Align agmatinase (EC 3.5.3.11) (characterized)
to candidate SMc01967 SMc01967 agmatinase
Query= BRENDA::Q9BSE5 (352 letters) >FitnessBrowser__Smeli:SMc01967 Length = 352 Score = 243 bits (620), Expect = 5e-69 Identities = 128/274 (46%), Positives = 182/274 (66%), Gaps = 5/274 (1%) Query: 71 LDAAFIGVPLDTGTSNRPGARFGPRRIREESVMLGTVNPSTGALPFQSLMVADLGDVNV- 129 L A IGVP+D G +NRPG+RFGPR +R +G N G P L VAD+GDV Sbjct: 70 LQVAMIGVPMDLGVTNRPGSRFGPRALRAIE-RIGPYNHVLGCAPVHDLRVADIGDVPFR 128 Query: 130 NLYNLQDSCRRIQEAYEKIVAAGCIPLTLGGDHTITYPILQAMAKKHGPVGLLHVDAHTD 189 + Y L+ S I++ +IV AG +PL++GGDH+IT+PIL+A+ +K PVG++H+DAH D Sbjct: 129 SRYRLEISHEDIEKRISQIVDAGVLPLSVGGDHSITHPILKAVGRKQ-PVGMIHIDAHCD 187 Query: 190 TTDKALGEKLYHGAPFRRCVDEGLLDCKRVVQIGIRGSSTTLDPYRYNRSQGFRVVLAED 249 T K +HG PFR V +G+LD RV+QIGIRGS+ L + Y G V+ AE+ Sbjct: 188 TGGAFDLTKFHHGGPFRNAVLDGVLDPTRVIQIGIRGSAEYLWEFSYE--SGMTVIHAEE 245 Query: 250 CWMKSLVPLMGEVRQQMGGKPIYISFDIDALDPAYAPGTGTPEIAGLTPSQALEIIRGCQ 309 + ++ + ++ +G P Y+SFD+D+LDP++APGTGTPE+ GLT + LE+IRG + Sbjct: 246 VTGLGIPAIIEKAKKIVGDGPTYLSFDVDSLDPSFAPGTGTPEVGGLTTREVLELIRGLK 305 Query: 310 GLNVMGCDLVEVSPPYDLSGNTALLAANLLFEML 343 G+N++G D+VEV+P YD + NTA A +LFE+L Sbjct: 306 GVNLVGGDVVEVAPQYDTTTNTAHAGAQVLFEIL 339 Lambda K H 0.320 0.139 0.424 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: 395 Number of extensions: 27 Number of successful extensions: 5 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: 352 Length of database: 352 Length adjustment: 29 Effective length of query: 323 Effective length of database: 323 Effective search space: 104329 Effective search space used: 104329 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 SMc01967 SMc01967 (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.27291.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-61 192.9 0.0 5.6e-61 192.6 0.0 1.1 1 lcl|FitnessBrowser__Smeli:SMc01967 SMc01967 agmatinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc01967 SMc01967 agmatinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 192.6 0.0 5.6e-61 5.6e-61 13 273 .. 70 339 .. 60 341 .. 0.89 Alignments for each domain: == domain 1 score: 192.6 bits; conditional E-value: 5.6e-61 TIGR01230 13 AevvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdarem.vekieev 85 +v ++g+P+d + rpGsr+gp a+r + + y++ l+ + +l+v+D gd+p+ e+ e ie++ lcl|FitnessBrowser__Smeli:SMc01967 70 LQVAMIGVPMDLGVTNRPGSRFGPRALRAI-ERIGPYNHVLGcAPVHDLRVADIGDVPFRSRYRLEIsHEDIEKR 143 567899********************9976.6899*******667888**********9776655551689**** PP TIGR01230 86 veelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvmr.....rvlelgln 155 +++++++g ++++GG+Hsit p+++Av +k +++ ++++DAH+D+ f+ k+ h + r +vl+++ + lcl|FitnessBrowser__Smeli:SMc01967 144 ISQIVDAGVLPLSVGGDHSITHPILKAVGRK-QPVGMIHIDAHCDTGGAFDLTKFHHGGPFRnavldGVLDPT-R 216 ****************************998.6899***********88888888877666611111566776.* PP TIGR01230 156 vlqigiRsgikeeadlarennikvlk.relede.....iaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgG 224 v+qigiR + +++ e ++ v++ e++ i++++++v d p y+++D+D lDP+faPG+gtpe+gG lcl|FitnessBrowser__Smeli:SMc01967 217 VIQIGIRGSAEYLWEFSYESGMTVIHaEEVTGLgipaiIEKAKKIVGDGPTYLSFDVDSLDPSFAPGTGTPEVGG 291 **************************7777765778879999999****************************** PP TIGR01230 225 ltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalell 273 lt++e+l+ + ++ k +++vG DvvEvaP yd++ ta + a++ e+l lcl|FitnessBrowser__Smeli:SMc01967 292 LTTREVLE-LIRGLKGVNLVGGDVVEVAPQYDTTTNTAHAGAQVLFEIL 339 ********.99**********************************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (352 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: 11.54 // [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