Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_034997207.1 DL88_RS14000 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Smeli:SMc01801 (310 letters) >NCBI__GCF_000745425.1:WP_034997207.1 Length = 306 Score = 278 bits (711), Expect = 1e-79 Identities = 151/311 (48%), Positives = 202/311 (64%), Gaps = 12/311 (3%) Query: 1 MKPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPD 60 M +IFIDGE GTTGL I+ R+AGR D+EL+S+P +R+ A ++ + D+ ILCLPD Sbjct: 1 MPARIFIDGEAGTTGLGIKERLAGRADVELVSLPAGDRKTAEAKQTVYKGVDLVILCLPD 60 Query: 61 DASREAVAMVA--GNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCY 118 DA++EAV + G+ R++D STAHR AP W YGF E+ K Q + I A V NPGCY Sbjct: 61 DAAKEAVVLAGALGDAAPRLLDASTAHRTAPGWTYGFPELTKGQAEAIAKAPRVGNPGCY 120 Query: 119 PTGAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHF-LYG 177 TGAIAL+RPL +AG+LP V+++AVSGY+GGGK MIA E AP F Y Sbjct: 121 ATGAIALLRPLTEAGLLPSTASVSIHAVSGYSGGGKTMIAAYEAGT------APAFEAYA 174 Query: 178 LTLKHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVD 237 L L HKHVPE+ +G L+ P+F+PSVG F QGM+V +PL+L+ L + + L Sbjct: 175 LGLGHKHVPEIMAYGQLQNRPIFTPSVGNFRQGMLVFIPLFLDSLPQKPGRKDLAAVLQA 234 Query: 238 HYAGQSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGAS 297 HYAG V ++E+ + R++ L ++ ++LFV G + G V L A LDNLGKGAS Sbjct: 235 HYAGSRHVH-TRMEEAPE--RLEPQALNDTNELELFVCGPEEGRQVVLAARLDNLGKGAS 291 Query: 298 GAAVQNMDLML 308 GAA+QN +LML Sbjct: 292 GAALQNTELML 302 Lambda K H 0.319 0.136 0.395 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: 300 Number of extensions: 16 Number of successful extensions: 4 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: 310 Length of database: 306 Length adjustment: 27 Effective length of query: 283 Effective length of database: 279 Effective search space: 78957 Effective search space used: 78957 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 WP_034997207.1 DL88_RS14000 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01851 (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/TIGR01851.hmm # target sequence database: /tmp/gapView.31270.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01851 [M=310] Accession: TIGR01851 Description: argC_other: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-117 378.4 0.0 1.6e-117 378.2 0.0 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034997207.1 DL88_RS14000 N-acetyl-gamma-glut Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034997207.1 DL88_RS14000 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.2 0.0 1.6e-117 1.6e-117 3 310 .] 4 304 .. 2 304 .. 0.96 Alignments for each domain: == domain 1 score: 378.2 bits; conditional E-value: 1.6e-117 TIGR01851 3 kvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd. 70 ++fidGeaGttGl i+erla+r d+el+s+ + rk a+++ + +d +ilclpddaa+eav l lcl|NCBI__GCF_000745425.1:WP_034997207.1 4 RIFIDGEAGTTGLGIKERLAGRADVELVSLPAGDRKTAEAKQTVYKGVDLVILCLPDDAAKEAVVLAGa 72 79***************************************************************9752 PP TIGR01851 71 ..npntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadf 137 +++ ++ldasta+rta++w+yGfpel+ +q e ia+a rv nPGcyatgaiallrPl+eaG+lP+ lcl|NCBI__GCF_000745425.1:WP_034997207.1 73 lgDAAPRLLDASTAHRTAPGWTYGFPELTKGQAEAIAKAPRVGNPGCYATGAIALLRPLTEAGLLPSTA 141 226899*************************************************************** PP TIGR01851 138 PvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfa 206 v+i+avsGysGGGk++ia+ye + af +y+l l+hkh+pe++ +++l ++PiftP+vG+f lcl|NCBI__GCF_000745425.1:WP_034997207.1 142 SVSIHAVSGYSGGGKTMIAAYEA-----GTAPAFEAYALGLGHKHVPEIMAYGQLQNRPIFTPSVGNFR 205 **********************2.....334689*********************************** PP TIGR01851 207 qGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvf 275 qG+lv ipl l l +k+ +d++++l+ +y+G ++v+ +++a+ + l++q+ln+tn+lelfv lcl|NCBI__GCF_000745425.1:WP_034997207.1 206 QGMLVFIPLFLDSLPQKPGRKDLAAVLQAHYAGSRHVHTR-MEEAP----ERLEPQALNDTNELELFVC 269 *************************************975.56665....578**************** PP TIGR01851 276 gsddgerallvarldnlGkGasGaavqnlnialGl 310 g ++g++++l+arldnlGkGasGaa+qn +++lGl lcl|NCBI__GCF_000745425.1:WP_034997207.1 270 GPEEGRQVVLAARLDNLGKGASGAALQNTELMLGL 304 **********************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (306 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 10.96 // [ok]
This GapMind analysis is from Apr 10 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