Align Ribose-phosphate pyrophosphokinase 2; Phosphoribosyl pyrophosphate synthase 2; EC 2.7.6.1 (characterized)
to candidate BWI76_RS25955 BWI76_RS25955 ribose-phosphate pyrophosphokinase
Query= SwissProt::P38620 (318 letters) >FitnessBrowser__Koxy:BWI76_RS25955 Length = 289 Score = 96.3 bits (238), Expect = 8e-25 Identities = 73/226 (32%), Positives = 113/226 (50%), Gaps = 23/226 (10%) Query: 66 EINDFLMELLILIHACKTASVRRITAV------IPNFPYARQDKKDKSRAPITAKLIANL 119 ++NDF++ L L+ A VR +T V +P P+ARQD+ K+ A Sbjct: 50 DMNDFML-LAQLVEA-----VRHVTDVAFSHLELPWLPWARQDRHMVPGDSFALKVFARQ 103 Query: 120 LETAGCDHVITMDLH----ASQIQGFFHIPVDNLYGEPSVLNYIRTKTDFNNAILVSPDA 175 L T G D V+ +D H A+ + + + + +VL R +LV+PDA Sbjct: 104 LNTLGFDKVVVLDPHSDAAAAAVNNMVAVAQQHCLLQSAVL---RQAIATGELMLVAPDA 160 Query: 176 GGAKRVASLADKLDMN-FALIHKERQKANEV--SRMLLVGDVAGKSCLLIDDMADTCGTL 232 G K++ +A FA++ KER A+ S LL GDVAGK+ L++DD+ D GT Sbjct: 161 GALKKIHPVAKACGAGEFAILGKERDLASGALTSFSLLAGDVAGKAVLIVDDLCDAGGTF 220 Query: 233 VKACDTLMDHGAKEVIAIVTHGIFSGSAREKLINSRLSRIVCTNTV 278 + + L + GA+ V VTHGIFS E L+N+ + + T ++ Sbjct: 221 IGSAQVLREAGARSVSLYVTHGIFSKGV-EHLLNNGIDAVYATTSL 265 Lambda K H 0.320 0.135 0.385 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: 163 Number of extensions: 8 Number of successful extensions: 3 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: 318 Length of database: 289 Length adjustment: 27 Effective length of query: 291 Effective length of database: 262 Effective search space: 76242 Effective search space used: 76242 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate BWI76_RS25955 BWI76_RS25955 (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.956.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-44 137.5 0.0 2.6e-44 137.4 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS25955 BWI76_RS25955 ribose-phosphate p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS25955 BWI76_RS25955 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 137.4 0.0 2.6e-44 2.6e-44 24 288 .. 13 281 .. 1 286 [. 0.82 Alignments for each domain: == domain 1 score: 137.4 bits; conditional E-value: 2.6e-44 TIGR01251 24 lgdvevkkFadgElyvrieesvrgkdvfiiv.qstsapvndalmellllidalkrasaksv.taviPyygY 92 F+dg + ++ +++ + + + + t +++n + m l l++a+++ ++ +P +++ lcl|FitnessBrowser__Koxy:BWI76_RS25955 13 AFTLASGVFPDGAVWLKVTDQLPPSARLMRIrAVTLRDMN-DFMLLAQLVEAVRHVTDVAFsHLELPWLPW 82 5556666788888888888888776665544144444444.5788889999999965444415679***** PP TIGR01251 93 aRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkkke..lknl 161 aRqd+++ ++++ + k++a+ l+++G d+v+++d Hs++ + + v+ + + l + ++ +l lcl|FitnessBrowser__Koxy:BWI76_RS25955 83 ARQDRHMVPGDSFALKVFARQLNTLGFDKVVVLDPHSDAAAAAVNNMVAVAQQHCLLQSAVLRQAiaTGEL 153 ***************************************999988766666666666666555556899** PP TIGR01251 162 vvvsPDkGaverakkvakklg.lelaiieKeRdskenev.evtnllgdvegkdvvivDDiisTggTlvkaa 230 ++v+PD+Ga++ + vak+ g e+ai+ KeRd ++ + l gdv+gk v+ivDD+ + ggT + +a lcl|FitnessBrowser__Koxy:BWI76_RS25955 154 MLVAPDAGALKKIHPVAKACGaGEFAILGKERDLASGALtSFSLLAGDVAGKAVLIVDDLCDAGGTFIGSA 224 *********************89**********8766551556678************************* PP TIGR01251 231 elLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekklpkvseisva 288 ++L+e+GA++v ++thg+fs+ +e l ++g+++v++t ++ + + p+++ i++ lcl|FitnessBrowser__Koxy:BWI76_RS25955 225 QVLREAGARSVSLYVTHGIFSKG-VEHLLNNGIDAVYATTSLTSPALAHPQLELIDID 281 ********************975.67777778*********99977788888888875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (289 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.11 // [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