Align N-succinylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_055434902.1 ASC41_RS01635 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Pedo557:CA265_RS18540 (326 letters) >NCBI__GCF_001418085.1:WP_055434902.1 Length = 327 Score = 406 bits (1043), Expect = e-118 Identities = 202/325 (62%), Positives = 243/325 (74%) Query: 2 KIKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFVSD 61 K++ GIIGGAGYT GE++R+L+NHP I F+ STSNAGN IS VH DLIG TDL+F S Sbjct: 3 KLEIGIIGGAGYTAGELIRLLLNHPKTNINFIYSTSNAGNKISKVHQDLIGSTDLEFSSQ 62 Query: 62 IPQDIDVLFLCVGHGDAKKFLTANPIKDNIKIIDLSQDFRLHANASFSTKDFVYGLPELN 121 I +++VLFLC+GHG++K FL N KIIDLS DFRL + F +K FVYGLPELN Sbjct: 63 INSEVEVLFLCLGHGNSKAFLVKNSFSAETKIIDLSNDFRLTKDTIFDSKTFVYGLPELN 122 Query: 122 RDKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNEVHINATTGSTGAGQSLSTTSHFSW 181 ++ IK A IANPGCFA+ IQL LLPLA ++QN+VHINA TG+TGAG SLS T+HF+W Sbjct: 123 KEAIKKANYIANPGCFASAIQLALLPLAEAEVLQNDVHINAVTGATGAGTSLSATTHFTW 182 Query: 182 RNNNLSIYKAFEHQHLNEISESLLQLQPSISEALNFIPQRGAFTRGILAAMYLESDLSLE 241 R+NN S YKAF HQHL EI++S+ LQ + +NF+P RG F+RGI A MY + SLE Sbjct: 183 RDNNFSHYKAFTHQHLGEINQSVKLLQSDFNSDINFMPNRGDFSRGIFATMYTKFKGSLE 242 Query: 242 EAQNIYEAYYSAHPFTHVSRKNIDLKQVVNTNKALVHLEKHGGKLFIISIIDNLLKGASG 301 +A+ +Y A+Y FT VS I LKQVVNTNK ++HL KH KL + SIIDNLLKGASG Sbjct: 243 DAKALYNAFYKDAAFTVVSDDEIHLKQVVNTNKCILHLHKHEDKLLVTSIIDNLLKGASG 302 Query: 302 QAVQNMNLMFGLDETAGLKLKAAYF 326 QAVQNMNLMFG DET GLKLKA YF Sbjct: 303 QAVQNMNLMFGFDETEGLKLKATYF 327 Lambda K H 0.319 0.135 0.387 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: 338 Number of extensions: 6 Number of successful extensions: 1 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: 326 Length of database: 327 Length adjustment: 28 Effective length of query: 298 Effective length of database: 299 Effective search space: 89102 Effective search space used: 89102 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_055434902.1 ASC41_RS01635 (N-acetyl-gamma-glutamyl-phosphate reductase)
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.1906557.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-97 312.0 0.1 3.7e-97 311.5 0.1 1.1 1 NCBI__GCF_001418085.1:WP_055434902.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001418085.1:WP_055434902.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 311.5 0.1 3.7e-97 3.7e-97 2 342 .. 5 324 .. 4 326 .. 0.93 Alignments for each domain: == domain 1 score: 311.5 bits; conditional E-value: 3.7e-97 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflA 74 +++i+G+ GYt++eL+rll +Hp+++++ ++s+++ag+k+s+vh+ l g +dl++++ +i++e++v+fl+ NCBI__GCF_001418085.1:WP_055434902.1 5 EIGIIGGAGYTAGELIRLLLNHPKTNINFIYSTSNAGNKISKVHQDLIGSTDLEFSS----QINSEVEVLFLC 73 699************************************************999995....57789******* PP TIGR01850 75 lphgvsael.vpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146 l hg s+++ v++ ++++k+idlS dfRl++ +++ +++vYGlpEln+e+ikka++ian NCBI__GCF_001418085.1:WP_055434902.1 74 LGHGNSKAFlVKNSFSAETKIIDLSNDFRLTKDTIFD------------SKTFVYGLPELNKEAIKKANYIAN 134 ******986277888999*************886553............3689******************** PP TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219 PGC+a a++Lal Pl+++++++++ + ++a++G +gAG++ s++++f+ +++n++ Yk+++H+H Ei+q+++ NCBI__GCF_001418085.1:WP_055434902.1 135 PGCFASAIQLALLPLAEAEVLQND-VHINAVTGATGAGTSLSATTHFTWRDNNFSHYKAFTHQHLGEINQSVK 206 *********************985.************************************************ PP TIGR01850 220 klaek.kvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnf 291 l+++ + ++f+p+ +++rGi+at+y+k+k +l e+ ++ly+++Y+d f v + +e+ ++k+v+ +n NCBI__GCF_001418085.1:WP_055434902.1 207 LLQSDfNSDINFMPNRGDFSRGIFATMYTKFKGSL--EDAKALYNAFYKDAAFTVVSD-DEI-HLKQVVNTNK 275 999887777************************66..9999************99998.555.9********* PP TIGR01850 292 vdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklp 342 + + ++ +e ++++v+s iDNL+KGa+gqAvqn+Nlm+gfdetegL+ ++ NCBI__GCF_001418085.1:WP_055434902.1 276 CILHLHKHE--DKLLVTSIIDNLLKGASGQAVQNMNLMFGFDETEGLKLKA 324 *99888777..89**********************************9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (327 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: 00:00:00.00 # Mc/sec: 19.26 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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