Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate BWI76_RS00290 BWI76_RS00290 ribokinase
Query= reanno::Koxy:BWI76_RS00290 (309 letters) >FitnessBrowser__Koxy:BWI76_RS00290 Length = 309 Score = 598 bits (1541), Expect = e-176 Identities = 309/309 (100%), Positives = 309/309 (100%) Query: 1 MKTAGKLVVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISF 60 MKTAGKLVVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISF Sbjct: 1 MKTAGKLVVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISF 60 Query: 61 IACTGDDDIGERVRRQLESDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAAL 120 IACTGDDDIGERVRRQLESDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAAL Sbjct: 61 IACTGDDDIGERVRRQLESDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAAL 120 Query: 121 CVAQVDAEKERIASAQALLMQLESPLESVLAAAKIAHQNQTSVILNPAPARELPDELLTL 180 CVAQVDAEKERIASAQALLMQLESPLESVLAAAKIAHQNQTSVILNPAPARELPDELLTL Sbjct: 121 CVAQVDAEKERIASAQALLMQLESPLESVLAAAKIAHQNQTSVILNPAPARELPDELLTL 180 Query: 181 VDIITPNETEAEKLTGVRVENDEDAAKAAKVLHDKGIGTVIITLGSRGVWASSEGNGRRV 240 VDIITPNETEAEKLTGVRVENDEDAAKAAKVLHDKGIGTVIITLGSRGVWASSEGNGRRV Sbjct: 181 VDIITPNETEAEKLTGVRVENDEDAAKAAKVLHDKGIGTVIITLGSRGVWASSEGNGRRV 240 Query: 241 PGFKVQAVDTIAAGDTFNGALVTALLEGRELAEAIRFAHAAAAIAVTRKGAQPSVPWRKE 300 PGFKVQAVDTIAAGDTFNGALVTALLEGRELAEAIRFAHAAAAIAVTRKGAQPSVPWRKE Sbjct: 241 PGFKVQAVDTIAAGDTFNGALVTALLEGRELAEAIRFAHAAAAIAVTRKGAQPSVPWRKE 300 Query: 301 IDEFLRQQG 309 IDEFLRQQG Sbjct: 301 IDEFLRQQG 309 Lambda K H 0.315 0.131 0.366 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: 485 Number of extensions: 13 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: 309 Length of database: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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 (21.5 bits) S2: 48 (23.1 bits)
Align candidate BWI76_RS00290 BWI76_RS00290 (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.5417.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-115 370.1 5.7 4.7e-115 370.0 5.7 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS00290 BWI76_RS00290 ribokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS00290 BWI76_RS00290 ribokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.0 5.7 4.7e-115 4.7e-115 2 297 .. 8 302 .. 7 303 .. 0.99 Alignments for each domain: == domain 1 score: 370.0 bits; conditional E-value: 4.7e-115 TIGR02152 2 vvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlk 72 vv+GSin+D++l+ +++p pGetv+++++++a GGKGANQAvaa r ga++s+i++ G+D++ge+++++l+ lcl|FitnessBrowser__Koxy:BWI76_RS00290 8 VVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISFIACTGDDDIGERVRRQLE 78 8********************************************************************** PP TIGR02152 73 kegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletv 143 +++id+ v+ v+ +stGvAli+v+ egeN+I + aGan+ l ++v+a++e+i++++ +l+QlE+ple+v lcl|FitnessBrowser__Koxy:BWI76_RS00290 79 SDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAALCVAQVDAEKERIASAQALLMQLESPLESV 149 *********************************************************************** PP TIGR02152 144 eealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvka 214 +a+kia+++++ v+lnPAPa++ l++ell+lvdii+pNetEae Ltg++ve+ eda kaa+ l++kg+ + lcl|FitnessBrowser__Koxy:BWI76_RS00290 150 LAAAKIAHQNQTSVILNPAPARE-LPDELLTLVDIITPNETEAEKLTGVRVENDEDAAKAAKVLHDKGIGT 219 *********************65.99********************************************* PP TIGR02152 215 viitlGskGallvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkG 285 viitlGs+G+ +s+++ + +p +kv+avDt aAGDtF+gal++aL eg++l++a+rfa+aaaa++VtrkG lcl|FitnessBrowser__Koxy:BWI76_RS00290 220 VIITLGSRGVWASSEGNGRRVPGFKVQAVDTIAAGDTFNGALVTALLEGRELAEAIRFAHAAAAIAVTRKG 290 *********************************************************************** PP TIGR02152 286 aqssiPtkeeve 297 aq+s+P ++e++ lcl|FitnessBrowser__Koxy:BWI76_RS00290 291 AQPSVPWRKEID 302 **********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (309 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.72 // [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