Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate 6938451 Sama_2570 ribose-phosphate pyrophosphokinase (RefSeq)
Query= BRENDA::P0A719 (315 letters) >FitnessBrowser__SB2B:6938451 Length = 315 Score = 531 bits (1368), Expect = e-156 Identities = 262/315 (83%), Positives = 293/315 (93%) Query: 1 MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60 MPD+KLFAGNATP LA++IA+RL+ LG+A VGRFSDGE+SVQINENVRG D+FIIQSTC Sbjct: 1 MPDIKLFAGNATPSLAKKIADRLFCKLGEAEVGRFSDGEISVQINENVRGADVFIIQSTC 60 Query: 61 APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120 APTNDNLMEL+VMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV Sbjct: 61 APTNDNLMELIVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120 Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180 GVDRVLT DLHAEQIQGFFDVPVDNVFGSP+LLEDM+ LDNP+VVSPDIGGVVRARA+ Sbjct: 121 GVDRVLTCDLHAEQIQGFFDVPVDNVFGSPVLLEDMVAKKLDNPVVVSPDIGGVVRARAV 180 Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240 AKLLND+D+AIIDKRRP+ANV+QVMHIIGDV GRDC++VDDMIDTGGTLCKAAEALKE G Sbjct: 181 AKLLNDSDLAIIDKRRPQANVAQVMHIIGDVEGRDCIIVDDMIDTGGTLCKAAEALKEHG 240 Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300 A RVFAYATHP+FSG AA N++NSVIDEV+V DT+PLS+E+ + V LT+S +LAEAI Sbjct: 241 ANRVFAYATHPVFSGKAAENIKNSVIDEVIVTDTVPLSEEMMKVGKVSQLTMSALLAEAI 300 Query: 301 RRISNEESISAMFEH 315 RR+SNEESISAMF+H Sbjct: 301 RRVSNEESISAMFQH 315 Lambda K H 0.321 0.137 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: 418 Number of extensions: 5 Number of successful extensions: 1 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: 315 Length of database: 315 Length adjustment: 27 Effective length of query: 288 Effective length of database: 288 Effective search space: 82944 Effective search space used: 82944 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate 6938451 Sama_2570 (ribose-phosphate pyrophosphokinase (RefSeq))
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.14840.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-131 423.3 2.7 2.6e-131 423.1 2.7 1.0 1 lcl|FitnessBrowser__SB2B:6938451 Sama_2570 ribose-phosphate pyrop Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938451 Sama_2570 ribose-phosphate pyrophosphokinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 423.1 2.7 2.6e-131 2.6e-131 2 309 .] 5 314 .. 4 314 .. 0.98 Alignments for each domain: == domain 1 score: 423.1 bits; conditional E-value: 2.6e-131 TIGR01251 2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkra 78 k+++g+++++la+k+a++l +lg++ev +F+dgE++v+i+e+vrg dvfii qst+ap+nd+lmel++++dal+ra lcl|FitnessBrowser__SB2B:6938451 5 KLFAGNATPSLAKKIADRLFCKLGEAEVGRFSDGEISVQINENVRGADVFII-QSTCAPTNDNLMELIVMVDALRRA 80 89**************************************************.************************ PP TIGR01251 79 saksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelk 154 sa+++taviPy+gYaRqd++++ r pi+ak+va++l+++G+drvlt dlH+eqiqgfFdvpv+n+ +sp+l+e++ lcl|FitnessBrowser__SB2B:6938451 81 SAGRITAVIPYFGYARQDRRVRsARVPITAKVVADFLSSVGVDRVLTCDLHAEQIQGFFDVPVDNVFGSPVLLEDMV 157 ********************9857***************************************************** PP TIGR01251 155 kkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaa 230 +k+l+n+vvvsPD G+v ra++vak l+ ++laii+K+R+ ++n+++v++++gdveg+d++ivDD+i+TggTl+kaa lcl|FitnessBrowser__SB2B:6938451 158 AKKLDNPVVVSPDIGGVVRARAVAKLLNdSDLAIIDKRRP-QANVAQVMHIIGDVEGRDCIIVDDMIDTGGTLCKAA 233 ****************************9***********.888********************************* PP TIGR01251 231 elLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiarihenesvs 305 e+Lke+GA++v+++ath+vfsg+A+e++++++++evivt+t++ ee k+ kvs+++++ l+aeai+r++++es+s lcl|FitnessBrowser__SB2B:6938451 234 EALKEHGANRVFAYATHPVFSGKAAENIKNSVIDEVIVTDTVPLsEEmMKVGKVSQLTMSALLAEAIRRVSNEESIS 310 ********************************************877899*************************** PP TIGR01251 306 slfd 309 ++f+ lcl|FitnessBrowser__SB2B:6938451 311 AMFQ 314 **96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (315 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: 00:00:00.01 # Mc/sec: 8.55 // [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