Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate CA265_RS24735 CA265_RS24735 ribose-phosphate pyrophosphokinase
Query= BRENDA::E7EAU9 (317 letters) >FitnessBrowser__Pedo557:CA265_RS24735 Length = 313 Score = 290 bits (743), Expect = 2e-83 Identities = 158/307 (51%), Positives = 210/307 (68%), Gaps = 3/307 (0%) Query: 10 LKIFSLNSNPELAKEIADNVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSAPV 69 +K+FS + L+ +IA++ G LG ++ +FSDGE Q + +ESIRG D ++IQST P Sbjct: 8 VKLFSGTGSRGLSLKIAEHYGKPLGSVTIHKFSDGEFQPSFDESIRGSDVFLIQSTYQP- 66 Query: 70 NEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATR 129 ++++MELL+MVDA KRASA I V+PYYG ARQDRK + R I AKL ANLL++AG R Sbjct: 67 SDNLMELLLMVDAAKRASAHYITAVVPYYGLARQDRKDKPRVAIGAKLVANLLKSAGIHR 126 Query: 130 VIALDLHAPQIQGFFDIPIDHLMGVPILGHYFEGKDLKDIVIVSPDHGGVTRARKLADRL 189 ++ +DLHA QIQGFFDIP+DHL G I Y + LK++ I SPD GG RAR A Sbjct: 127 IMTMDLHAAQIQGFFDIPVDHLDGSVIFVPYIKSLGLKNLTIASPDMGGSYRARTFAKFF 186 Query: 190 KAPIAIIDKRRPRPNEVEVMNIVGNVEGKTAILIDDIIDTAGTITLAANALVENGAAEVY 249 A + I DKRR R NE+E M+I+G+V G+ +LIDDI DTAGT++ AA ++ENGAA V Sbjct: 187 NAEVIICDKRRKRANEIESMSIIGDVTGQDVVLIDDICDTAGTLSKAAALIMENGAASVR 246 Query: 250 ACCTHPVLSGPAVERINNSKIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEK 309 A CTH VLSG A+E + NS + EL+VT++I L +E + + LS L A AI V+E Sbjct: 247 AVCTHAVLSGKAIETVENSVLTELIVTDTIPLKQES--PKIRVLSTAGLFARAIANVNEH 304 Query: 310 QSVSYLF 316 S+S LF Sbjct: 305 GSISDLF 311 Lambda K H 0.319 0.136 0.383 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: 203 Number of extensions: 5 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: 317 Length of database: 313 Length adjustment: 27 Effective length of query: 290 Effective length of database: 286 Effective search space: 82940 Effective search space used: 82940 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate CA265_RS24735 CA265_RS24735 (ribose-phosphate pyrophosphokinase)
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.10824.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-110 352.7 0.1 8e-110 352.5 0.1 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS24735 CA265_RS24735 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS24735 CA265_RS24735 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 352.5 0.1 8e-110 8e-110 2 309 .] 9 312 .. 8 312 .. 0.99 Alignments for each domain: == domain 1 score: 352.5 bits; conditional E-value: 8e-110 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 k++sg+ s+ l+ k+a++ g +lg+v+++kF+dgE++ ++es+rg+dvf+i qst++ +d+lmell lcl|FitnessBrowser__Pedo557:CA265_RS24735 9 KLFSGTGSRGLSLKIAEHYGKPLGSVTIHKFSDGEFQPSFDESIRGSDVFLI-QSTYQ-PSDNLMELL 74 79**************************************************.99995.799****** PP TIGR01251 70 llidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFd 137 l++da+krasa+ +tav+Pyyg aRqd+k+k+r +i aklva+ll++aG++r++t+dlH+ qiqgfFd lcl|FitnessBrowser__Pedo557:CA265_RS24735 75 LMVDAAKRASAHYITAVVPYYGLARQDRKDKPRVAIGAKLVANLLKSAGIHRIMTMDLHAAQIQGFFD 142 ******************************************************************** PP TIGR01251 138 vpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnll 205 +pv++l++s ++ ++k+ lknl++ sPD G+ ra+++ak ++e+ i +K+R+ ++ne+e++ ++ lcl|FitnessBrowser__Pedo557:CA265_RS24735 143 IPVDHLDGSVIFVPYIKSLGLKNLTIASPDMGGSYRARTFAKFFNAEVIICDKRRK-RANEIESMSII 209 ******************99************************************.889******** PP TIGR01251 206 gdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntil 273 gdv g+dvv++DDi +T+gTl kaa l+ e+GA +v +++th+v+sg+A+e +++++++e+ivt+ti+ lcl|FitnessBrowser__Pedo557:CA265_RS24735 210 GDVTGQDVVLIDDICDTAGTLSKAAALIMENGAASVRAVCTHAVLSGKAIETVENSVLTELIVTDTIP 277 ******************************************************************** PP TIGR01251 274 veekklpkvseisvapliaeaiarihenesvsslfd 309 +++ pk++++s a l+a+aia+++e+ s+s lf+ lcl|FitnessBrowser__Pedo557:CA265_RS24735 278 L-KQESPKIRVLSTAGLFARAIANVNEHGSISDLFR 312 *.8899****************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (313 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.35 // [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