Align N-succinylglutamylphosphate reductase (EC 1.2.1.-) (characterized)
to candidate 353285 BT3759 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file)
Query= reanno::Btheta:353285 (322 letters) >FitnessBrowser__Btheta:353285 Length = 322 Score = 652 bits (1681), Expect = 0.0 Identities = 322/322 (100%), Positives = 322/322 (100%) Query: 1 MIKAGIIGGAGYTAGELIRLLLNHPETEIVFINSSSNAGNRITDVHEGLYGETDLRFTDQ 60 MIKAGIIGGAGYTAGELIRLLLNHPETEIVFINSSSNAGNRITDVHEGLYGETDLRFTDQ Sbjct: 1 MIKAGIIGGAGYTAGELIRLLLNHPETEIVFINSSSNAGNRITDVHEGLYGETDLRFTDQ 60 Query: 61 LPLDAIDVLFFCTAHGDTKKFMESHNVPEDLKIIDLSMDYRIKSDDHDFIYGLPELNRRA 120 LPLDAIDVLFFCTAHGDTKKFMESHNVPEDLKIIDLSMDYRIKSDDHDFIYGLPELNRRA Sbjct: 61 LPLDAIDVLFFCTAHGDTKKFMESHNVPEDLKIIDLSMDYRIKSDDHDFIYGLPELNRRA 120 Query: 121 TCTAKHVANPGCFATCIQLGLLPLAKNLMLTGDVSVNAITGSTGAGVKPGATSHFSWRNN 180 TCTAKHVANPGCFATCIQLGLLPLAKNLMLTGDVSVNAITGSTGAGVKPGATSHFSWRNN Sbjct: 121 TCTAKHVANPGCFATCIQLGLLPLAKNLMLTGDVSVNAITGSTGAGVKPGATSHFSWRNN 180 Query: 181 NISIYKAFDHQHVPEIKQSLKQLQNSFDSEIDFIPYRGDFPRGIFATLVVKTKVALEEIV 240 NISIYKAFDHQHVPEIKQSLKQLQNSFDSEIDFIPYRGDFPRGIFATLVVKTKVALEEIV Sbjct: 181 NISIYKAFDHQHVPEIKQSLKQLQNSFDSEIDFIPYRGDFPRGIFATLVVKTKVALEEIV 240 Query: 241 RMYEEYYAKDSFVHIVDKNIDLKQVVNTNKCLIHLEKHGDKLLIISCIDNLLKGASGQAV 300 RMYEEYYAKDSFVHIVDKNIDLKQVVNTNKCLIHLEKHGDKLLIISCIDNLLKGASGQAV Sbjct: 241 RMYEEYYAKDSFVHIVDKNIDLKQVVNTNKCLIHLEKHGDKLLIISCIDNLLKGASGQAV 300 Query: 301 HNMNLMFNLEETVGLRLKPSAF 322 HNMNLMFNLEETVGLRLKPSAF Sbjct: 301 HNMNLMFNLEETVGLRLKPSAF 322 Lambda K H 0.321 0.138 0.409 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: 500 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: 322 Length of database: 322 Length adjustment: 28 Effective length of query: 294 Effective length of database: 294 Effective search space: 86436 Effective search space used: 86436 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: 48 (23.1 bits)
Align candidate 353285 BT3759 (N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file))
to HMM TIGR01850 (argC: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))
# 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.aa/TIGR01850.hmm # target sequence database: /tmp/gapView.13279.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01850 [M=345] Accession: TIGR01850 Description: argC: N-acetyl-gamma-glutamyl-phosphate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-94 301.1 0.0 1.1e-93 300.1 0.0 1.4 1 lcl|FitnessBrowser__Btheta:353285 BT3759 N-acetyl-gamma-glutamyl-p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:353285 BT3759 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 300.1 0.0 1.1e-93 1.1e-93 1 342 [. 2 319 .. 2 321 .. 0.94 Alignments for each domain: == domain 1 score: 300.1 bits; conditional E-value: 1.1e-93 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflAlp 76 ik++i+G+ GYt++eL+rll +Hpe+e++ + ss++ag+++++vh+ l g++dl+++++ l+++dv+f++++ lcl|FitnessBrowser__Btheta:353285 2 IKAGIIGGAGYTAGELIRLLLNHPETEIVFINSSSNAGNRITDVHEGLYGETDLRFTDQLP---LDAIDVLFFCTA 74 689**************************9999999*****************99996544...5799******** PP TIGR01850 77 hgvsaelvpelle.kgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCya 151 hg +++++++ +++k+idlS d+R+k+ + ++++YGlpElnr++ +ak +anPGC+a lcl|FitnessBrowser__Btheta:353285 75 HGDTKKFMESHNVpEDLKIIDLSMDYRIKSDD----------------HDFIYGLPELNRRATCTAKHVANPGCFA 134 ********98765478*************774................468************************* PP TIGR01850 152 TaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaek.kv 226 T+++L+l Pl+k+ +++ + + v+a++G++gAG k+ ++s+f+ +n+n+++Yk+++H+H pEi+q+l++l+++ + lcl|FitnessBrowser__Btheta:353285 135 TCIQLGLLPLAKNLMLTGD-VSVNAITGSTGAGVKPGATSHFSWRNNNISIYKAFDHQHVPEIKQSLKQLQNSfDS 209 ***********99999975.***************************************************99888 PP TIGR01850 227 kvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeet 302 ++ f+p ++ rGi+at+ +k+k ee+ ++yee+Y++++fv++++ ++ ++k+v+ +n + i ++ + lcl|FitnessBrowser__Btheta:353285 210 EIDFIPYRGDFPRGIFATLVVKTKVA--LEEIVRMYEEYYAKDSFVHIVD-KN-IDLKQVVNTNKCLIHLEKHG-- 279 8******************9999885..59*******************9.44.49***********9987766.. PP TIGR01850 303 krvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklp 342 ++++++s iDNL+KGa+gqAv n+Nlm++++et gL+ +p lcl|FitnessBrowser__Btheta:353285 280 DKLLIISCIDNLLKGASGQAVHNMNLMFNLEETVGLRLKP 319 89**********************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (322 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 2.55 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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