Align agmatinase (EC 3.5.3.11) (characterized)
to candidate PfGW456L13_4435 Agmatinase (EC 3.5.3.11)
Query= BRENDA::W5PHZ9 (361 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4435 Length = 316 Score = 406 bits (1043), Expect = e-118 Identities = 199/308 (64%), Positives = 237/308 (76%) Query: 51 NQPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFGPRRIREES 110 +QP + R GI +MMRLP T GLDAA VGVPLDIGTS RPG RFGPR IR ES Sbjct: 6 HQPLGGNEMPRFGGIATMMRLPHLNTAAGLDAAFVGVPLDIGTSLRPGTRFGPREIRAES 65 Query: 111 VMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLGGD 170 VM+R N +TGA PF L VAD+GD+ +N +NL D+ R+I Y I+ +PLTLGGD Sbjct: 66 VMIRPYNMATGAAPFDSLSVADIGDIAINTFNLLDAVRIIEESYDNILEHDVIPLTLGGD 125 Query: 171 HTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGLLDCKRVVQ 230 HTIT PIL+AI +KHG VGLVH+DAH D D GEK+ HGT FRR V+EGLLD RVVQ Sbjct: 126 HTITLPILRAIHKKHGKVGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDPDRVVQ 185 Query: 231 IGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLD 290 IG+R T D + +SR+QGFRVV AE+CW KSL PLM EVR+++GG P+Y+SFDIDG+D Sbjct: 186 IGLRAQGYTADDFNWSRNQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDGID 245 Query: 291 PAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANLLFE 350 PA+APGTGTPEI GLT QA+EI+RGCQGL++VGCDLVEVSP YD +GNT+L+AANLL+E Sbjct: 246 PAWAPGTGTPEIGGLTTIQAIEIVRGCQGLDLVGCDLVEVSPAYDTTGNTSLLAANLLYE 305 Query: 351 MLCVLPKV 358 MLCVLP V Sbjct: 306 MLCVLPGV 313 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: 416 Number of extensions: 11 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 PfGW456L13_4435 (Agmatinase (EC 3.5.3.11))
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.23499.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-68 217.0 0.0 2.4e-68 216.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4435 Agmatinase (EC 3.5.3.11) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4435 Agmatinase (EC 3.5.3.11) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.7 0.0 2.4e-68 2.4e-68 14 274 .. 36 308 .. 24 309 .. 0.94 Alignments for each domain: == domain 1 score: 216.7 bits; conditional E-value: 2.4e-68 TIGR01230 14 evvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagd 67 ++ vg+P+d ts rpG+r+gp ir s+ + y+ + ++ l v+D gd lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4435 36 DAAFVGVPLDIGTSLRPGTRFGPREIRAESVMIRPYNMATGaAPFDSLSVADIGD 90 56678********************************9998678*********** PP TIGR01230 68 lplaaGdaremvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklav 122 + + + + + v iee +++le+ ++++GG+H+itlp++rA++kk++k+ + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4435 91 IAINTFNLLDAVRIIEESYDNILEHDVIPLTLGGDHTITLPILRAIHKKHGKVGL 145 *******9*********************************************** PP TIGR01230 123 vqfDAHtDlrdefegeklshacvmrrvlelg....lnvlqigiRsg..ikeeadl 171 v++DAH+D+ d+ gek+ h ++ rr++e g +v+qig+R++ + +++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4435 146 VHIDAHADVNDHMFGEKIAHGTTFRRAVEEGlldpDRVVQIGLRAQgyTADDFNW 200 *****************************99777779*******97446899*** PP TIGR01230 172 arennikvlk.relede.....iaevlakvldkpvyvtiDiDvlDPafaPGvgtp 220 r+++ +v++ e ++ +aev kv + pvy+++DiD++DPa+aPG+gtp lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4435 201 SRNQGFRVVQaEECWHKsleplMAEVREKVGGGPVYLSFDIDGIDPAWAPGTGTP 255 *******99855555555666699999**************************** PP TIGR01230 221 epgGltskellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274 e+gGlt+ ++++ v++ + +vG+D+vEv+P+yd++ t l+aa+l +e+l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4435 256 EIGGLTTIQAIE-IVRGCQGLDLVGCDLVEVSPAYDTTGNTSLLAANLLYEMLC 308 ************.99*************************************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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.27 // [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