Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_012334742.1 M446_RS24185 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Korea:Ga0059261_0351 (310 letters) >NCBI__GCF_000019365.1:WP_012334742.1 Length = 315 Score = 302 bits (773), Expect = 8e-87 Identities = 162/303 (53%), Positives = 200/303 (66%), Gaps = 8/303 (2%) Query: 4 SVFIDGAAGTTGLEIRERLATRSDISLIGLDDAHRKDAGKRAEAINSADFVILCLPDDAA 63 SVFIDG AGTTGL IRERL +I+L L A RKD + + D V+LCLPDDAA Sbjct: 10 SVFIDGEAGTTGLGIRERLEPSHEITLRSLPPAQRKDPDAKRALLAEVDLVVLCLPDDAA 69 Query: 64 REAVAL---IANDTTRVIDASTAHRVADGWTYGFAELEPAQAAAIAEARYVSNPGCWPTG 120 +E VA+ + R++DASTAHRVA GWTYGFAEL P Q AA+ +R V+NPGC+PTG Sbjct: 70 KETVAMADALPGGGPRILDASTAHRVAPGWTYGFAELAPEQRAALRASRRVANPGCYPTG 129 Query: 121 FLALVRPLVRAGLIPPDWVLTAGGASGYSGGGKSMIAEFEDGSEPTGFRAYGLDLEHKHL 180 +AL+RPLV AGLIP D ++ SGYSGGG+ MI +EDG+ P F YGL HKHL Sbjct: 130 AIALLRPLVDAGLIPADHPISINAVSGYSGGGRKMIGAYEDGTAP-AFELYGLGFAHKHL 188 Query: 181 PEMQKHARIDHAPIFQPAVARSYRGMLIEVPLPLQMLPRKPAPAQIEQVLADAYRDSPIV 240 PE Q ++R+ PIF P+V +GML+ +PL L LP +P P +EQ LA Y +V Sbjct: 189 PETQAYSRLTRRPIFVPSVGNFRQGMLVSIPLHLDALPGRPHPGDLEQALAARYAGEELV 248 Query: 241 RVL--PSDDVSLVRIEDDA--GTDRLTIRVFGNAERGQARLVATLDNLGKGAGGAAVQNL 296 RV+ + R+E +A GTD L +RVFG+ GQA LVA LDNLGKGA GAAVQNL Sbjct: 249 RVVTGAEEGAHRERLEPEALNGTDGLELRVFGSDAHGQAVLVARLDNLGKGASGAAVQNL 308 Query: 297 NIM 299 +M Sbjct: 309 RLM 311 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: 300 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: 315 Length adjustment: 27 Effective length of query: 283 Effective length of database: 288 Effective search space: 81504 Effective search space used: 81504 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_012334742.1 M446_RS24185 (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.12791.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-123 396.1 0.0 6.5e-123 395.9 0.0 1.0 1 lcl|NCBI__GCF_000019365.1:WP_012334742.1 M446_RS24185 N-acetyl-gamma-glut Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019365.1:WP_012334742.1 M446_RS24185 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 395.9 0.0 6.5e-123 6.5e-123 2 309 .. 9 313 .. 8 314 .. 0.96 Alignments for each domain: == domain 1 score: 395.9 bits; conditional E-value: 6.5e-123 TIGR01851 2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd 70 p vfidGeaGttGl irerl +++ l s+ + +rkd+d++ ll +d ++lclpddaa+e+v++ d lcl|NCBI__GCF_000019365.1:WP_012334742.1 9 PSVFIDGEAGTTGLGIRERLEPSHEITLRSLPPAQRKDPDAKRALLAEVDLVVLCLPDDAAKETVAMAD 77 78*****************************************************************99 PP TIGR01851 71 n...pntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPad 136 + +ildasta+r+a++w+yGf+ela+eqr +++++rvanPGcy+tgaiallrPlv+aG++Pad lcl|NCBI__GCF_000019365.1:WP_012334742.1 78 AlpgGGPRILDASTAHRVAPGWTYGFAELAPEQRAALRASRRVANPGCYPTGAIALLRPLVDAGLIPAD 146 73224679************************************************************* PP TIGR01851 137 fPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdf 205 +P++inavsGysGGG+++i +ye+++ af ygl + hkhlpe++ +s+l+++Pif+P+vG+f lcl|NCBI__GCF_000019365.1:WP_012334742.1 147 HPISINAVSGYSGGGRKMIGAYEDGT-----APAFELYGLGFAHKHLPETQAYSRLTRRPIFVPSVGNF 210 ***********************554.....4579********************************** PP TIGR01851 206 aqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfv 274 qG+lv iplhl l +++ + d+++ala y+Ge+ v+v+ +++ + + l++++lngt+ lel v lcl|NCBI__GCF_000019365.1:WP_012334742.1 211 RQGMLVSIPLHLDALPGRPHPGDLEQALAARYAGEELVRVVTGAEEGAH-RERLEPEALNGTDGLELRV 278 *****************************************99998865.689**************** PP TIGR01851 275 fgsddgerallvarldnlGkGasGaavqnlnialG 309 fgsd+ ++a+lvarldnlGkGasGaavqnl ++l lcl|NCBI__GCF_000019365.1:WP_012334742.1 279 FGSDAHGQAVLVARLDNLGKGASGAAVQNLRLMLD 313 *********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (315 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: 00:00:00.01 # Mc/sec: 6.34 // [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