Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate PfGW456L13_3908 Ribokinase (EC 2.7.1.15)
Query= reanno::pseudo1_N1B4:Pf1N1B4_6031 (305 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 Length = 305 Score = 525 bits (1351), Expect = e-154 Identities = 271/305 (88%), Positives = 287/305 (94%) Query: 1 MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG 60 M AKVVVIGSLNMDLVTRAPRLP+GGETLIG+SF TVSGGKGANQAVAAARLGAQVSM+G Sbjct: 1 MSAKVVVIGSLNMDLVTRAPRLPKGGETLIGQSFTTVSGGKGANQAVAAARLGAQVSMIG 60 Query: 61 CVGNDAYGEALRGALLAEQIDCQAVSTVEDSSGVALIVVDDNSQNAIVIVAGANGALTPE 120 CVGNDAYGEALRGALLAEQIDC+AVSTV+ SSGVALIVVDD+SQN+IVIV GANGALT E Sbjct: 61 CVGNDAYGEALRGALLAEQIDCRAVSTVDGSSGVALIVVDDSSQNSIVIVPGANGALTAE 120 Query: 121 VIDRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAID 180 IDRFD+V++AADV+ICQLEVPDA+VGHALKRGRELGKTVILNPAPASRPLP DWYA+ID Sbjct: 121 TIDRFDSVIRAADVLICQLEVPDASVGHALKRGRELGKTVILNPAPASRPLPSDWYASID 180 Query: 181 YLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPA 240 YLIPNESEAS LSGL VDSL TA+ AATRLIA+GAGKVIITLG+QGSLFADGQRFEHFPA Sbjct: 181 YLIPNESEASALSGLSVDSLDTAQAAATRLIALGAGKVIITLGAQGSLFADGQRFEHFPA 240 Query: 241 AKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQ 300 VKAVDTTAAGDTFVGGFAAALAAG EA AIRFGQVAAALSVTRAGAQPSIP LSDVQ Sbjct: 241 PVVKAVDTTAAGDTFVGGFAAALAAGNDEAQAIRFGQVAAALSVTRAGAQPSIPALSDVQ 300 Query: 301 AFKAP 305 AFK P Sbjct: 301 AFKTP 305 Lambda K H 0.316 0.132 0.369 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: 401 Number of extensions: 7 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 PfGW456L13_3908 (Ribokinase (EC 2.7.1.15))
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.6398.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-115 370.2 2.4 4.4e-115 370.0 2.4 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 Ribokinase (EC 2.7.1.15) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 Ribokinase (EC 2.7.1.15) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.0 2.4 4.4e-115 4.4e-115 1 297 [. 5 300 .. 5 301 .. 0.99 Alignments for each domain: == domain 1 score: 370.0 bits; conditional E-value: 4.4e-115 TIGR02152 1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmi 55 +vv+GS+n+Dlv+r++rlpk Get+ +++f++++GGKGANQAvaaarlga+vsmi lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 5 VVVIGSLNMDLVTRAPRLPKGGETLIGQSFTTVSGGKGANQAVAAARLGAQVSMI 59 79***************************************************** PP TIGR02152 56 gkvGkDefgeellenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGa 110 g+vG+D++ge+l+ +l +e+id+ v++v + s+GvAli+vd++++NsIv+v Ga lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 60 GCVGNDAYGEALRGALLAEQIDCRAVSTV-DGSSGVALIVVDDSSQNSIVIVPGA 113 ***************************99.5677********************* PP TIGR02152 111 neeltpedvkaaeekikesdlvllQlEipletveealkiakkagvkvllnPAPae 165 n lt+e++++ + i+++d++++QlE+p ++v +alk ++ g++v+lnPAPa+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 114 NGALTAETIDRFDSVIRAADVLICQLEVPDASVGHALKRGRELGKTVILNPAPAS 168 ******************************************************* PP TIGR02152 166 kkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitlG 220 + l++++++ +d+++pNe+Ea++L+g +v++l++a++aa++l + g+ +viitlG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 169 RPLPSDWYASIDYLIPNESEASALSGLSVDSLDTAQAAATRLIALGAGKVIITLG 223 ******************************************************* PP TIGR02152 221 skGallvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfana 275 ++G+l+++ ++ +++pa vkavDttaAGDtF+g++a+aLa+g++ ++a+rf++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 224 AQGSLFADGQRFEHFPAPVVKAVDTTAAGDTFVGGFAAALAAGNDEAQAIRFGQV 278 ******************************************************* PP TIGR02152 276 aaalsVtrkGaqssiPtkeeve 297 aaalsVtr+Gaq+siP++++v+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 279 AAALSVTRAGAQPSIPALSDVQ 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.83 // [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