Align agmatinase (EC 3.5.3.11) (characterized)
to candidate GFF1959 PGA1_c19920 agmatinase SpeB
Query= BRENDA::W5PHZ9 (361 letters) >FitnessBrowser__Phaeo:GFF1959 Length = 315 Score = 351 bits (900), Expect = e-101 Identities = 169/309 (54%), Positives = 223/309 (72%) Query: 51 NQPPSSEFVARSVGICSMMRLPMQATPEGLDAALVGVPLDIGTSNRPGARFGPRRIREES 110 NQP S +AR G + MRLP + +GLD A++GVP+DIGTS R G RFGP++IR ES Sbjct: 5 NQPISGNDLARFSGPNTFMRLPQATSLDGLDVAILGVPMDIGTSWRSGTRFGPKQIRAES 64 Query: 111 VMLRTANPSTGAVPFQFLKVADLGDVNVNLYNLQDSCRLIRADYQKIVAAGCVPLTLGGD 170 M+R N ++GA PF L + D+GD+ +N ++L DS R+I+ Y I+A+ P+ +GGD Sbjct: 65 AMIRPYNMTSGAAPFDSLNIGDIGDLAINTFSLPDSLRIIQESYSAILASDVTPVAMGGD 124 Query: 171 HTITYPILQAIAEKHGPVGLVHVDAHMDTADKALGEKLYHGTPFRRCVDEGLLDCKRVVQ 230 H+IT PIL+A+AEK+GPV LVHVDAH D D GE+ HGT FRR +EGL+ + Q Sbjct: 125 HSITLPILRAVAEKYGPVALVHVDAHADVNDDMFGERETHGTVFRRAYEEGLIVADKTYQ 184 Query: 231 IGIRGSSTTLDTYRYSRSQGFRVVLAEDCWLKSLVPLMGEVRQQMGGRPIYISFDIDGLD 290 IG+RG+ D ++ ++ GF+ A + W +SL + E+R+ +G RP+Y+S+DID LD Sbjct: 185 IGLRGTGYGADDFKEAQRWGFQHFPASELWNRSLHGMGAEIRRDIGNRPVYVSYDIDSLD 244 Query: 291 PAYAPGTGTPEIAGLTPSQALEIIRGCQGLNVVGCDLVEVSPPYDPSGNTALVAANLLFE 350 PAYAPGTGTPEI GLT QALE+IR +GLN+VGCD+VEVSPPYD SGNTAL AANLL+E Sbjct: 245 PAYAPGTGTPEIGGLTTPQALELIRALRGLNIVGCDMVEVSPPYDTSGNTALTAANLLYE 304 Query: 351 MLCVLPKVT 359 +LCVLP VT Sbjct: 305 LLCVLPGVT 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: 372 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: 315 Length adjustment: 28 Effective length of query: 333 Effective length of database: 287 Effective search space: 95571 Effective search space used: 95571 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 GFF1959 PGA1_c19920 (agmatinase SpeB)
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.30990.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-69 220.6 0.0 1.9e-69 220.3 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF1959 PGA1_c19920 agmatinase SpeB Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF1959 PGA1_c19920 agmatinase SpeB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 220.3 0.0 1.9e-69 1.9e-69 13 274 .. 34 307 .. 22 308 .. 0.89 Alignments for each domain: == domain 1 score: 220.3 bits; conditional E-value: 1.9e-69 TIGR01230 13 AevvivgiPydattsyrpGsrhgpeaireastnLeayseeld.rdlallkvvDagdlplaaGdaremvekieevve 87 +v i+g+P+d ts+r G+r+gp++ir s + y+ + + ++ l++ D gdl + + + +++ i+e + lcl|FitnessBrowser__Phaeo:GFF1959 34 LDVAILGVPMDIGTSWRSGTRFGPKQIRAESAMIRPYNMTSGaAPFDSLNIGDIGDLAINTFSLPDSLRIIQESYS 109 5889*********************************99988678**************99999************ PP TIGR01230 88 elleegkfvvaiGGeHsitlpvirAvkkkfeklavvqfDAHtDlrdefegeklshacvmrrvlelg....lnvlqi 159 +l+ +va+GG+Hsitlp++rAv++k++++a+v++DAH+D+ d+ ge+ +h +v rr++e g +++qi lcl|FitnessBrowser__Phaeo:GFF1959 110 AILASDVTPVAMGGDHSITLPILRAVAEKYGPVALVHVDAHADVNDDMFGERETHGTVFRRAYEEGlivaDKTYQI 185 ****************************************************************987676799*** PP TIGR01230 160 giRsg......ikeead..larennikvlkreledeiaevlakvldkpvyvtiDiDvlDPafaPGvgtpepgGlts 227 g+R +ke ++ + + + ++ +r+l+ ae + ++pvyv+ DiD lDPa+aPG+gtpe+gGlt+ lcl|FitnessBrowser__Phaeo:GFF1959 186 GLRGTgygaddFKEAQRwgFQHFPASELWNRSLHGMGAEIRRDIGNRPVYVSYDIDSLDPAYAPGTGTPEIGGLTT 261 ***7622111133333200333334444456777779999999********************************* PP TIGR01230 228 kellklfvlaekekkvvGlDvvEvaPvydssevtaltaaklalelll 274 ++l+ + +a ++vG+D+vEv+P yd+s taltaa+l +ell lcl|FitnessBrowser__Phaeo:GFF1959 262 PQALE-LIRALRGLNIVGCDMVEVSPPYDTSGNTALTAANLLYELLC 307 *****.999***********************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 1 (315 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: 11.20 // [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