Align candidate CA265_RS03655 CA265_RS03655 (phosphoribosylpyrophosphate synthetase)
to HMM TIGR01251 (prs: ribose-phosphate diphosphokinase (EC 2.7.6.1))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01251.hmm # target sequence database: /tmp/gapView.24363.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01251 [M=309] Accession: TIGR01251 Description: ribP_PPkin: ribose-phosphate diphosphokinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-42 130.8 0.0 3.1e-42 130.5 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS03655 CA265_RS03655 phosphoribosylpyro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS03655 CA265_RS03655 phosphoribosylpyrophosphate synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 130.5 0.0 3.1e-42 3.1e-42 24 285 .. 16 271 .. 11 277 .] 0.85 Alignments for each domain: == domain 1 score: 130.5 bits; conditional E-value: 3.1e-42 TIGR01251 24 lgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkrasaksvtaviPyyg 91 l++ + Fa gE ++i+++ + i +++ +++ nd + + +++dalkr ++k++++ iPy++ lcl|FitnessBrowser__Pedo557:CA265_RS03655 16 LIEYKSFLFAGGEPHIKISNNFDA-ALPITITHRINSFNDLGL-ICITVDALKRMGVKEIHLFIPYFP 81 55666667999**********988.555555888888888555.55789******************* PP TIGR01251 92 YaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkkkelk 159 aRqd+ + ++ep+s+k+ a++++++ +v ++d Hse + ++ ++s +++i+++ +k+ + lcl|FitnessBrowser__Pedo557:CA265_RS03655 82 AARQDRVMIPGEPLSVKVYADIINAMALANVTIFDPHSEVSPALLN-NCVTISN-HEFIKQVIAKIGT 147 *************************************987766666.4666766.566666666689* PP TIGR01251 160 nlvvvsPDkGaverakkvakklg.lelaiieKeRdskeneve.vtnllgdvegkdvvivDDiisTggT 225 ++ ++sPD Ga++ kv++ l+ +e+ K Rd k+ + + + d++g d++ivDDi + ggT lcl|FitnessBrowser__Pedo557:CA265_RS03655 148 DVKLISPDGGALKKIYKVSEFLDgAEVIECSKSRDVKTGKLSgFKVYAEDLAGADCLIVDDICDGGGT 215 **********************999**********999888724556789****************** PP TIGR01251 226 lvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.eekklpkvsei 285 + +e+Lk k A k + a++hg+fs+ l++ +e+++ t++i+ ++k + ++i lcl|FitnessBrowser__Pedo557:CA265_RS03655 216 FIGLSEALKAKNAGKLYLAISHGIFSK-GFDELDKY-FEQIFTTDSIKEvDHKGV---TQI 271 *************************96.57888887.**********99444433...333 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (277 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 8.97 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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