Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate YP_004143601.1 Mesci_4441 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Smeli:SMc01801 (310 letters) >NCBI__GCF_000185905.1:YP_004143601.1 Length = 308 Score = 322 bits (826), Expect = 5e-93 Identities = 170/311 (54%), Positives = 214/311 (68%), Gaps = 8/311 (2%) Query: 1 MKPKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPD 60 MKPKIFIDGEHGTTGLQIR +A R DLE++SIP R+ A R + LN+AD+AILCLPD Sbjct: 1 MKPKIFIDGEHGTTGLQIRALLAERGDLEIISIPTERRKETAARAEFLNAADVAILCLPD 60 Query: 61 DASREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPT 120 DA++E+V+++A N+ R+ID STAHRVA WAYGFAEMDK Q + I A+ VANPGC+P Sbjct: 61 DAAKESVSLIA-NDTTRVIDASTAHRVAEGWAYGFAEMDKDQAKAIASAKRVANPGCWPQ 119 Query: 121 GAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFL-YGLT 179 G IA +RPL AG+LP +P+TVN +SGY+GGG+ MI +D A FL YGLT Sbjct: 120 GPIATLRPLVTAGLLPADFPITVNGISGYSGGGRPMI----EDYVAKGEDASEFLPYGLT 175 Query: 180 LKHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHY 239 L+HKHVPE++ + L P+ P+VG FAQGMI VPL L L T +H A+ DH+ Sbjct: 176 LQHKHVPELRAYARLSHDPIMQPAVGNFAQGMITVVPLQLGGLDHVPTGAELHAAIADHF 235 Query: 240 AG--QSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGAS 297 A +VEV P S ++ ID G++ MK++VF A L+A+ DNLGKGAS Sbjct: 236 AAIKGGVVEVAPYAHSERMPEIDPEIYNGTNRMKVYVFANDKRAQALLLAVYDNLGKGAS 295 Query: 298 GAAVQNMDLML 308 GAAVQNMDLML Sbjct: 296 GAAVQNMDLML 306 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: 305 Number of extensions: 15 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: 308 Length adjustment: 27 Effective length of query: 283 Effective length of database: 281 Effective search space: 79523 Effective search space used: 79523 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 YP_004143601.1 Mesci_4441 (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.31455.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-129 417.0 0.0 2.8e-129 416.8 0.0 1.0 1 lcl|NCBI__GCF_000185905.1:YP_004143601.1 Mesci_4441 N-acetyl-gamma-glutam Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185905.1:YP_004143601.1 Mesci_4441 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 416.8 0.0 2.8e-129 2.8e-129 1 310 [] 2 308 .] 2 308 .] 0.97 Alignments for each domain: == domain 1 score: 416.8 bits; conditional E-value: 2.8e-129 TIGR01851 1 kpkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslv 69 kpk+fidGe GttGlqir laer dle++si +++rk++++ra++lnaadvailclpddaa+e+vsl+ lcl|NCBI__GCF_000185905.1:YP_004143601.1 2 KPKIFIDGEHGTTGLQIRALLAERGDLEIISIPTERRKETAARAEFLNAADVAILCLPDDAAKESVSLI 70 79******************************************************************* PP TIGR01851 70 dnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfP 138 n t+++dasta+r+ae+w+yGf+e++ +q + ia+akrvanPGc++ g ia lrPlv+aG+lPadfP lcl|NCBI__GCF_000185905.1:YP_004143601.1 71 ANDTTRVIDASTAHRVAEGWAYGFAEMDKDQAKAIASAKRVANPGCWPQGPIATLRPLVTAGLLPADFP 139 ********************************************************************* PP TIGR01851 139 vtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaq 207 +t+n++sGysGGG+ +i++y + + + f +ygl+l+hkh+pe+r +++l + Pi+ PavG+faq lcl|NCBI__GCF_000185905.1:YP_004143601.1 140 ITVNGISGYSGGGRPMIEDYVAKGE---DASEFLPYGLTLQHKHVPELRAYARLSHDPIMQPAVGNFAQ 205 ********************94433...3569************************************* PP TIGR01851 208 GllveiplhlaeldskvsaedihkalaeyykGek..fvkvaelddaellddtildaqglngtnrlelfv 274 G++ +pl+l ld ++++++h+a+a++++ k v+va+ +++e + +d++ ngtnr++++v lcl|NCBI__GCF_000185905.1:YP_004143601.1 206 GMITVVPLQLGGLDHVPTGAELHAAIADHFAAIKggVVEVAPYAHSERM--PEIDPEIYNGTNRMKVYV 272 ******************************9865448**********76..789*************** PP TIGR01851 275 fgsddgerallvarldnlGkGasGaavqnlnialGl 310 f++d+ +all a dnlGkGasGaavqn++++lGl lcl|NCBI__GCF_000185905.1:YP_004143601.1 273 FANDKRAQALLLAVYDNLGKGASGAAVQNMDLMLGL 308 ***********************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (308 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: 7.09 // [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