Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate H281DRAFT_01116 H281DRAFT_01116 ribokinase
Query= reanno::Burk376:H281DRAFT_01116 (320 letters) >FitnessBrowser__Burk376:H281DRAFT_01116 Length = 320 Score = 618 bits (1593), Expect = 0.0 Identities = 320/320 (100%), Positives = 320/320 (100%) Query: 1 MSSQPQQSGRVVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGA 60 MSSQPQQSGRVVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGA Sbjct: 1 MSSQPQQSGRVVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGA 60 Query: 61 EVVFCTRIGNDAFGSIAQATWAREGITARASVVEGVSTGAAHIFVDDTTGMNAIIVAAGA 120 EVVFCTRIGNDAFGSIAQATWAREGITARASVVEGVSTGAAHIFVDDTTGMNAIIVAAGA Sbjct: 61 EVVFCTRIGNDAFGSIAQATWAREGITARASVVEGVSTGAAHIFVDDTTGMNAIIVAAGA 120 Query: 121 AGTLSAADVDAIEADIAGSRVFVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALPLDDD 180 AGTLSAADVDAIEADIAGSRVFVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALPLDDD Sbjct: 121 AGTLSAADVDAIEADIAGSRVFVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALPLDDD 180 Query: 181 IFPLCDYITPNETEAAALTGVPIANVDDARRAADVLLAKGVGTVIVTLGEGGALLHDATQ 240 IFPLCDYITPNETEAAALTGVPIANVDDARRAADVLLAKGVGTVIVTLGEGGALLHDATQ Sbjct: 181 IFPLCDYITPNETEAAALTGVPIANVDDARRAADVLLAKGVGTVIVTLGEGGALLHDATQ 240 Query: 241 SIWLPAFRCGAVVETAGAGDGFTGGFAAALARGEDAISAMRFGCALAGISVTRAGTAPSM 300 SIWLPAFRCGAVVETAGAGDGFTGGFAAALARGEDAISAMRFGCALAGISVTRAGTAPSM Sbjct: 241 SIWLPAFRCGAVVETAGAGDGFTGGFAAALARGEDAISAMRFGCALAGISVTRAGTAPSM 300 Query: 301 PTLAEVNRVLSESAQPAQAS 320 PTLAEVNRVLSESAQPAQAS Sbjct: 301 PTLAEVNRVLSESAQPAQAS 320 Lambda K H 0.318 0.132 0.377 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: 436 Number of extensions: 8 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: 320 Length of database: 320 Length adjustment: 28 Effective length of query: 292 Effective length of database: 292 Effective search space: 85264 Effective search space used: 85264 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 H281DRAFT_01116 H281DRAFT_01116 (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.8415.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-95 304.8 4.3 3.6e-95 304.7 4.3 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_01116 H281DRAFT_01116 ribokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_01116 H281DRAFT_01116 ribokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 304.7 4.3 3.6e-95 3.6e-95 1 297 [. 11 307 .. 11 308 .. 0.97 Alignments for each domain: == domain 1 score: 304.7 bits; conditional E-value: 3.6e-95 TIGR02152 1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgee 66 +v++G + +Dl++r+ r+p Get++++ f +++GGKG+NQAvaaar gaev + +++G+D+fg+ lcl|FitnessBrowser__Burk376:H281DRAFT_01116 11 VVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGAEVVFCTRIGNDAFGSI 76 799*************************************************************** PP TIGR02152 67 llenlkkegidteyvkkvkktstGvAlilvde.egeNsIvvvaGaneeltpedvkaaeekikesdl 131 + ++++egi t + v+ +stG A+i+vd+ +g N+I+v+aGa +l+++dv+a e++i+ s++ lcl|FitnessBrowser__Burk376:H281DRAFT_01116 77 AQATWAREGI-TARASVVEGVSTGAAHIFVDDtTGMNAIIVAAGAAGTLSAADVDAIEADIAGSRV 141 **********.7778899************983589****************************** PP TIGR02152 132 vllQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedl 197 + QlE pl+++++ l++a+k+gv++++nPAPa + ld++++ l+d+i+pNetEa++Ltg+ ++++ lcl|FitnessBrowser__Burk376:H281DRAFT_01116 142 FVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALP-LDDDIFPLCDYITPNETEAAALTGVPIANV 206 *********************************76.99**************************** PP TIGR02152 198 edaekaaekllekgvkaviitlGskGallvskdekklipalkvka.vDttaAGDtFigalavaLae 262 +da++aa+ ll+kgv +vi+tlG+ Gall++++++ +pa++ a v t++AGD F+g++a+aLa+ lcl|FitnessBrowser__Burk376:H281DRAFT_01116 207 DDARRAADVLLAKGVGTVIVTLGEGGALLHDATQSIWLPAFRCGAvVETAGAGDGFTGGFAAALAR 272 ******************************************97626999**************** PP TIGR02152 263 gksledavrfanaaaalsVtrkGaqssiPtkeeve 297 g+++ +a+rf+ a+a +sVtr+G+++s+Pt++ev+ lcl|FitnessBrowser__Burk376:H281DRAFT_01116 273 GEDAISAMRFGCALAGISVTRAGTAPSMPTLAEVN 307 *********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (320 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: 9.25 // [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