP+I A +++ Sbjct: 249 LRIPGFLTLGLIYFLIQVASYGLNFWAPQLIRSAGTESPVMIGLLTAIPYICGAISMVVI 308 Query: 307 PRFARTEQRSRSMLMAGYLVMATGMAIGAIAGHGVALLGFSLAAFMFFAMQSIIFNWL-- 364 R + R + V A G I L +L + SI W Sbjct: 309 GRLSDASGERRKFVAGLVAVGAVGFFCAGIFASHTTFLIVALGLLGAGIIASIPSFWTLP 368 Query: 365 PSIM--SGHMLAGSFGLLNCLGLCGGFLGPFILGAFEDRTGAATSGLW-------FAVAL 415 P ++ +G AG ++N LG GG + P ++G +D TG+ T L+ AVAL Sbjct: 369 PKLLAGAGAGAAGGIAVINTLGQFGGIVSPVMVGRIKDLTGSTTPALYVIGVCALIAVAL 428 Query: 416 LIVG 419 L+ G Sbjct: 429 LLWG 432 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: 465 Number of extensions: 24 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: 445 Length of database: 443 Length adjustment: 32 Effective length of query: 413 Effective length of database: 411 Effective search space: 169743 Effective search space used: 169743 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