Align agmatinase (EC 3.5.3.11) (characterized)
to candidate PP_4523 PP_4523 putative Agmatinase
Query= BRENDA::W5PHZ9 (361 letters) >FitnessBrowser__Putida:PP_4523 Length = 320 Score = 407 bits (1045), Expect = e-118 Identities = 197/316 (62%), Positives = 240/316 (75%) Query: 43 RQASDGPRNQPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFG 102 R D +QP + R GI +M+RLP + +GLDAA +GVPLDIGTS R G RFG Sbjct: 2 RPTVDKTLHQPLGGNEMPRFGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRFG 61 Query: 103 PRRIREESVMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGC 162 PR+IR ESVM+R N +TGA PF L VAD+GDV +N +NL D+ R+I Y +IV Sbjct: 62 PRQIRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHNV 121 Query: 163 VPLTLGGDHTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGL 222 +P+TLGGDHTIT PIL+A+ +KHG +GLVH+DAH D D GEK+ HGT FRR V+EGL Sbjct: 122 IPMTLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGL 181 Query: 223 LDCKRVVQIGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYI 282 LDC RVVQIG+R T D + +SR QGFRVV AE+CW KSL PLM EVR+++GG P+Y+ Sbjct: 182 LDCDRVVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYL 241 Query: 283 SFDIDGLDPAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTAL 342 SFDIDG+DPA+APGTGTPEI GLT QA+EIIRGC GL+++GCDLVEVSPPYD +GNT+L Sbjct: 242 SFDIDGIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTSL 301 Query: 343 VAANLLFEMLCVLPKV 358 + ANLLFEMLCVLP V Sbjct: 302 LGANLLFEMLCVLPGV 317 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: 421 Number of extensions: 14 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: 320 Length adjustment: 28 Effective length of query: 333 Effective length of database: 292 Effective search space: 97236 Effective search space used: 97236 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 PP_4523 PP_4523 (putative 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.19504.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-65 207.0 0.0 2.7e-65 206.7 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_4523 PP_4523 putative Agmatinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4523 PP_4523 putative Agmatinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 206.7 0.0 2.7e-65 2.7e-65 14 274 .. 40 312 .. 31 313 .. 0.94 Alignments for each domain: == domain 1 score: 206.7 bits; conditional E-value: 2.7e-65 TIGR01230 14 evvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdaremvekieevve 87 ++ +g+P+d ts r G+r+gp +ir s+ + y+ + ++ l v+D gd+ + + + + v iee + lcl|FitnessBrowser__Putida:PP_4523 40 DAAFIGVPLDIGTSLRSGTRFGPRQIRAESVMIRPYNMATGaAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYD 114 45578********************************9998678******************9************ PP TIGR01230 88 elleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvmrrvlelg....lnvlq 158 e++e++ ++++GG+H+itlp++rA +kk++k+ +v++DAH+D+ d+ gek+ h ++ rr++e g +v+q lcl|FitnessBrowser__Putida:PP_4523 115 EIVEHNVIPMTLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGlldcDRVVQ 189 ****************************************************************99777779*** PP TIGR01230 159 igiRsg..ikeeadlarennikvlk.relede.....iaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGl 225 ig+R++ + +++++ r+++ +v++ e ++ +aev kv + pvy+++DiD++DPa+aPG+gtpe+gGl lcl|FitnessBrowser__Putida:PP_4523 190 IGLRAQgyTADDFNWSRRQGFRVVQaEECWHKsleplMAEVREKVGGGPVYLSFDIDGIDPAWAPGTGTPEIGGL 264 ****97446899**********99855555555666699999********************************* PP TIGR01230 226 tskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274 t+ ++++ ++ + ++G+D+vEv+P yd++ t l+ a+l e+l lcl|FitnessBrowser__Putida:PP_4523 265 TTIQAME-IIRGCHGLDLIGCDLVEVSPPYDTTGNTSLLGANLLFEMLC 312 *******.89999**********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (320 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: 10.75 // [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