Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate GFF3591 PS417_18385 ribokinase
Query= reanno::pseudo3_N2E3:AO353_20835 (305 letters) >lcl|FitnessBrowser__WCS417:GFF3591 PS417_18385 ribokinase Length = 305 Score = 477 bits (1228), Expect = e-139 Identities = 245/305 (80%), Positives = 274/305 (89%) Query: 1 MPAKVVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIG 60 MPAKVVVVGSLNMDLVTRA RLP AGETL G++F+TV GGKGANQAVASARLGA VSMIG Sbjct: 1 MPAKVVVVGSLNMDLVTRASRLPRAGETLIGQTFSTVPGGKGANQAVASARLGADVSMIG 60 Query: 61 CVGDDAYGEQLRAALLAEQIDCQALTSVEGSSGVALIVVDDNSQNAIVIVAGANGQLTPG 120 CVG DAYG QLR ALL E IDCQA+++V+GSSGVALIVVDD+SQNAIVIVAG+NG+LTP Sbjct: 61 CVGSDAYGSQLREALLVEGIDCQAVSTVDGSSGVALIVVDDSSQNAIVIVAGSNGELTPA 120 Query: 121 MVAGFDAVLAAADVIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSID 180 + FDAVL AADVI+CQLEVPM+TVGY LKRGRELGKTVILNPAPA+ PLPA+WY+SID Sbjct: 121 SLQAFDAVLQAADVIVCQLEVPMNTVGYALKRGRELGKTVILNPAPASGPLPAEWYASID 180 Query: 181 YLIPNESEASALSGLPVDSLESAELAASRLIAAGAGKVIITLGPQGSLFANGQSCEHFPA 240 YLIPNESEASALSG+ VDS+++A++AA++LI AGAGKVI+TLG QG+LF +GQ EH A Sbjct: 181 YLIPNESEASALSGVTVDSIDAAKVAATQLIQAGAGKVIVTLGAQGALFTDGQRFEHLQA 240 Query: 241 PKVKSVDTTAAGDTFVGGFAAALAAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDVQ 300 PKVK+VDTTAAGDTFVGGFAAALA GKSE EAIRFGQVAAALSVTRAGAQPSIP+L DVQ Sbjct: 241 PKVKAVDTTAAGDTFVGGFAAALANGKSEAEAIRFGQVAAALSVTRAGAQPSIPTLHDVQ 300 Query: 301 AFKAS 305 F S Sbjct: 301 GFVPS 305 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: 396 Number of extensions: 6 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: 305 Length adjustment: 27 Effective length of query: 278 Effective length of database: 278 Effective search space: 77284 Effective search space used: 77284 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 GFF3591 PS417_18385 (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.5606.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-116 373.3 6.4 5.2e-116 373.1 6.4 1.0 1 lcl|FitnessBrowser__WCS417:GFF3591 PS417_18385 ribokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF3591 PS417_18385 ribokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 373.1 6.4 5.2e-116 5.2e-116 1 297 [. 5 300 .. 5 301 .. 0.99 Alignments for each domain: == domain 1 score: 373.1 bits; conditional E-value: 5.2e-116 TIGR02152 1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkkeg 75 +vvvGS+n+Dlv+r++rlp++Get+ +++f++++GGKGANQAva arlga+vsmig+vG+D++g++l+e+l eg lcl|FitnessBrowser__WCS417:GFF3591 5 VVVVGSLNMDLVTRASRLPRAGETLIGQTFSTVPGGKGANQAVASARLGADVSMIGCVGSDAYGSQLREALLVEG 79 79************************************************************************* PP TIGR02152 76 idteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveealkia 150 id++ v++v + s+GvAli+vd++++N+Iv+vaG+n eltp+ ++a + ++++d++++QlE+p++tv +alk lcl|FitnessBrowser__WCS417:GFF3591 80 IDCQAVSTV-DGSSGVALIVVDDSSQNAIVIVAGSNGELTPASLQAFDAVLQAADVIVCQLEVPMNTVGYALKRG 153 *******99.5677************************************************************* PP TIGR02152 151 kkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitlGskGal 225 ++ g++v+lnPAPa+ l++e+++ +d+++pNe+Ea++L+g++v+++++a+ aa++l + g+ +vi+tlG++Gal lcl|FitnessBrowser__WCS417:GFF3591 154 RELGKTVILNPAPASGPLPAEWYASIDYLIPNESEASALSGVTVDSIDAAKVAATQLIQAGAGKVIVTLGAQGAL 228 *************************************************************************** PP TIGR02152 226 lvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPtkeeve 297 +++ ++ ++++a kvkavDttaAGDtF+g++a+aLa+gks ++a+rf++ aaalsVtr+Gaq+siPt+++v+ lcl|FitnessBrowser__WCS417:GFF3591 229 FTDGQRFEHLQAPKVKAVDTTAAGDTFVGGFAAALANGKSEAEAIRFGQVAAALSVTRAGAQPSIPTLHDVQ 300 *********************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (305 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: 7.81 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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