Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate GFF1073 Psest_1106 ribose-phosphate pyrophosphokinase
Query= BRENDA::P0A719 (315 letters) >FitnessBrowser__psRCH2:GFF1073 Length = 329 Score = 426 bits (1096), Expect = e-124 Identities = 210/310 (67%), Positives = 258/310 (83%), Gaps = 1/310 (0%) Query: 4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63 M +F GNA P+LA+R+ +L+ LGDA VG+FSDGE+SV+INENVRG D+F+IQ TCAPT Sbjct: 20 MMVFTGNANPDLARRVVRQLHIPLGDAYVGKFSDGEISVEINENVRGKDVFLIQPTCAPT 79 Query: 64 NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123 NDNLMELVV+ DA RR+SA RITAVIPYFGYARQDRR RSARVPI+AKVVAD L VGV+ Sbjct: 80 NDNLMELVVLADAFRRSSASRITAVIPYFGYARQDRRPRSARVPISAKVVADMLDVVGVN 139 Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183 RVLTVDLHA+QIQGFFD+PVDN++GSP+L++D+ +N ++VSPDIGGVVRARA+AK Sbjct: 140 RVLTVDLHADQIQGFFDMPVDNIYGSPVLVDDIQAQRFENLMIVSPDIGGVVRARAVAKS 199 Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243 L D+AIIDKRRP+AN S+VMHIIGD+ GR C+LVDDM+DT GTLC AA+ALK+ GA + Sbjct: 200 LG-VDLAIIDKRRPKANQSEVMHIIGDIEGRTCILVDDMVDTAGTLCHAAKALKDHGAAK 258 Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRI 303 V+AY THPI SG A N+ SV+DE+VV +TIPLS +S +R L ++ ++AEA+RRI Sbjct: 259 VYAYCTHPILSGRAIENIEGSVLDELVVTNTIPLSAAAQSCTRIRQLDIAPVVAEAVRRI 318 Query: 304 SNEESISAMF 313 SN ESISAMF Sbjct: 319 SNAESISAMF 328 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: 355 Number of extensions: 9 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: 315 Length of database: 329 Length adjustment: 28 Effective length of query: 287 Effective length of database: 301 Effective search space: 86387 Effective search space used: 86387 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 GFF1073 Psest_1106 (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.21695.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-126 405.4 0.9 7e-126 405.3 0.9 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1073 Psest_1106 ribose-phosphate pyro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1073 Psest_1106 ribose-phosphate pyrophosphokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.3 0.9 7e-126 7e-126 1 309 [] 20 329 .] 20 329 .] 0.98 Alignments for each domain: == domain 1 score: 405.3 bits; conditional E-value: 7e-126 TIGR01251 1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidal 75 ++++ g+++++la++v ++l+++lgd+ v kF+dgE++v+i+e+vrgkdvf+i q t+ap+nd+lmel++l+da+ lcl|FitnessBrowser__psRCH2:GFF1073 20 MMVFTGNANPDLARRVVRQLHIPLGDAYVGKFSDGEISVEINENVRGKDVFLI-QPTCAPTNDNLMELVVLADAF 93 799**************************************************.********************* PP TIGR01251 76 krasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspkl 149 +r+sa+++taviPy+gYaRqd++ + r pisak+va++l +G++rvltvdlH++qiqgfFd+pv+n+++sp+l lcl|FitnessBrowser__psRCH2:GFF1073 94 RRSSASRITAVIPYFGYARQDRRPRsARVPISAKVVADMLDVVGVNRVLTVDLHADQIQGFFDMPVDNIYGSPVL 168 **********************97758************************************************ PP TIGR01251 150 ieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTgg 224 +++++++ +nl++vsPD G+v ra++vak+lg++laii+K+R+ k+n+ ev++++gd+eg+++++vDD+++T+g lcl|FitnessBrowser__psRCH2:GFF1073 169 VDDIQAQRFENLMIVSPDIGGVVRARAVAKSLGVDLAIIDKRRP-KANQSEVMHIIGDIEGRTCILVDDMVDTAG 242 ********************************************.899*************************** PP TIGR01251 225 TlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiar 297 Tl++aa++Lk++GA kv++++th+++sg+A+e+++ ++++e++vtnti+ +++ +++++++ap++aea++r lcl|FitnessBrowser__psRCH2:GFF1073 243 TLCHAAKALKDHGAAKVYAYCTHPILSGRAIENIEGSVLDELVVTNTIPLsAAaQSCTRIRQLDIAPVVAEAVRR 317 **************************************************65579******************** PP TIGR01251 298 ihenesvsslfd 309 i++ es+s++f+ lcl|FitnessBrowser__psRCH2:GFF1073 318 ISNAESISAMFR 329 **********95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (309 nodes) Target sequences: 1 (329 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.30 // [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