Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PfGW456L13_3929 Nitrate/nitrite transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3929 Length = 431 Score = 345 bits (885), Expect = 2e-99 Identities = 179/412 (43%), Positives = 248/412 (60%), Gaps = 9/412 (2%) Query: 20 KLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALSEIPSNLIM 79 +L+P L++ YI++FLDR N+ AK D IS AA+ GAG+FF+ YAL E+PSNLI+ Sbjct: 15 RLLPFLLLMYIMAFLDRANVGFAKQAFQADTNISDAAFAFGAGVFFVGYALLEVPSNLIL 74 Query: 80 HKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVMLYLTYWFNR 139 H+VGAR W+ RIMVTWGL+SAAM F ETSFY+LR LLG+AEAG FPGV+LYLTYWF Sbjct: 75 HRVGARLWMCRIMVTWGLVSAAMVFAHTETSFYILRFLLGVAEAGFFPGVILYLTYWFPS 134 Query: 140 EQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAVAFA-WVVW 198 R +A G+F G A I G P+ L+ +DG G+HGWQW+F +EGL A A W W Sbjct: 135 AVRGKAMGFFYFGAPLAFIFGSPLSGLLLELDGFAGFHGWQWLFAVEGLMATAVGIWAYW 194 Query: 199 RKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTPQILLAIFVYFCHQI 258 L +RP+ A WL+ EE + ++ + QE G L P +L +Y Q Sbjct: 195 -YLDNRPADAKWLTVEERQQVQSLLNQEDSHKQNHGRSLLNVICQPSVLYLCLIYLLIQA 253 Query: 259 TIYTVIFFLPSIISKYGELST---MSVGLLTSLPWIAAALGALLIPRFATTPGRCRRLLV 315 ++Y V+F+LPS + G L T + VGL+T++PWI A + A LIP ++ G RR Sbjct: 254 SVYGVVFYLPSQVG--GLLGTKVGLMVGLVTAIPWICALIAAYLIPGYSDRTGERRRTAC 311 Query: 316 TGLLTMALGLGIA-SVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALAGGLGFV 374 LL A G+ + + S P+ ++ C +A F VQ + + +P+S L G A A G+ + Sbjct: 312 LTLLMAAAGIACSVTFSNPLLGIIALCFAASGFIAVQPVFWTFPSSYLAGSAAAAGIALI 371 Query: 375 NACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRM-GHE 425 N+ G LGGF+ P + E + + GL V+A V+AAL L +R GH+ Sbjct: 372 NSFGALGGFIAPVLKNWAEGAFHSPAAGLYVLAATTVIAALLVLGIRAPGHK 423 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: 576 Number of extensions: 29 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: 438 Length of database: 431 Length adjustment: 32 Effective length of query: 406 Effective length of database: 399 Effective search space: 161994 Effective search space used: 161994 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