Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate H281DRAFT_05229 H281DRAFT_05229 ribokinase
Query= reanno::pseudo3_N2E3:AO353_20835 (305 letters) >FitnessBrowser__Burk376:H281DRAFT_05229 Length = 307 Score = 368 bits (945), Expect = e-107 Identities = 200/299 (66%), Positives = 232/299 (77%), Gaps = 1/299 (0%) Query: 3 AKVVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIGCV 62 A+V VVGSLNMDLV RA RLPH GETL G +FA V+GGKG NQAVA+ARLGAQVSM+GCV Sbjct: 8 ARVAVVGSLNMDLVARAPRLPHPGETLAGRTFAQVAGGKGGNQAVAAARLGAQVSMLGCV 67 Query: 63 GDDAYGEQLRAALLAEQIDCQALTSVEGSSGVALIVVDDNSQNAIVIVAGANGQLTPGMV 122 G DA G QLRA L AE IDC A+ + ++GVALIVVDD SQNAIVIVAG+NG++TP + Sbjct: 68 GADANGAQLRAGLEAEGIDCAAVETGREATGVALIVVDDASQNAIVIVAGSNGEVTPETI 127 Query: 123 AGFDAVLAAADVIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSIDYL 182 A +AVLAAADV+ICQLE P+ TV L R LGKTVILNPAPAT PLPA+W IDYL Sbjct: 128 ARHEAVLAAADVVICQLETPLDTVQAALATARRLGKTVILNPAPATGPLPAEWLPLIDYL 187 Query: 183 IPNESEASALSGLPVDSLESAELAASRLIAAGAGKVIITLGPQGSLFA-NGQSCEHFPAP 241 IPNE EA+ L+GLPV S E A AA+ L AAGA V++TLGP+G A G + + AP Sbjct: 188 IPNELEAATLTGLPVGSPEEAATAAAVLRAAGARNVLVTLGPRGVQAALEGAAPALYDAP 247 Query: 242 KVKSVDTTAAGDTFVGGFAAALAAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDVQ 300 KVK++DTTAAGDTF+GGFAA LA G S AIRF Q AAALSVTRAGAQPSIP+ ++V+ Sbjct: 248 KVKAIDTTAAGDTFIGGFAAQLAQGASVDAAIRFAQRAAALSVTRAGAQPSIPTWTEVE 306 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: 323 Number of extensions: 11 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: 307 Length adjustment: 27 Effective length of query: 278 Effective length of database: 280 Effective search space: 77840 Effective search space used: 77840 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 H281DRAFT_05229 H281DRAFT_05229 (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.23594.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-112 359.8 5.4 6.5e-112 359.7 5.4 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_05229 H281DRAFT_05229 ribokinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_05229 H281DRAFT_05229 ribokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 359.7 5.4 6.5e-112 6.5e-112 1 297 [. 10 306 .. 10 307 .] 0.98 Alignments for each domain: == domain 1 score: 359.7 bits; conditional E-value: 6.5e-112 TIGR02152 1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgee 66 ++vvGS+n+Dlv+r++rlp+pGet+++++f ++aGGKG NQAvaaarlga+vsm+g+vG D+ g++ lcl|FitnessBrowser__Burk376:H281DRAFT_05229 10 VAVVGSLNMDLVARAPRLPHPGETLAGRTFAQVAGGKGGNQAVAAARLGAQVSMLGCVGADANGAQ 75 78**************************************************************** PP TIGR02152 67 llenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlv 132 l+ l++egid+ v++ +++tGvAli+vd+ ++N+Iv+vaG+n e+tpe+++++e+ ++++d+v lcl|FitnessBrowser__Burk376:H281DRAFT_05229 76 LRAGLEAEGIDCAAVETG-REATGVALIVVDDASQNAIVIVAGSNGEVTPETIARHEAVLAAADVV 140 ***************965.7889******************************************* PP TIGR02152 133 llQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedle 198 ++QlE+pl+tv++al +a++ g++v+lnPAPa+ l++e+l l+d+++pNe Ea++Ltg v + e lcl|FitnessBrowser__Burk376:H281DRAFT_05229 141 ICQLETPLDTVQAALATARRLGKTVILNPAPATGPLPAEWLPLIDYLIPNELEAATLTGLPVGSPE 206 ****************************************************************** PP TIGR02152 199 daekaaekllekgvkaviitlGskGallvskd.ekklipalkvkavDttaAGDtFigalavaLaeg 263 +a +aa+ l++ g+++v++tlG +G+ + ++ +l +a kvka+DttaAGDtFig++a++La+g lcl|FitnessBrowser__Burk376:H281DRAFT_05229 207 EAATAAAVLRAAGARNVLVTLGPRGVQAALEGaAPALYDAPKVKAIDTTAAGDTFIGGFAAQLAQG 272 **************************9988876899****************************** PP TIGR02152 264 ksledavrfanaaaalsVtrkGaqssiPtkeeve 297 s+++a+rfa++aaalsVtr+Gaq+siPt +eve lcl|FitnessBrowser__Burk376:H281DRAFT_05229 273 ASVDAAIRFAQRAAALSVTRAGAQPSIPTWTEVE 306 ********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (307 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: 00:00:00.00 # Mc/sec: 11.19 // [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