Align agmatinase; EC 3.5.3.11 (characterized)
to candidate 5209143 Shew_1621 agmatinase (RefSeq)
Query= CharProtDB::CH_024895 (306 letters) >FitnessBrowser__PV4:5209143 Length = 307 Score = 407 bits (1047), Expect = e-118 Identities = 190/302 (62%), Positives = 247/302 (81%), Gaps = 1/302 (0%) Query: 1 MSTLGHQYDNSLVSNAFGFLRLPMNFQPYDSDADWVITGVPFDMATSGRAGGRHGPAAIR 60 M+T+ + D SL SNAFG+LR P++F+P +SDAD V+ G+PFDMAT+GR+GGR GP AIR Sbjct: 1 MTTIADKPDYSLYSNAFGYLRQPLDFKPLESDADVVVIGLPFDMATTGRSGGRMGPGAIR 60 Query: 61 QVSTNLAWEHNRFPWNFDMRERLNVVDCGDLVYAFGDAREMSEKLQAHAEKLLAAGKRML 120 Q S NLAWE R+PW+F + + L +VD GDLV+ GDA + +++++ A +L +GK ++ Sbjct: 61 QASVNLAWEECRWPWDFKLSDHLKMVDAGDLVFDCGDAADFTQRVEDFATAVLDSGKALM 120 Query: 121 SFGGDHFVTLPLLRAHAKHFGKMALVHFDAHTDTYANGCEFDHGTMFYTAPKEGLIDPNH 180 SFGGDHFVTLPLLRAH K GKMAL+HFDAHTDTY+ G ++DHGTMF+ AP EG+ID +H Sbjct: 121 SFGGDHFVTLPLLRAHYKKHGKMALLHFDAHTDTYSQGSKYDHGTMFFHAPNEGIIDASH 180 Query: 181 SVQIGIRTEFDKDNG-FTVLDACQVNDRSVDDVIAQVKQIVGDMPVYLTFDIDCLDPAFA 239 SVQ+GIRTE+DK + F V+DA N+ + D+++AQ+K VGDMP+Y+TFDIDCLDPAFA Sbjct: 181 SVQVGIRTEYDKPSHLFKVIDAAAANEMTADEIVAQIKDRVGDMPLYVTFDIDCLDPAFA 240 Query: 240 PGTGTPVIGGLTSDRAIKLVRGLKDLNIVGMDVVEVAPAYDQSEITALAAATLALEMLYI 299 PGTGTPV GGLTSD+A+K++RGL+ +N+VGMDVVEVAPAYD +EITALA ATL LEML++ Sbjct: 241 PGTGTPVCGGLTSDKAMKIIRGLRGMNVVGMDVVEVAPAYDSAEITALAGATLGLEMLHV 300 Query: 300 QA 301 A Sbjct: 301 WA 302 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: 380 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: 306 Length of database: 307 Length adjustment: 27 Effective length of query: 279 Effective length of database: 280 Effective search space: 78120 Effective search space used: 78120 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 5209143 Shew_1621 (agmatinase (RefSeq))
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.28667.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-91 292.5 0.0 2.2e-91 292.3 0.0 1.0 1 lcl|FitnessBrowser__PV4:5209143 Shew_1621 agmatinase (RefSeq) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209143 Shew_1621 agmatinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 292.3 0.0 2.2e-91 2.2e-91 1 274 [. 21 299 .. 21 300 .. 0.96 Alignments for each domain: == domain 1 score: 292.3 bits; conditional E-value: 2.2e-91 TIGR01230 1 klfleseaeyeeAevvivgiPydattsyrpGsrhgpeaireastnLeayseeldrdlal...lkvvDagdlplaaGda 75 +++l +++ ++A+vv++g+P+d++t +r G+r gp air+as+nL++++ + ++d++l lk+vDagdl++ Gda lcl|FitnessBrowser__PV4:5209143 21 RQPLDFKPLESDADVVVIGLPFDMATTGRSGGRMGPGAIRQASVNLAWEECRWPWDFKLsdhLKMVDAGDLVFDCGDA 98 578999***************************************************98889**************** PP TIGR01230 76 remvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlr...defegeklshacvmrrvl 150 + +++e+ ++ +l+ gk ++++GG+H++tlp++rA++kk++k+a+++fDAHtD++ +++++++++ ++ ++++ lcl|FitnessBrowser__PV4:5209143 99 ADFTQRVEDFATAVLDSGKALMSFGGDHFVTLPLLRAHYKKHGKMALLHFDAHTDTYsqgSKYDHGTMFFHAPNEGII 176 *********************************************************99999**************** PP TIGR01230 151 elglnvlqigiRsgikeeadlar.ennikvlkreledeiaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGlts 227 + +++q+giR++ ++ +l + ++ +++ ++ a+ + +v d+p+yvt+DiD+lDPafaPG+gtp+ gGlts lcl|FitnessBrowser__PV4:5209143 177 DAS-HSVQVGIRTEYDKPSHLFKvIDAAAANEMTADEIVAQIKDRVGDMPLYVTFDIDCLDPAFAPGTGTPVCGGLTS 253 **9.99**********9988766167777788999999**************************************** PP TIGR01230 228 kellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274 ++++k ++ +vvG+DvvEvaP+yds+e+tal+ a+l le+l lcl|FitnessBrowser__PV4:5209143 254 DKAMK-IIRGLRGMNVVGMDVVEVAPAYDSAEITALAGATLGLEMLH 299 *****.89999**********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 11.51 // [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