Align agmatinase (EC 3.5.3.11) (characterized)
to candidate AO356_04095 AO356_04095 agmatinase
Query= BRENDA::W5PHZ9 (361 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_04095 Length = 316 Score = 413 bits (1061), Expect = e-120 Identities = 201/308 (65%), Positives = 238/308 (77%) Query: 51 NQPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFGPRRIREES 110 +QP + R GI +MMRLP T GLDAA VGVPLDIGTS R G RFGPR IR ES Sbjct: 6 HQPLGGNEMPRFGGIATMMRLPHLQTAAGLDAAFVGVPLDIGTSLRAGTRFGPREIRAES 65 Query: 111 VMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLGGD 170 VM+R N +TGA PF L VAD+GDV +N +NL D+ R+I Y KI+ +PLTLGGD Sbjct: 66 VMIRPYNMATGAAPFDSLSVADIGDVPINTFNLLDAVRIIEESYHKILEHNVIPLTLGGD 125 Query: 171 HTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGLLDCKRVVQ 230 HTIT PIL+AI +KHG VGLVH+DAH D D GEK+ HGT FRR V+EGLLDC RVVQ Sbjct: 126 HTITLPILRAIHKKHGKVGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDCDRVVQ 185 Query: 231 IGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLD 290 IG+R T D + +SR+QGFRVV AE+CW KSL PLM EVR+++GG P+Y+SFDIDG+D Sbjct: 186 IGLRAQGYTADDFNWSRNQGFRVVQAEECWHKSLAPLMAEVREKVGGGPVYLSFDIDGID 245 Query: 291 PAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANLLFE 350 PA+APGTGTPEI GLT QA+EI+RGCQGL++VGCDLVEVSPPYD +GNT+L+ ANLL+E Sbjct: 246 PAWAPGTGTPEIGGLTTIQAIEIVRGCQGLDLVGCDLVEVSPPYDTTGNTSLLGANLLYE 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: 430 Number of extensions: 9 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 AO356_04095 AO356_04095 (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.11627.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-67 212.5 0.0 5.6e-67 212.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04095 AO356_04095 agmatinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04095 AO356_04095 agmatinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 212.2 0.0 5.6e-67 5.6e-67 14 274 .. 36 308 .. 24 309 .. 0.94 Alignments for each domain: == domain 1 score: 212.2 bits; conditional E-value: 5.6e-67 TIGR01230 14 evvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGda 75 ++ vg+P+d ts r+G+r+gp ir s+ + y+ + ++ l v+D gd+p+ + + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04095 36 DAAFVGVPLDIGTSLRAGTRFGPREIRAESVMIRPYNMATGaAPFDSLSVADIGDVPINTFNL 98 56678********************************9998678******************9 PP TIGR01230 76 remvekieevveelleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefege 138 + v iee +++le++ ++++GG+H+itlp++rA++kk++k+ +v++DAH+D+ d+ ge lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04095 99 LDAVRIIEESYHKILEHNVIPLTLGGDHTITLPILRAIHKKHGKVGLVHIDAHADVNDHMFGE 161 *************************************************************** PP TIGR01230 139 klshacvmrrvlelg....lnvlqigiRsg..ikeeadlarennikvlk.relede.....ia 189 k+ h ++ rr++e g +v+qig+R++ + +++++ r+++ +v++ e ++ +a lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04095 162 KIAHGTTFRRAVEEGlldcDRVVQIGLRAQgyTADDFNWSRNQGFRVVQaEECWHKslaplMA 224 *************99777779*******97446899**********99866665556677799 PP TIGR01230 190 evlakvldkpvyvtiDiDvlDPafaPGvgtpepgGltskellklfvlaekekkvvGlDvvEva 252 ev kv + pvy+++DiD++DPa+aPG+gtpe+gGlt+ ++++ v++ + +vG+D+vEv+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04095 225 EVREKVGGGPVYLSFDIDGIDPAWAPGTGTPEIGGLTTIQAIE-IVRGCQGLDLVGCDLVEVS 286 999****************************************.99***************** PP TIGR01230 253 Pvydssevtaltaaklalelll 274 P yd++ t l+ a+l +e+l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_04095 287 PPYDTTGNTSLLGANLLYEMLC 308 ********************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: 7.40 // [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