Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate PP_2458 PP_2458 ribokinase
Query= reanno::pseudo3_N2E3:AO353_20835 (305 letters) >FitnessBrowser__Putida:PP_2458 Length = 302 Score = 379 bits (974), Expect = e-110 Identities = 204/300 (68%), Positives = 228/300 (76%), Gaps = 1/300 (0%) Query: 1 MPAKVVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIG 60 M AKVVVVGSLNMDLV RAQRLP AGETL G+SF TV GGKGANQAVA ARLG V+MIG Sbjct: 1 MNAKVVVVGSLNMDLVVRAQRLPRAGETLPGDSFFTVPGGKGANQAVAVARLGGSVAMIG 60 Query: 61 CVGDDAYGEQLRAALLAEQIDCQALTSVEG-SSGVALIVVDDNSQNAIVIVAGANGQLTP 119 VGDD YG QL AL E IDCQ +++ SSGVALI VD SQN IVI+ GANG LTP Sbjct: 61 NVGDDDYGRQLHRALYVEGIDCQGVSTCPAMSSGVALITVDAASQNCIVIIPGANGLLTP 120 Query: 120 GMVAGFDAVLAAADVIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSI 179 V FDA+L AA+VIICQLEVP TV + L RG ELGK VILNPAPAT PLPADW++ I Sbjct: 121 QSVRRFDALLQAAEVIICQLEVPASTVAWTLARGHELGKQVILNPAPATGPLPADWFAHI 180 Query: 180 DYLIPNESEASALSGLPVDSLESAELAASRLIAAGAGKVIITLGPQGSLFANGQSCEHFP 239 DYL PNESEA AL+G+ V +SA A RL+ GAGKVIITLG QG+L Q +H+P Sbjct: 181 DYLTPNESEAEALTGVVVTDQDSARRAGERLLQLGAGKVIITLGAQGALLVTAQGHQHYP 240 Query: 240 APKVKSVDTTAAGDTFVGGFAAALAAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDV 299 AP V+ +DTTAAGDTF+GGFAA L G E EAI FGQ AAALSVTRAGAQPSIP L+++ Sbjct: 241 APHVQPLDTTAAGDTFIGGFAAGLVRGLEEGEAIAFGQRAAALSVTRAGAQPSIPYLAEL 300 Lambda K H 0.315 0.130 0.363 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: 313 Number of extensions: 11 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: 305 Length of database: 302 Length adjustment: 27 Effective length of query: 278 Effective length of database: 275 Effective search space: 76450 Effective search space used: 76450 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
Align candidate PP_2458 PP_2458 (ribokinase)
to HMM TIGR02152 (rbsK: ribokinase (EC 2.7.1.15))
# 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.carbon/TIGR02152.hmm # target sequence database: /tmp/gapView.17028.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02152 [M=298] Accession: TIGR02152 Description: D_ribokin_bact: ribokinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-113 363.2 0.0 5.9e-113 363.1 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_2458 PP_2458 ribokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_2458 PP_2458 ribokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 363.1 0.0 5.9e-113 5.9e-113 1 296 [. 5 300 .. 5 302 .] 0.99 Alignments for each domain: == domain 1 score: 363.1 bits; conditional E-value: 5.9e-113 TIGR02152 1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkkeg 75 +vvvGS+n+Dlv+r++rlp++Get+ +++f +++GGKGANQAva+arlg +v+mig+vG+D++g++l ++l eg lcl|FitnessBrowser__Putida:PP_2458 5 VVVVGSLNMDLVVRAQRLPRAGETLPGDSFFTVPGGKGANQAVAVARLGGSVAMIGNVGDDDYGRQLHRALYVEG 79 79************************************************************************* PP TIGR02152 76 idteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveealkia 150 id++ v++ +s+GvAli+vd ++N+Iv++ Gan ltp+ v++ + +++++++++QlE+p +tv l lcl|FitnessBrowser__Putida:PP_2458 80 IDCQGVSTCPAMSSGVALITVDAASQNCIVIIPGANGLLTPQSVRRFDALLQAAEVIICQLEVPASTVAWTLARG 154 *************************************************************************** PP TIGR02152 151 kkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitlGskGal 225 ++ g++v+lnPAPa+ l++++++++d+++pNe+Eae+Ltg+ v+d+++a++a e+ll+ g+ +viitlG++Gal lcl|FitnessBrowser__Putida:PP_2458 155 HELGKQVILNPAPATGPLPADWFAHIDYLTPNESEAEALTGVVVTDQDSARRAGERLLQLGAGKVIITLGAQGAL 229 *************************************************************************** PP TIGR02152 226 lvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPtkeev 296 lv+++ +++ pa +v+ +DttaAGDtFig++a+ L +g + +a+ f+++aaalsVtr+Gaq+siP+++e+ lcl|FitnessBrowser__Putida:PP_2458 230 LVTAQGHQHYPAPHVQPLDTTAAGDTFIGGFAAGLVRGLEEGEAIAFGQRAAALSVTRAGAQPSIPYLAEL 300 ********************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (302 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: 00:00:00.00 # Mc/sec: 9.61 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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