Align ribokinase (characterized)
to candidate 5208184 Shew_0696 ribokinase (RefSeq)
Query= CharProtDB::CH_024905 (309 letters) >FitnessBrowser__PV4:5208184 Length = 304 Score = 271 bits (693), Expect = 1e-77 Identities = 145/298 (48%), Positives = 200/298 (67%), Gaps = 3/298 (1%) Query: 7 LVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGAN---IAFIAC 63 L++LGS NADH++NL+ P+ G+T+ Y++ GGKGANQAVAA R + + FI Sbjct: 4 LLILGSANADHVMNLEHLPSAGQTLMSRGYRLEHGGKGANQAVAAARLSKDETRVDFICH 63 Query: 64 TGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPA 123 G D+IG+++ Q D I ++ + TG A+IFV +GEN+IG+ AGANA L+P Sbjct: 64 LGRDAIGQAMAQAWQQDGIMPYGITYTDDQPTGTAMIFVADKGENIIGVSAGANATLTPE 123 Query: 124 LVEAQRERIANASALLMQLESPLESVMAAAKIAHQNKTIVALNPAPARELPDELLALVDI 183 +EA E I A LL+QLE+P +V+ A K A ++ LNPAPA + +L LVD+ Sbjct: 124 ALEAHLELIEKADYLLVQLETPAVTVLDALKHAKKHGVTTILNPAPAMVIGKDLFRLVDV 183 Query: 184 ITPNETEAEKLTGIRVENDEDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGF 243 ITPNETEAE +TGI V +++ A AAQ+LH+ G +TV+ITLG +G S +PG Sbjct: 184 ITPNETEAEAITGIEVTDEQSARMAAQMLHQFGPQTVIITLGKQGALLSTKDYCALIPGV 243 Query: 244 RVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEI 301 +V+AVDT+AAGDTFNGAL+ AL E K + EA+ FAH AAAI+VTR GAQ ++P+R E+ Sbjct: 244 QVKAVDTVAAGDTFNGALMVALGEGKSVEEAVAFAHRAAAISVTRAGAQRAIPYRHEL 301 Lambda K H 0.314 0.131 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: 270 Number of extensions: 10 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: 309 Length of database: 304 Length adjustment: 27 Effective length of query: 282 Effective length of database: 277 Effective search space: 78114 Effective search space used: 78114 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: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate 5208184 Shew_0696 (ribokinase (RefSeq))
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.26654.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-114 367.7 3.3 2.6e-114 367.5 3.3 1.0 1 lcl|FitnessBrowser__PV4:5208184 Shew_0696 ribokinase (RefSeq) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5208184 Shew_0696 ribokinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 367.5 3.3 2.6e-114 2.6e-114 2 297 .. 5 302 .. 4 303 .. 0.99 Alignments for each domain: == domain 1 score: 367.5 bits; conditional E-value: 2.6e-114 TIGR02152 2 vvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlg...aevsmigkvGkDefgeellenlkkegi 76 +++GS+n+D+v++ ++lp++G+t+ ++ +++ +GGKGANQAvaaarl+ ++v++i+++G+D++g+++ ++++++gi lcl|FitnessBrowser__PV4:5208184 5 LILGSANADHVMNLEHLPSAGQTLMSRGYRLEHGGKGANQAVAAARLSkdeTRVDFICHLGRDAIGQAMAQAWQQDGI 82 79**********************************************88889************************* PP TIGR02152 77 dteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveealkiakkag 154 ++ +++++tG+A+i+v+++geN I v aGan++ltpe ++a+ e i+++d++l+QlE+p tv alk akk+g lcl|FitnessBrowser__PV4:5208184 83 MPYGITYTDDQPTGTAMIFVADKGENIIGVSAGANATLTPEALEAHLELIEKADYLLVQLETPAVTVLDALKHAKKHG 160 ****************************************************************************** PP TIGR02152 155 vkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitlGskGallvskdek 232 v+++lnPAPa + ++l++lvd+i+pNetEae++tgiev+d+++a+ aa+ l++ g ++viitlG++Gall++kd + lcl|FitnessBrowser__PV4:5208184 161 VTTILNPAPAMV-IGKDLFRLVDVITPNETEAEAITGIEVTDEQSARMAAQMLHQFGPQTVIITLGKQGALLSTKDYC 237 **********55.889************************************************************** PP TIGR02152 233 klipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPtkeeve 297 +lip ++vkavDt+aAGDtF+gal vaL egks+e+av fa++aaa+sVtr+Gaq++iP+++e++ lcl|FitnessBrowser__PV4:5208184 238 ALIPGVQVKAVDTVAAGDTFNGALMVALGEGKSVEEAVAFAHRAAAISVTRAGAQRAIPYRHELA 302 **************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (304 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: 10.43 // [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