Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate Pf1N1B4_4622 Nitrate/nitrite transporter
Query= reanno::Koxy:BWI76_RS23715 (445 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4622 Length = 440 Score = 324 bits (830), Expect = 4e-93 Identities = 179/440 (40%), Positives = 255/440 (57%), Gaps = 14/440 (3%) Query: 12 TQLQRTHKKIYRHLMPLLIVAYIISFIDRTNIGMAKATMSVDIGLSATAFGLGAGLFFLT 71 +Q R ++I L+P LI+ Y+I+++DR+ +G AK M DIGL A+GLGAGLFF+ Sbjct: 2 SQELRLIRRITLKLIPFLILLYLIAYVDRSAVGFAKLHMGADIGLGDAAYGLGAGLFFIG 61 Query: 72 YAVLEIPSNLFLTRIGARRWIARIMITWGIISCGMAFVTGPTSFYVMRLLLGAAEAGLYP 131 Y +LEIPSNL L R GARRW ARIM+TWG I+ GMAFV GP SFYVMR LLGAAEAG +P Sbjct: 62 YFLLEIPSNLMLDRFGARRWFARIMVTWGAITIGMAFVQGPNSFYVMRFLLGAAEAGFFP 121 Query: 132 GIIYYLTLWFGREERAKATGLFLLGVCLANIIGAPLGGLLLSLDGMSGWHGWQWMFFIEG 191 G++YY+T WF R K GLF+L +A +I P+ G LL +DG+ G HGWQW+F + G Sbjct: 122 GVLYYITQWFPIRHRGKILGLFILSQPIAMMITGPVSGGLLGMDGIFGLHGWQWLFIVIG 181 Query: 192 LPAIALAFVVWRRLPDKPADARWLDSHDVQAITAVLEKEAE---ETRHTPSRFSLKTALT 248 +PAI L + V R LPD P +W+D + +T L+K+ E +TRH +LK Sbjct: 182 MPAILLTWPVLRYLPDGPQQVKWMDQSEKDWLTGELKKDLEVYGQTRHGNPLHALK---- 237 Query: 249 TRVFLLLVLIYFTHQFSVYGLSYFLPGIIGSWGQLTPLQIGLLTAIPWIAAAAGGILLPR 308 + LLL L Y S+YGL +LP +I +G T L G ++++P+I G +++PR Sbjct: 238 DKRVLLLALFYLPVTLSIYGLGLWLPTLIKQFGG-TDLVTGFVSSVPYIFGIIGLLIIPR 296 Query: 309 FARTEQRSRSMLMAGYLVMATGMAIGA-IAGHGVALLGFSLAAFMFFAMQSIIFNWLPSI 367 + L Y++ A G+ + A + + L L AF F+ ++ + Sbjct: 297 SSDRLNDRYGHLAVLYVLGAIGLFLSAWLTVPVLQLAALCLVAFALFSCTAVFWTLPGRF 356 Query: 368 MSGHMLAGSFGLLNCLGLCGGFLGPFILGAFEDRTGAATSGLWF-----AVALLIVGALA 422 +G A L+N +G GG++GPF++GA ++ TG SGL+F L++ G + Sbjct: 357 FAGASAAAGIALINSVGNLGGYIGPFVIGALKEYTGNLASGLYFLSCVMVFGLVLTGVVY 416 Query: 423 SLLIKSSSSSTPASAKQARG 442 LL + A ARG Sbjct: 417 RLLERKHVLPADQFAASARG 436 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: 562 Number of extensions: 25 Number of successful extensions: 2 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: 440 Length adjustment: 32 Effective length of query: 413 Effective length of database: 408 Effective search space: 168504 Effective search space used: 168504 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