Align Probable N-acetyl-gamma-glutamyl-phosphate reductase, chloroplastic; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate AZOBR_RS07795 AZOBR_RS07795 N-acetyl-gamma-glutamyl-phosphate reductase
Query= SwissProt::Q93Z70 (401 letters) >FitnessBrowser__azobra:AZOBR_RS07795 Length = 350 Score = 415 bits (1066), Expect = e-120 Identities = 206/343 (60%), Positives = 252/343 (73%) Query: 59 IRIGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQSMESVFPHLRAQKLPTLVSVK 118 IR+G+LGASGYTGAE+VR+L HP ++ +TA+R+AG+ M VFPHL LP LV ++ Sbjct: 8 IRVGILGASGYTGAELVRMLLRHPGVEICALTAERQAGKPMAEVFPHLGQFNLPGLVKIE 67 Query: 119 DADFSTVDAVFCCLPHGTTQEIIKELPTALKIVDLSADFRLRNIAEYEEWYGQPHKAVEL 178 + + +DAVFC LPHGTTQE+I LP +K+VDLSADFRL + AEY WYG H+AVEL Sbjct: 68 EVAWDKLDAVFCALPHGTTQEVIAGLPRHIKVVDLSADFRLSDPAEYATWYGHEHRAVEL 127 Query: 179 QKEVVYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLKANLIKHENIIIDAKSGVSG 238 QKEV YGLTE R+ ++KAR+VANPGCYPT L L+PLL +I+ I+IDAKSGVSG Sbjct: 128 QKEVAYGLTEFNRQGVRKARVVANPGCYPTCSLLALLPLLMDEMIEPGGIVIDAKSGVSG 187 Query: 239 AGRGAKEANLYSEIAEGISSYGVTRHRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIRGMQ 298 AGR AK+ NL++E++EG ++YGV HRH+PEIEQ L A VTVSFTPHL+PM RGM Sbjct: 188 AGRDAKQQNLFTEVSEGFNAYGVGHHRHMPEIEQELRLAAGRPVTVSFTPHLVPMNRGMM 247 Query: 299 STIYVEMAPGVRTEDLHQQLKTSYEDEEFVKVLDEGVVPRTHNVRGSNYCHMSVFPDRIP 358 +TIYV MA GV +DL L YE E FV V G+ P T +VR SN + VFPDR P Sbjct: 248 ATIYVRMADGVTADDLRATLTARYESEPFVNVTAAGIAPATRHVRASNQALIGVFPDRTP 307 Query: 359 GRAIIISVIDNLVKGASGQALQNLNIMLGYPETTGLLHQPLFP 401 AII+SVIDNLVKGASGQA+QN+N+M G ETTGL PLFP Sbjct: 308 RGAIIVSVIDNLVKGASGQAIQNMNVMFGLGETTGLEQAPLFP 350 Lambda K H 0.318 0.134 0.386 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: 437 Number of extensions: 11 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: 401 Length of database: 350 Length adjustment: 30 Effective length of query: 371 Effective length of database: 320 Effective search space: 118720 Effective search space used: 118720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate AZOBR_RS07795 AZOBR_RS07795 (N-acetyl-gamma-glutamyl-phosphate reductase)
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.12849.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-133 430.8 0.0 2.3e-133 430.6 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS07795 AZOBR_RS07795 N-acetyl-gamma-glu Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS07795 AZOBR_RS07795 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 430.6 0.0 2.3e-133 2.3e-133 1 345 [] 8 350 .] 8 350 .] 0.97 Alignments for each domain: == domain 1 score: 430.6 bits; conditional E-value: 2.3e-133 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileead 69 i+v+i+GasGYtGaeL+r+l +Hp ve+ +l+++r+agk+++ev+phl ++ l ++ee + ++ d lcl|FitnessBrowser__azobra:AZOBR_RS07795 8 IRVGILGASGYTGAELVRMLLRHPGVEICALTAERQAGKPMAEVFPHLGQFNLPGLVKIEEV-AWDKLD 75 69**********************************************99888777777776.4679** PP TIGR01850 70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138 +vf+Alphg+++e+++ l +++kv+dlSadfRl+d+++Y++wYg++h++ el++e++YGl+E+nr+ + lcl|FitnessBrowser__azobra:AZOBR_RS07795 76 AVFCALPHGTTQEVIA-GLPRHIKVVDLSADFRLSDPAEYATWYGHEHRAVELQKEVAYGLTEFNRQGV 143 ***************5.57899*********************************************** PP TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtk 207 +ka+++anPGCy+T++lLal Pll +++iep i++daksGvSgAGr a++++lf+ev+e +++Y v + lcl|FitnessBrowser__azobra:AZOBR_RS07795 144 RKARVVANPGCYPTCSLLALLPLLMDEMIEPGGIVIDAKSGVSGAGRDAKQQNLFTEVSEGFNAYGVGH 212 ********************************************************************* PP TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlk 276 HrH pEieqel+ +a++ v+vsftphlvpm rG++atiy+++++++t+++lr++++++Ye+epfv+v lcl|FitnessBrowser__azobra:AZOBR_RS07795 213 HRHMPEIEQELRLAAGRPVTVSFTPHLVPMNRGMMATIYVRMADGVTADDLRATLTARYESEPFVNVTA 281 ************88888999************************************************* PP TIGR01850 277 egelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 +g +P+t++v++sn++ igv d++ + +++vs+iDNLvKGa+gqA+qn+N+m+g+ et+gLe+ pl+p lcl|FitnessBrowser__azobra:AZOBR_RS07795 282 AGIAPATRHVRASNQALIGVFPDRTPRGAIIVSVIDNLVKGASGQAIQNMNVMFGLGETTGLEQAPLFP 350 ******************************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (350 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: 00:00:00.01 # Mc/sec: 11.91 // [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