Align agmatine deiminase (EC 3.5.3.12) (characterized)
to candidate WP_090446711.1 BLS63_RS16690 agmatine deiminase
Query= BRENDA::Q9I6J9 (368 letters) >NCBI__GCF_900100495.1:WP_090446711.1 Length = 368 Score = 647 bits (1669), Expect = 0.0 Identities = 303/367 (82%), Positives = 331/367 (90%) Query: 1 MSNPTSTPRADGFRMPAEWEPHEQTWMVWPERPDNWRNGGKPAQAAFAAVAKAIARFEPV 60 M+ STPRADGFRMPAEWE H QTWMVWPERPDNWR GGKPAQAAF+AVAKAIA FEPV Sbjct: 1 MTTLNSTPRADGFRMPAEWETHSQTWMVWPERPDNWRLGGKPAQAAFSAVAKAIAAFEPV 60 Query: 61 TVCASAGQYENARARLDDGNIRVVEISSDDAWVRDTGPTFVIDDKGDVRGVDWGFNAWGG 120 TVC SA QYENARARLD IRV+E+SSDDAWVRDTGPTFV + G+VRGVDW FNAWGG Sbjct: 61 TVCVSACQYENARARLDHAAIRVLEMSSDDAWVRDTGPTFVCNASGEVRGVDWSFNAWGG 120 Query: 121 FEGGLYFPWQRDDQVARKILEIERRARYRTDDFVLEGGSIHVDGEGTLITTEECLLNHNR 180 F+GGLYFPWQRDDQVA KILEIER ARYRT+ FVLEGGSIHVDGEGTLITTEECLLN NR Sbjct: 121 FDGGLYFPWQRDDQVAGKILEIERCARYRTEGFVLEGGSIHVDGEGTLITTEECLLNRNR 180 Query: 181 NPHLSQAEIERTLRDYLAVESIIWLPNGLYNDETDGHVDNFCCYARPGEVLLAWTDDQDD 240 NPHLS+ E E+ LR++LA++ +IWLP+GL+NDETDGHVDNFCC+ RPGEVLLAWTDD D Sbjct: 181 NPHLSREETEQVLREHLAIDRVIWLPDGLFNDETDGHVDNFCCFVRPGEVLLAWTDDPQD 240 Query: 241 PNYLRCQAALRVLEESRDAKGRKLVVHKMPIPGPLYATQEECDGVDIVEGSQPRDPSIRL 300 PNY RCQAALRVLE +RDAKGR+L+VHK+PIPGPLYAT EC GVD+V GSQPRDPSIRL Sbjct: 241 PNYPRCQAALRVLESARDAKGRQLIVHKLPIPGPLYATDAECAGVDLVAGSQPRDPSIRL 300 Query: 301 AGSYVNFLIVNGGIIAPSFDDPKDAEARAILQRVFPEHEVVMVPGREILLGGGNIHCITQ 360 AGSYVNFLIVNGGIIAPSFDDP+D ARAILQR+FPEH VV+VPGREILLGGGNIHCITQ Sbjct: 301 AGSYVNFLIVNGGIIAPSFDDPQDEAARAILQRLFPEHRVVLVPGREILLGGGNIHCITQ 360 Query: 361 QQPAPRK 367 QQPAP++ Sbjct: 361 QQPAPQR 367 Lambda K H 0.319 0.138 0.439 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: 678 Number of extensions: 20 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: 368 Length of database: 368 Length adjustment: 30 Effective length of query: 338 Effective length of database: 338 Effective search space: 114244 Effective search space used: 114244 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_090446711.1 BLS63_RS16690 (agmatine deiminase)
to HMM TIGR03380 (aguA: agmatine deiminase (EC 3.5.3.12))
# 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/TIGR03380.hmm # target sequence database: /tmp/gapView.683301.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03380 [M=357] Accession: TIGR03380 Description: agmatine_aguA: agmatine deiminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-181 589.5 0.0 1.2e-181 589.3 0.0 1.0 1 NCBI__GCF_900100495.1:WP_090446711.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100495.1:WP_090446711.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 589.3 0.0 1.2e-181 1.2e-181 1 357 [] 6 364 .. 6 364 .. 0.99 Alignments for each domain: == domain 1 score: 589.3 bits; conditional E-value: 1.2e-181 TIGR03380 1 ttpkedgfrlPaefekqkevwliWPerpDnWregakpaqkafaevakaiakvepvtvlvskeqyenarkalpe 73 +tp++dgfr+Pae+e+++++w++WPerpDnWr g+kpaq+af +vakaia +epvtv+vs+ qyenar++l++ NCBI__GCF_900100495.1:WP_090446711.1 6 STPRADGFRMPAEWETHSQTWMVWPERPDNWRLGGKPAQAAFSAVAKAIAAFEPVTVCVSACQYENARARLDH 78 58*********************************************************************87 PP TIGR03380 74 .eirvvemssnDawirDvGPtfvvndkgelrgvdwefnawgglkdGlyfpWdkDdkvarkvleleridryra. 144 +irv+emss+Daw+rD+GPtfv n +ge+rgvdw+fnawgg+++GlyfpW++Dd+va k+le+er +ryr+ NCBI__GCF_900100495.1:WP_090446711.1 79 aAIRVLEMSSDDAWVRDTGPTFVCNASGEVRGVDWSFNAWGGFDGGLYFPWQRDDQVAGKILEIERCARYRTe 151 58**********************************************************************8 PP TIGR03380 145 dlvleggsihvDGeGtlltteeclLsegrnpelskeeieeklkeylgvekviWlkeGlyldetnGhvDnllnf 217 +vleggsihvDGeGtl+tteeclL+++rnp+ls+ee e++l+e+l++++viWl++Gl++det+GhvDn+++f NCBI__GCF_900100495.1:WP_090446711.1 152 GFVLEGGSIHVDGEGTLITTEECLLNRNRNPHLSREETEQVLREHLAIDRVIWLPDGLFNDETDGHVDNFCCF 224 9************************************************************************ PP TIGR03380 218 vrPGevvlswtddesdPqyeiskealevLenetDakGrklkvhklklpeplllteeeakgvdavegtlpreag 290 vrPGev+l+wtdd +dP+y ++++al+vLe+++DakGr+l vhkl++p+pl++t++e++gvd v g++pr+++ NCBI__GCF_900100495.1:WP_090446711.1 225 VRPGEVLLAWTDDPQDPNYPRCQAALRVLESARDAKGRQLIVHKLPIPGPLYATDAECAGVDLVAGSQPRDPS 297 ************************************************************************* PP TIGR03380 291 erlaasyvnyliankaiilPlfddekDkeakkllqelfPdrkvvgvkareillgGGnihcitqqipa 357 rla+syvn+li+n++ii+P+fdd++D+ a+++lq+lfP+++vv v+ reillgGGnihcitqq+pa NCBI__GCF_900100495.1:WP_090446711.1 298 IRLAGSYVNFLIVNGGIIAPSFDDPQDEAARAILQRLFPEHRVVLVPGREILLGGGNIHCITQQQPA 364 *****************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 1 (368 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 24.28 // [ok]
This GapMind analysis is from Sep 24 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