Align agmatinase (EC 3.5.3.11) (characterized)
to candidate GFF31 PGA1_c00310 guanidinobutyrase
Query= BRENDA::W5PHZ9 (361 letters) >FitnessBrowser__Phaeo:GFF31 Length = 324 Score = 268 bits (686), Expect = 1e-76 Identities = 138/307 (44%), Positives = 196/307 (63%), Gaps = 6/307 (1%) Query: 53 PPSSEFVARSVGICSMMRLPMQATPEGL----DAALVGVPLDIGTSNRPGARFGPRRIRE 108 P S + R G+ + MRLP + + LVGVP D GT+NRPG R GPR++R+ Sbjct: 11 PVSGMEMPRFAGLPTFMRLPHVTVSDPIIDQVQLGLVGVPWDAGTTNRPGPRHGPRQLRD 70 Query: 109 ESVMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLG 168 S M+R NP TG PF + ADLGDV N ++ D I A Y + + LT+G Sbjct: 71 LSTMIRAGNPVTGINPFSMINCADLGDVAPNPVDIIDCMERISAFYADLKSRDIFALTVG 130 Query: 169 GDHTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLY-HGTPFRRCVDEGLLDCKR 227 GDH ++ P+L+ +A PVGL+ D+H D D G Y HGTPFRR ++EGL+D KR Sbjct: 131 GDHLVSLPVLRGLASG-APVGLIQFDSHTDLFDSYFGGNKYTHGTPFRRAIEEGLVDPKR 189 Query: 228 VVQIGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDID 287 +VQIGIRG++ + + ++QG R++ E+ + + + +M EVR+ +G +P Y ++DID Sbjct: 190 MVQIGIRGTAYNTEDVEWGQAQGVRIIRIEEFFDRGVSDVMREVREIVGDQPTYCTYDID 249 Query: 288 GLDPAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANL 347 +DPA+APGTGTPE+ G QAL+++R G+ +VG DLVEVSPP+D +GNTA + A++ Sbjct: 250 FVDPAFAPGTGTPEVGGPNSFQALQVVRELAGVQLVGADLVEVSPPFDTNGNTAWLGASI 309 Query: 348 LFEMLCV 354 LFEMLCV Sbjct: 310 LFEMLCV 316 Lambda K H 0.321 0.139 0.426 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: 391 Number of extensions: 21 Number of successful extensions: 3 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: 361 Length of database: 324 Length adjustment: 29 Effective length of query: 332 Effective length of database: 295 Effective search space: 97940 Effective search space used: 97940 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate GFF31 PGA1_c00310 (guanidinobutyrase)
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.9423.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-57 181.2 0.0 1.9e-57 180.9 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF31 PGA1_c00310 guanidinobutyrase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF31 PGA1_c00310 guanidinobutyrase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.9 0.0 1.9e-57 1.9e-57 6 274 .. 35 315 .. 31 316 .. 0.90 Alignments for each domain: == domain 1 score: 180.9 bits; conditional E-value: 1.9e-57 TIGR01230 6 seaeyeeAevvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdaremveki 82 s+++ ++ + +vg+P+da t rpG rhgp ++r+ st + a ++ + +++++ +D+gd+ d + +e+i lcl|FitnessBrowser__Phaeo:GFF31 35 SDPIIDQVQLGLVGVPWDAGTTNRPGPRHGPRQLRDLSTMIRAGNPVTGiNPFSMINCADLGDVAPNPVDIIDCMERI 112 5666677777799************************************5559***********999999999***** PP TIGR01230 83 eevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrde.fegeklshacvmrrvlelg....ln 155 + ++l f +++GG+H+++lpv+r ++ ++ ++qfD HtDl d f g+k++h ++ rr++e g ++ lcl|FitnessBrowser__Phaeo:GFF31 113 SAFYADLKSRDIFALTVGGDHLVSLPVLRGLASG-APVGLIQFDSHTDLFDSyFGGNKYTHGTPFRRAIEEGlvdpKR 189 ******999999******************9986.689************87257899************9988889* PP TIGR01230 156 vlqigiRsg..ikeeadlarennikvlk.relede.....iaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGl 225 ++qigiR e+ ++ + +++++++ e+ d+ + ev +v d+p y t DiD +DPafaPG+gtpe+gG lcl|FitnessBrowser__Phaeo:GFF31 190 MVQIGIRGTayNTEDVEWGQAQGVRIIRiEEFFDRgvsdvMREVREIVGDQPTYCTYDIDFVDPAFAPGTGTPEVGGP 267 *******65225899********99876444444443333999999******************************** PP TIGR01230 226 tskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274 +s ++l+ v++ +++vG+D+vEv+P +d++ ta + a + e+l lcl|FitnessBrowser__Phaeo:GFF31 268 NSFQALQ-VVRELAGVQLVGADLVEVSPPFDTNGNTAWLGASILFEMLC 315 *******.8999***********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (324 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: 00:00:00.01 # Mc/sec: 6.88 // [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