Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_041565990.1 NPUN_RS07920 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Korea:Ga0059261_0351 (310 letters) >NCBI__GCF_000020025.1:WP_041565990.1 Length = 322 Score = 295 bits (754), Expect = 1e-84 Identities = 155/317 (48%), Positives = 207/317 (65%), Gaps = 13/317 (4%) Query: 5 VFIDGAAGTTGLEIRERLATRSDISLIGLDDAHRKDAGKRAEAINSADFVILCLPDDAAR 64 +FIDG +GTTGL+I RL R DI L+ ++ + RKDA +RA+ IN+ D VILCLPDDAAR Sbjct: 6 IFIDGESGTTGLQIYSRLNQRDDIELVSIEASKRKDASERAKLINTVDVVILCLPDDAAR 65 Query: 65 EAVALIANDTTRVIDASTAHRVADGWTYGFAELEPAQAAAIAEARYVSNPGCWPTGFLAL 124 EAV+L+++ T +++DAS+AHR A+GW YGF EL P Q IA A+YVSNPGC+PTGFLA Sbjct: 66 EAVSLVSSTTVKILDASSAHRTANGWVYGFPELNPGQREKIASAQYVSNPGCYPTGFLAC 125 Query: 125 VRPLVRAGLIPPDWVLTAGGASGYSGGGKSMIAEFE-------DGSEPTGFRAYGLDLEH 177 +RPL+ GL ++ +T SGYSGGGK++I ++ G F YGL H Sbjct: 126 IRPLIAKGLFKSNFPITVNAVSGYSGGGKNLIKQYHTFHEQQAGGESLYPFGIYGLQFGH 185 Query: 178 KHLPEMQKHARIDHAPIFQPAVARSYRGMLIEVPLPLQMLPRKPAPAQIEQVLADAYRDS 237 KH+ EM ++ + P+F P+V +GML++VPLPL L P+ I + +AD Y+ Sbjct: 186 KHVKEMHYYSGLASPPLFVPSVGDFEQGMLVQVPLPLGTLDNPPSGEVIYEAIADYYQGE 245 Query: 238 PIVRVLPSDDVSLVR--IEDDA----GTDRLTIRVFGNAERGQARLVATLDNLGKGAGGA 291 V+V P D +L+R I DA GT+ + + VF N +A LVA LDNLGKGA GA Sbjct: 246 KFVQVAPFQDSTLLRDGIFLDAIAVNGTNIVQVFVFANDTTKEALLVARLDNLGKGASGA 305 Query: 292 AVQNLNIMAGFDQTAGL 308 A+QNLNIM GF + GL Sbjct: 306 AIQNLNIMLGFPEELGL 322 Lambda K H 0.319 0.136 0.400 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: 264 Number of extensions: 9 Number of successful extensions: 3 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: 322 Length adjustment: 27 Effective length of query: 283 Effective length of database: 295 Effective search space: 83485 Effective search space used: 83485 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 WP_041565990.1 NPUN_RS07920 (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.13935.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-159 514.7 0.0 4.9e-159 514.6 0.0 1.0 1 lcl|NCBI__GCF_000020025.1:WP_041565990.1 NPUN_RS07920 N-acetyl-gamma-glut Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020025.1:WP_041565990.1 NPUN_RS07920 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 514.6 0.0 4.9e-159 4.9e-159 1 309 [. 3 315 .. 3 316 .. 0.99 Alignments for each domain: == domain 1 score: 514.6 bits; conditional E-value: 4.9e-159 TIGR01851 1 kpkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslv 69 kpk+fidGe+GttGlqi++rl++rdd+el+si+++krkda+erakl+n++dv+ilclpddaareavslv lcl|NCBI__GCF_000020025.1:WP_041565990.1 3 KPKIFIDGESGTTGLQIYSRLNQRDDIELVSIEASKRKDASERAKLINTVDVVILCLPDDAAREAVSLV 71 79******************************************************************* PP TIGR01851 70 dnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfP 138 +++ +kildas+a+rta++wvyGfpel+++qrekia+a++v+nPGcy+tg++a++rPl+++G++ ++fP lcl|NCBI__GCF_000020025.1:WP_041565990.1 72 SSTTVKILDASSAHRTANGWVYGFPELNPGQREKIASAQYVSNPGCYPTGFLACIRPLIAKGLFKSNFP 140 ********************************************************************* PP TIGR01851 139 vtinavsGysGGGkaliakye...eesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGd 204 +t+navsGysGGGk+li++y+ e++a+ ++ ++f iygl+++hkh++em+ +sglas+P+f+P+vGd lcl|NCBI__GCF_000020025.1:WP_041565990.1 141 ITVNAVSGYSGGGKNLIKQYHtfhEQQAGGESLYPFGIYGLQFGHKHVKEMHYYSGLASPPLFVPSVGD 209 *******************988889999***************************************** PP TIGR01851 205 faqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaelldd.tildaqglngtnrlel 272 f+qG+lv++pl+l +ld+++s+e i +a+a+yy+Gekfv+va+++d++ll+d +lda ++ngtn++++ lcl|NCBI__GCF_000020025.1:WP_041565990.1 210 FEQGMLVQVPLPLGTLDNPPSGEVIYEAIADYYQGEKFVQVAPFQDSTLLRDgIFLDAIAVNGTNIVQV 278 ****************************************************7789************* PP TIGR01851 273 fvfgsddgerallvarldnlGkGasGaavqnlnialG 309 fvf++d +++allvarldnlGkGasGaa+qnlni+lG lcl|NCBI__GCF_000020025.1:WP_041565990.1 279 FVFANDTTKEALLVARLDNLGKGASGAAIQNLNIMLG 315 ************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.17 // [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