Align ribokinase (EC 2.7.1.15) (characterized)
to candidate 352330 BT2803 ribokinase (NCBI ptt file)
Query= reanno::Btheta:352330 (321 letters) >FitnessBrowser__Btheta:352330 Length = 321 Score = 619 bits (1596), Expect = 0.0 Identities = 321/321 (100%), Positives = 321/321 (100%) Query: 1 MIIAFICIVLIFNTMETISIHRPKIVVIGSCNTDMVVKANRLPVPGETILGGTFYMNPGG 60 MIIAFICIVLIFNTMETISIHRPKIVVIGSCNTDMVVKANRLPVPGETILGGTFYMNPGG Sbjct: 1 MIIAFICIVLIFNTMETISIHRPKIVVIGSCNTDMVVKANRLPVPGETILGGTFYMNPGG 60 Query: 61 KGANQAIAAARLGAEVTFISKIGYDLFGLQALEIYRSEKINTEYIFTDQKSPSGVALISV 120 KGANQAIAAARLGAEVTFISKIGYDLFGLQALEIYRSEKINTEYIFTDQKSPSGVALISV Sbjct: 61 KGANQAIAAARLGAEVTFISKIGYDLFGLQALEIYRSEKINTEYIFTDQKSPSGVALISV 120 Query: 121 DSFGENSIIVAPGASRSLSIEDINKAEEKIKEADIILMQLEIPIDTVEYAATIACKYGKK 180 DSFGENSIIVAPGASRSLSIEDINKAEEKIKEADIILMQLEIPIDTVEYAATIACKYGKK Sbjct: 121 DSFGENSIIVAPGASRSLSIEDINKAEEKIKEADIILMQLEIPIDTVEYAATIACKYGKK 180 Query: 181 VILNPAPASSLSNSFLMNVHTILPNRIEAEMLSGIKVMNIESAHRAAQAIGEKGIENVVI 240 VILNPAPASSLSNSFLMNVHTILPNRIEAEMLSGIKVMNIESAHRAAQAIGEKGIENVVI Sbjct: 181 VILNPAPASSLSNSFLMNVHTILPNRIEAEMLSGIKVMNIESAHRAAQAIGEKGIENVVI 240 Query: 241 TLGKDGAYVKEKDEYTMIPAKEVETIDTTGAGDVFCGAFSVCLSEGHSLAKSVKFANAAA 300 TLGKDGAYVKEKDEYTMIPAKEVETIDTTGAGDVFCGAFSVCLSEGHSLAKSVKFANAAA Sbjct: 241 TLGKDGAYVKEKDEYTMIPAKEVETIDTTGAGDVFCGAFSVCLSEGHSLAKSVKFANAAA 300 Query: 301 AIAVTRIGAQSAIPYKREVVL 321 AIAVTRIGAQSAIPYKREVVL Sbjct: 301 AIAVTRIGAQSAIPYKREVVL 321 Lambda K H 0.318 0.134 0.370 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: 474 Number of extensions: 6 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: 321 Length of database: 321 Length adjustment: 28 Effective length of query: 293 Effective length of database: 293 Effective search space: 85849 Effective search space used: 85849 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate 352330 BT2803 (ribokinase (NCBI ptt file))
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.18753.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-123 396.8 4.5 3.5e-123 396.7 4.5 1.0 1 lcl|FitnessBrowser__Btheta:352330 BT2803 ribokinase (NCBI ptt file Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:352330 BT2803 ribokinase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 396.7 4.5 3.5e-123 3.5e-123 1 296 [. 25 319 .. 25 321 .] 0.99 Alignments for each domain: == domain 1 score: 396.7 bits; conditional E-value: 3.5e-123 TIGR02152 1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkkegi 76 ivv+GS+n+D+v++++rlp+pGet+ + +f++++GGKGANQA+aaarlgaev++i+k+G D fg ++le +++e+i lcl|FitnessBrowser__Btheta:352330 25 IVVIGSCNTDMVVKANRLPVPGETILGGTFYMNPGGKGANQAIAAARLGAEVTFISKIGYDLFGLQALEIYRSEKI 100 89************************************************************************** PP TIGR02152 77 dteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveealkiakk 152 +tey+ +++k+++GvAli vd+ geNsI+v+ Ga+++l+ ed+++aeekike+d++l+QlEip++tve+a++ia k lcl|FitnessBrowser__Btheta:352330 101 NTEYIFTDQKSPSGVALISVDSFGENSIIVAPGASRSLSIEDINKAEEKIKEADIILMQLEIPIDTVEYAATIACK 176 **************************************************************************** PP TIGR02152 153 agvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitlGskGallvs 228 g+kv+lnPAPa+ +l++++l +v++i+pN+ Eae+L+gi+v+++e+a++aa+++ ekg+++v+itlG++Ga++++ lcl|FitnessBrowser__Btheta:352330 177 YGKKVILNPAPAS-SLSNSFLMNVHTILPNRIEAEMLSGIKVMNIESAHRAAQAIGEKGIENVVITLGKDGAYVKE 251 ************5.599*********************************************************** PP TIGR02152 229 kdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPtkeev 296 kde ++ipa +v+++Dtt+AGD+F+ga++v+L+eg+sl+++v+fanaaaa++Vtr+Gaqs+iP+k+ev lcl|FitnessBrowser__Btheta:352330 252 KDEYTMIPAKEVETIDTTGAGDVFCGAFSVCLSEGHSLAKSVKFANAAAAIAVTRIGAQSAIPYKREV 319 *******************************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (321 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.16 // [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