Align agmatinase (EC 3.5.3.11) (characterized)
to candidate WP_086509701.1 BZY95_RS09505 agmatinase
Query= BRENDA::W5PHZ9 (361 letters) >NCBI__GCF_002151265.1:WP_086509701.1 Length = 316 Score = 387 bits (995), Expect = e-112 Identities = 189/308 (61%), Positives = 230/308 (74%) Query: 51 NQPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFGPRRIREES 110 NQP + R G +MMRLP Q T GLD A +GVPLDI TSNRPG R GPR+IR+ES Sbjct: 5 NQPLGGNEMPRFGGPATMMRLPTQPTAAGLDVAFIGVPLDIATSNRPGTRLGPRQIRDES 64 Query: 111 VMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLGGD 170 MLR N +T A PF L+VAD+GDV +N ++L S +I A Y ++++ GCVPLTLGGD Sbjct: 65 RMLRPYNMATRAAPFDSLQVADIGDVPINTFHLPKSVDIITAFYDEVLSHGCVPLTLGGD 124 Query: 171 HTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGLLDCKRVVQ 230 H IT PIL+AIA+KHGPVGL+HVDAH D + GE + HGTPFRR +EGLL +VVQ Sbjct: 125 HVITLPILRAIAKKHGPVGLIHVDAHADVNEHMFGEAIAHGTPFRRAQEEGLLAHGKVVQ 184 Query: 231 IGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLD 290 IG+RG+ + + + R QGFRVV AE+CW +SL PLM EVR+QMG P+Y++FDIDGLD Sbjct: 185 IGLRGTGYAAEDFDWCRQQGFRVVTAEECWYRSLAPLMAEVREQMGDTPVYVTFDIDGLD 244 Query: 291 PAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANLLFE 350 P+ APGTGT E+ GLT +Q LEI+RG GLN+VG DLVEVSPPYDPSGNTAL+ A LL+E Sbjct: 245 PSVAPGTGTVEMGGLTSAQGLEIVRGAAGLNIVGGDLVEVSPPYDPSGNTALMGATLLYE 304 Query: 351 MLCVLPKV 358 MLC LP V Sbjct: 305 MLCALPGV 312 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: 445 Number of extensions: 18 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: 361 Length of database: 316 Length adjustment: 28 Effective length of query: 333 Effective length of database: 288 Effective search space: 95904 Effective search space used: 95904 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 WP_086509701.1 BZY95_RS09505 (agmatinase)
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.28497.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-66 209.0 0.0 6.6e-66 208.7 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086509701.1 BZY95_RS09505 agmatinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086509701.1 BZY95_RS09505 agmatinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 208.7 0.0 6.6e-66 6.6e-66 7 274 .. 28 307 .. 22 308 .. 0.92 Alignments for each domain: == domain 1 score: 208.7 bits; conditional E-value: 6.6e-66 TIGR01230 7 eaeyeeAevvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGd 74 +++++ +v +g+P+d +ts rpG+r gp +ir+ s L y+ ++ l+v+D gd+p+ + lcl|NCBI__GCF_002151265.1:WP_086509701.1 28 QPTAAGLDVAFIGVPLDIATSNRPGTRLGPRQIRDESRMLRPYNMATRaAPFDSLQVADIGDVPINTFH 96 67778889999********************************98877588***************999 PP TIGR01230 75 aremvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklsha 143 ++v+ i++ +e+l +g ++++GG+H+itlp++rA++kk++++ ++++DAH+D+ + ge + h lcl|NCBI__GCF_002151265.1:WP_086509701.1 97 LPKSVDIITAFYDEVLSHGCVPLTLGGDHVITLPILRAIAKKHGPVGLIHVDAHADVNEHMFGEAIAHG 165 9******************************************************************** PP TIGR01230 144 cvmrrvlelg....lnvlqigiRsg..ikeeadlarennikvl.....k.reledeiaevlakvldkpv 200 ++ rr+ e g +v+qig+R e++d+ r+++ +v+ + r+l+ +aev ++ d pv lcl|NCBI__GCF_002151265.1:WP_086509701.1 166 TPFRRAQEEGllahGKVVQIGLRGTgyAAEDFDWCRQQGFRVVtaeecWyRSLAPLMAEVREQMGDTPV 234 ********98666569*******753378***********99722222334566669************ PP TIGR01230 201 yvtiDiDvlDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaakla 269 yvt+DiD+lDP+ aPG+gt+e+gGlts ++l+ v++ ++vG D+vEv+P yd s tal+ a+l lcl|NCBI__GCF_002151265.1:WP_086509701.1 235 YVTFDIDGLDPSVAPGTGTVEMGGLTSAQGLE-IVRGAAGLNIVGGDLVEVSPPYDPSGNTALMGATLL 302 ********************************.999********************************* PP TIGR01230 270 lelll 274 +e+l lcl|NCBI__GCF_002151265.1:WP_086509701.1 303 YEMLC 307 ***96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (316 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: 00:00:00.01 # Mc/sec: 7.07 // [ok]
This GapMind analysis is from Sep 24 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