Align N-succinylglutamylphosphate reductase (EC 1.2.1.-) (characterized)
to candidate Echvi_3847 Echvi_3847 N-acetyl-gamma-glutamyl-phosphate reductase, common form
Query= reanno::Cola:Echvi_3847 (322 letters) >FitnessBrowser__Cola:Echvi_3847 Length = 322 Score = 645 bits (1663), Expect = 0.0 Identities = 322/322 (100%), Positives = 322/322 (100%) Query: 1 MTKIKTAIIGAAGYTGGELLRILVHHPSCELVYIHSNSQKGKKIDEVHPDLIGDSDLVFT 60 MTKIKTAIIGAAGYTGGELLRILVHHPSCELVYIHSNSQKGKKIDEVHPDLIGDSDLVFT Sbjct: 1 MTKIKTAIIGAAGYTGGELLRILVHHPSCELVYIHSNSQKGKKIDEVHPDLIGDSDLVFT 60 Query: 61 DEVKTTGLDAVFLGLPHGQAKAFLAENKFDDQTVIIDLSTDFRDESNGFLYGLPEVNASQ 120 DEVKTTGLDAVFLGLPHGQAKAFLAENKFDDQTVIIDLSTDFRDESNGFLYGLPEVNASQ Sbjct: 61 DEVKTTGLDAVFLGLPHGQAKAFLAENKFDDQTVIIDLSTDFRDESNGFLYGLPEVNASQ 120 Query: 121 TGQAKRIANPGCFATGIQLALAPAIAAGLAKSDIHITGITGSTGAGKKLSETTHFSQRNQ 180 TGQAKRIANPGCFATGIQLALAPAIAAGLAKSDIHITGITGSTGAGKKLSETTHFSQRNQ Sbjct: 121 TGQAKRIANPGCFATGIQLALAPAIAAGLAKSDIHITGITGSTGAGKKLSETTHFSQRNQ 180 Query: 181 NVSVYKLFTHQHLKEISQTFGQLQTGFDQHLLFVPYRGNFSRGIWVTAYFPFEGSLEEAY 240 NVSVYKLFTHQHLKEISQTFGQLQTGFDQHLLFVPYRGNFSRGIWVTAYFPFEGSLEEAY Sbjct: 181 NVSVYKLFTHQHLKEISQTFGQLQTGFDQHLLFVPYRGNFSRGIWVTAYFPFEGSLEEAY 240 Query: 241 KIYHDFYQNAAFTHVSEKDIDLKQVVSTNKCIVHLKKEAGQLVIYSAIDNLLKGASGQAV 300 KIYHDFYQNAAFTHVSEKDIDLKQVVSTNKCIVHLKKEAGQLVIYSAIDNLLKGASGQAV Sbjct: 241 KIYHDFYQNAAFTHVSEKDIDLKQVVSTNKCIVHLKKEAGQLVIYSAIDNLLKGASGQAV 300 Query: 301 QNYNLAFGLNEKEGLRLKSVAF 322 QNYNLAFGLNEKEGLRLKSVAF Sbjct: 301 QNYNLAFGLNEKEGLRLKSVAF 322 Lambda K H 0.319 0.136 0.392 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: 481 Number of extensions: 13 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate Echvi_3847 Echvi_3847 (N-acetyl-gamma-glutamyl-phosphate reductase, common form)
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.14859.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-94 301.5 0.3 4.7e-93 298.1 0.3 1.9 1 lcl|FitnessBrowser__Cola:Echvi_3847 Echvi_3847 N-acetyl-gamma-glutam Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_3847 Echvi_3847 N-acetyl-gamma-glutamyl-phosphate reductase, common form # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 298.1 0.3 4.7e-93 4.7e-93 1 342 [. 4 319 .. 4 321 .. 0.93 Alignments for each domain: == domain 1 score: 298.1 bits; conditional E-value: 4.7e-93 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflA 74 ik+ai+Ga GYtG+eLlr+l +Hp++e+++++s++++gkk++evhp l g dl ++++ + ++ d+vfl+ lcl|FitnessBrowser__Cola:Echvi_3847 4 IKTAIIGAAGYTGGELLRILVHHPSCELVYIHSNSQKGKKIDEVHPDLIGDSDLVFTDEVK---TTGLDAVFLG 74 689***********************************************99998886433...3589****** PP TIGR01850 75 lphgvsaelvpe.llekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianP 147 lphg+++++ +e + ++++idlS dfR +++ + YGlpE+n ++ +ak+ianP lcl|FitnessBrowser__Cola:Echvi_3847 75 LPHGQAKAFLAEnKFDDQTVIIDLSTDFRDESN------------------GFLYGLPEVNASQTGQAKRIANP 130 ******998665156788***********7644..................589******************** PP TIGR01850 148 GCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelskl 221 GC+aT+++LalaP+++++l ++ +i +++++G++gAG+k se+++f+++n+n+++Yk+++H+H +Ei+q+ ++l lcl|FitnessBrowser__Cola:Echvi_3847 131 GCFATGIQLALAPAIAAGLAKS-DIHITGITGSTGAGKKLSETTHFSQRNQNVSVYKLFTHQHLKEISQTFGQL 203 ******************8887.5************************************************** PP TIGR01850 222 aek.kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdi 294 ++ + ++ f+p +++rGi+ t+y+ ++ +l ee +k+y+++Y++ f +v + +++ ++k+v+ +n + + lcl|FitnessBrowser__Cola:Echvi_3847 204 QTGfDQHLLFVPYRGNFSRGIWVTAYFPFEGSL--EEAYKIYHDFYQNAAFTHVSE-KDI-DLKQVVSTNKCIV 273 9998778************************66..899*****************8.555.9**********98 PP TIGR01850 295 gvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklp 342 ++ e++++v+ saiDNL+KGa+gqAvqn Nl++g++e+egL+ ++ lcl|FitnessBrowser__Cola:Echvi_3847 274 HLKK--EAGQLVIYSAIDNLLKGASGQAVQNYNLAFGLNEKEGLRLKS 319 7665..559***********************************9765 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 2.09 // [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