Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha
Query= TCDB::O05176 (512 letters) >FitnessBrowser__WCS417:GFF3463 Length = 502 Score = 353 bits (906), Expect = e-102 Identities = 200/503 (39%), Positives = 306/503 (60%), Gaps = 16/503 (3%) Query: 3 NTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEG 62 +++L++ NI K +PGV+AL+++NL+V+ GEIHAL+GENGAGKSTLMK+L GV EG Sbjct: 2 SSLLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQD--EG 59 Query: 63 EIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTF 121 +I +G + F D+ GI I+ QE +L+P L+ ENIFLG+E+++ G++ ++ Sbjct: 60 QILIDGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMV 119 Query: 122 NRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181 + L K++G+ + + + V +QQ VEIAKAL+ +LL+LDEPTA+L S++E Sbjct: 120 EASEALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAEL 179 Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNM 241 L ++ E + QG+ I I+H L E+ +V D+I+VLRDG V D +I D ++ M Sbjct: 180 LFEIMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDI--DHLVEMM 237 Query: 242 VGRDLEDRYPPRDV-PIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 VGR L +PP+ G +LEVK+ +R LH KGE++G AGL+G Sbjct: 238 VGRRLACSFPPKPTRERGPLLLEVKDIQLVRNGPHNRFQLH-------KGEILGFAGLVG 290 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 +GRTE A+ + G ++ DV + G+ + + +A+ G+ + E RK GL+ + + Sbjct: 291 SGRTELALGMMGALPS--VSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFS 348 Query: 361 ILHNTTLANLAGVSKAS-IIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVL 419 I N +L NL AS +ID +E +L I++ NLSGGNQQKVV+ Sbjct: 349 IRENISLNNLPKYQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVI 408 Query: 420 SKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIY 479 ++W+ + DVL+ DEPTRGIDVGAK +IY ++ L G ++MISSE+PE++G CDR+ Sbjct: 409 ARWINHHCDVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVA 468 Query: 480 VMNEGRIVAELPKGEASQESIMR 502 V ++G IV L + + +MR Sbjct: 469 VFHKGAIVKLLEASAVNPQEVMR 491 Lambda K H 0.316 0.135 0.374 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: 586 Number of extensions: 31 Number of successful extensions: 11 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: 512 Length of database: 502 Length adjustment: 34 Effective length of query: 478 Effective length of database: 468 Effective search space: 223704 Effective search space used: 223704 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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