Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate 6936059 Sama_0256 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)
Query= BRENDA::P11446 (334 letters) >FitnessBrowser__SB2B:6936059 Length = 331 Score = 293 bits (751), Expect = 3e-84 Identities = 163/330 (49%), Positives = 208/330 (63%), Gaps = 9/330 (2%) Query: 1 MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 60 M I+GASGY GA+L ++ PH+ + L VS S D GK +S L+P + L Sbjct: 6 MKKIAIIGASGYTGAQLTALIDAEPHLQVQGLYVSEGSADKGKPLSSLYPVYSHL-KYCL 64 Query: 61 QPMSDISEFS--PGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYY 118 P++D ++ + D V LAT H VS +LA F E G VFDLSGA+R D Y K+Y Sbjct: 65 SPLTDEAKDAIVAEADAVALATEHSVSLELAAYFYEKGLAVFDLSGAYRFADTAQYPKWY 124 Query: 119 GFTHQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWP 178 GF H +PE+L +A YGLAEW + + +IAVPGCYPTA+ ALKPL A L + P Sbjct: 125 GFEHSHPEVLAKAVYGLAEWNADAVAATRMIAVPGCYPTASLTALKPL-KAMLTEAR--P 181 Query: 179 VINATSGVSGAGRKAAISNSFCEVSLQPYGVFTHRHQPEIATHLGADVIFTPHLGNFPRG 238 VINA SGV+GAGRKA + SFCEVSL PYGV HRHQPEIAT LG +VIFTPHLGNF RG Sbjct: 182 VINAVSGVTGAGRKAQLHTSFCEVSLTPYGVLGHRHQPEIATQLGQEVIFTPHLGNFKRG 241 Query: 239 ILETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGVPALKNVVGLPFCDIG--FAVQ 296 IL TIT +LK G ++ VA+ Y P+V + + P + +VV P C +G F Sbjct: 242 ILATITVQLKPGTSREDVAKA-YSVYDQSPIVTVKEGQFPKVDDVVFTPNCHLGWKFDED 300 Query: 297 GEHLIIVATEDNLLKGAAAQAVQCANIRFG 326 +L++ + DNL+KGAA+QA+QC I FG Sbjct: 301 SGYLVVASAIDNLMKGAASQALQCIKIHFG 330 Lambda K H 0.321 0.136 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: 359 Number of extensions: 15 Number of successful extensions: 5 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: 334 Length of database: 331 Length adjustment: 28 Effective length of query: 306 Effective length of database: 303 Effective search space: 92718 Effective search space used: 92718 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 6936059 Sama_0256 (N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq))
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.23681.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-107 346.2 0.1 1.3e-107 346.0 0.1 1.0 1 lcl|FitnessBrowser__SB2B:6936059 Sama_0256 N-acetyl-gamma-glutamy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936059 Sama_0256 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 346.0 0.1 1.3e-107 1.3e-107 2 331 .. 8 330 .. 7 331 .] 0.96 Alignments for each domain: == domain 1 score: 346.0 bits; conditional E-value: 1.3e-107 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssre...agkklsevhphlkglvd..lkleeleeeeileeadvvfl 73 k+ai+GasGYtGa+L l+++ p+++v+ l++s+ +gk+ls+++p +++l + l+++++++i +ead+v l lcl|FitnessBrowser__SB2B:6936059 8 KIAIIGASGYTGAQLTALIDAEPHLQVQGLYVSEGsadKGKPLSSLYPVYSHLKYclSPLTDEAKDAIVAEADAVAL 84 89***************************998887789**********9988776556777777799********** PP TIGR01850 74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCy 150 A+ h vs el++ ++ekg+ v+dlS+++R+ d+++Y kwYg++h+++e+l++avYGl+E+n ++++ +++ia+PGCy lcl|FitnessBrowser__SB2B:6936059 85 ATEHSVSLELAAYFYEKGLAVFDLSGAYRFADTAQYPKWYGFEHSHPEVLAKAVYGLAEWNADAVAATRMIAVPGCY 161 ***************************************************************************** PP TIGR01850 151 aTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvk 227 +Ta+l al+Pl + ++++ +++++a+sGv+gAGrka+ +++f+ev +l+pY v +HrH+pEi+++l+ + lcl|FitnessBrowser__SB2B:6936059 162 PTASLTALKPLKA--MLTEARPVINAVSGVTGAGRKAQLHTSFCEV--SLTPYGVLGHRHQPEIATQLG------QE 228 ***********84..556667*************************..*********************......57 PP TIGR01850 228 vsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkr 304 v+ftphl +++rGilati+++lk ++++e+++k+y +vY+++p+v+v + g++P++ +v+ + +++g++ de+++ lcl|FitnessBrowser__SB2B:6936059 229 VIFTPHLGNFKRGILATITVQLKPGTSREDVAKAY-SVYDQSPIVTVKE-GQFPKVDDVVFTPNCHLGWKFDEDSGY 303 9*********************************9.69********997.9************************** PP TIGR01850 305 vvvvsaiDNLvKGaagqAvqnlNlmlg 331 +vv saiDNL+KGaa+qA+q++ +++g lcl|FitnessBrowser__SB2B:6936059 304 LVVASAIDNLMKGAASQALQCIKIHFG 330 ************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (331 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.91 // [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