Align agmatinase; EC 3.5.3.11 (characterized)
to candidate 17016 b2937 agmatinase (NCBI)
Query= CharProtDB::CH_024895 (306 letters) >FitnessBrowser__Keio:17016 Length = 306 Score = 626 bits (1614), Expect = 0.0 Identities = 306/306 (100%), Positives = 306/306 (100%) Query: 1 MSTLGHQYDNSLVSNAFGFLRLPMNFQPYDSDADWVITGVPFDMATSGRAGGRHGPAAIR 60 MSTLGHQYDNSLVSNAFGFLRLPMNFQPYDSDADWVITGVPFDMATSGRAGGRHGPAAIR Sbjct: 1 MSTLGHQYDNSLVSNAFGFLRLPMNFQPYDSDADWVITGVPFDMATSGRAGGRHGPAAIR 60 Query: 61 QVSTNLAWEHNRFPWNFDMRERLNVVDCGDLVYAFGDAREMSEKLQAHAEKLLAAGKRML 120 QVSTNLAWEHNRFPWNFDMRERLNVVDCGDLVYAFGDAREMSEKLQAHAEKLLAAGKRML Sbjct: 61 QVSTNLAWEHNRFPWNFDMRERLNVVDCGDLVYAFGDAREMSEKLQAHAEKLLAAGKRML 120 Query: 121 SFGGDHFVTLPLLRAHAKHFGKMALVHFDAHTDTYANGCEFDHGTMFYTAPKEGLIDPNH 180 SFGGDHFVTLPLLRAHAKHFGKMALVHFDAHTDTYANGCEFDHGTMFYTAPKEGLIDPNH Sbjct: 121 SFGGDHFVTLPLLRAHAKHFGKMALVHFDAHTDTYANGCEFDHGTMFYTAPKEGLIDPNH 180 Query: 181 SVQIGIRTEFDKDNGFTVLDACQVNDRSVDDVIAQVKQIVGDMPVYLTFDIDCLDPAFAP 240 SVQIGIRTEFDKDNGFTVLDACQVNDRSVDDVIAQVKQIVGDMPVYLTFDIDCLDPAFAP Sbjct: 181 SVQIGIRTEFDKDNGFTVLDACQVNDRSVDDVIAQVKQIVGDMPVYLTFDIDCLDPAFAP 240 Query: 241 GTGTPVIGGLTSDRAIKLVRGLKDLNIVGMDVVEVAPAYDQSEITALAAATLALEMLYIQ 300 GTGTPVIGGLTSDRAIKLVRGLKDLNIVGMDVVEVAPAYDQSEITALAAATLALEMLYIQ Sbjct: 241 GTGTPVIGGLTSDRAIKLVRGLKDLNIVGMDVVEVAPAYDQSEITALAAATLALEMLYIQ 300 Query: 301 AAKKGE 306 AAKKGE Sbjct: 301 AAKKGE 306 Lambda K H 0.322 0.138 0.419 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: 527 Number of extensions: 11 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: 306 Length of database: 306 Length adjustment: 27 Effective length of query: 279 Effective length of database: 279 Effective search space: 77841 Effective search space used: 77841 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
Align candidate 17016 b2937 (agmatinase (NCBI))
to HMM TIGR01230 (speB: agmatinase (EC 3.5.3.11))
# 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/TIGR01230.hmm # target sequence database: /tmp/gapView.26572.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01230 [M=275] Accession: TIGR01230 Description: agmatinase: agmatinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-123 395.5 0.0 8.6e-123 395.3 0.0 1.0 1 lcl|FitnessBrowser__Keio:17016 b2937 agmatinase (NCBI) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17016 b2937 agmatinase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 395.3 0.0 8.6e-123 8.6e-123 2 275 .] 22 299 .. 21 299 .. 0.99 Alignments for each domain: == domain 1 score: 395.3 bits; conditional E-value: 8.6e-123 TIGR01230 2 lfleseaeyeeAevvivgiPydattsyrpGsrhgpeaireastnLeayseeldrdlal...lkvvDagdlplaaGdare 77 l++++++++++A++vi+g+P+d++ts+r+G+rhgp+air++stnL+++++++++++++ l+vvD+gdl++a+Gdare lcl|FitnessBrowser__Keio:17016 22 LPMNFQPYDSDADWVITGVPFDMATSGRAGGRHGPAAIRQVSTNLAWEHNRFPWNFDMrerLNVVDCGDLVYAFGDARE 100 78***************************************************************************** PP TIGR01230 78 mvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlr...defegeklshacvmrrvlelg 153 m+ek+++++e+ll++gk+++++GG+H++tlp++rA++k+f+k+a+v+fDAHtD++ +ef++++++++++++++++++ lcl|FitnessBrowser__Keio:17016 101 MSEKLQAHAEKLLAAGKRMLSFGGDHFVTLPLLRAHAKHFGKMALVHFDAHTDTYangCEFDHGTMFYTAPKEGLIDPN 179 ******************************************************************************* PP TIGR01230 154 lnvlqigiRsgikeeadlarennikvlkreledeiaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGltskellk 232 +++qigiR+++++++++++ ++++v++r+++d+ia+v+++v d+pvy+t+DiD+lDPafaPG+gtp++gGlts++++k lcl|FitnessBrowser__Keio:17016 180 -HSVQIGIRTEFDKDNGFTVLDACQVNDRSVDDVIAQVKQIVGDMPVYLTFDIDCLDPAFAPGTGTPVIGGLTSDRAIK 257 .99**************************************************************************** PP TIGR01230 233 lfvlaekekkvvGlDvvEvaPvydssevtaltaaklalellli 275 +v++ k+ ++vG+DvvEvaP+yd+se+tal+aa+lale+l+i lcl|FitnessBrowser__Keio:17016 258 -LVRGLKDLNIVGMDVVEVAPAYDQSEITALAAATLALEMLYI 299 .9**************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (306 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.60 // [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