Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_010530711.1 ON01_RS09045 type I glutamate--ammonia ligase
Query= BRENDA::P12425 (444 letters) >NCBI__GCF_000224785.1:WP_010530711.1 Length = 445 Score = 725 bits (1871), Expect = 0.0 Identities = 342/440 (77%), Positives = 395/440 (89%) Query: 5 TREDIEKLVKEENVKYIRLQFTDILGTIKNVEIPVSQLGKALDNKVMFDGSSIEGFVRIE 64 TRE I K + EENV++IRLQFTD+LG IKNVEIP+SQL KALDNK+MFDGSSIEGFVRIE Sbjct: 6 TREQIMKRIDEENVRFIRLQFTDMLGNIKNVEIPLSQLDKALDNKMMFDGSSIEGFVRIE 65 Query: 65 ESDMYLYPDLNTFVIFPWTAEKGKVARFICDIYNPDGTPFEGDPRNNLKRILKEMEDLGF 124 ESDMYL PDL++FV+FPWT+EKGKVARFICDIYNPDGTPF G PR NLKR L++ME+LGF Sbjct: 66 ESDMYLQPDLDSFVVFPWTSEKGKVARFICDIYNPDGTPFAGCPRYNLKRKLQKMEELGF 125 Query: 125 SDFNLGPEPEFFLFKLDEKGEPTLELNDKGGYFDLAPTDLGENCRRDIVLELEEMGFEIE 184 + FN+G EPEFFLFKLDEKG+P++ELND GGYFDLAPTDLGENCRRDIVLELEEMGFEIE Sbjct: 126 NAFNIGTEPEFFLFKLDEKGQPSMELNDHGGYFDLAPTDLGENCRRDIVLELEEMGFEIE 185 Query: 185 ASHHEVAPGQHEIDFKYAGAVRSCDDIQTFKLVVKTIARKHGLHATFMPKPLFGVNGSGM 244 ASHHE APGQHEIDFKY+ AV+ DDIQTFKLVV+TIARKH LHATFMPKPLFGVNGSGM Sbjct: 186 ASHHEGAPGQHEIDFKYSDAVKHADDIQTFKLVVRTIARKHNLHATFMPKPLFGVNGSGM 245 Query: 245 HCNLSLFKNGVNAFFDENADLQLSETAKHFIAGIVKHATSFTAVTNPTVNSYKRLVPGYE 304 H N+SLF+NG NAFFD++ ++QLS+ A F AG++KHAT+FTAVTNPTVNSYKRLVPGYE Sbjct: 246 HVNMSLFRNGENAFFDKDGEMQLSDVAYQFTAGVIKHATNFTAVTNPTVNSYKRLVPGYE 305 Query: 305 APCYVAWSAQNRSPLIRIPASRGISTRVEVRSVDPAANPYLALSVLLAAGLDGIKNKLEA 364 APCYVAWS NRSPL+RIP SRG+STR+EVRSVDPAANPY+A+SVLLA+GLDG++NKL Sbjct: 306 APCYVAWSGTNRSPLVRIPYSRGLSTRIEVRSVDPAANPYMAMSVLLASGLDGVENKLTP 365 Query: 365 PAPIDRNIYVMSKEERMENGIVDLPATLAEALEEFKSNEVMVKALGEHLFEHFIEAKEIE 424 P +D+NIY M K+ER ENG+ DLPATL +ALE + +E +V+ALGEHL+EHF+EAK IE Sbjct: 366 PESVDQNIYDMDKKEREENGVKDLPATLMDALEVMQQDETIVEALGEHLYEHFVEAKTIE 425 Query: 425 WDMFRTQVHPWEREQYMSQY 444 WD+FRT VHPWEREQY++ Y Sbjct: 426 WDLFRTTVHPWEREQYLTTY 445 Lambda K H 0.319 0.137 0.406 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: 710 Number of extensions: 20 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: 444 Length of database: 445 Length adjustment: 32 Effective length of query: 412 Effective length of database: 413 Effective search space: 170156 Effective search space used: 170156 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: 51 (24.3 bits)
Align candidate WP_010530711.1 ON01_RS09045 (type I glutamate--ammonia ligase)
to HMM TIGR00653 (glnA: glutamine synthetase, type I (EC 6.3.1.2))
# 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/TIGR00653.hmm # target sequence database: /tmp/gapView.117851.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00653 [M=462] Accession: TIGR00653 Description: GlnA: glutamine synthetase, type I 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-181 590.2 0.3 9.1e-180 584.2 0.3 2.0 1 NCBI__GCF_000224785.1:WP_010530711.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010530711.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 584.2 0.3 9.1e-180 9.1e-180 1 461 [. 8 442 .. 8 443 .. 0.98 Alignments for each domain: == domain 1 score: 584.2 bits; conditional E-value: 9.1e-180 TIGR00653 1 eevlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlv 73 e+++k ++eenv+f++l+f+D+ G +k+veip+s+l+ +al+++++FDgss+eGf++ieesD++l+pd++++v NCBI__GCF_000224785.1:WP_010530711.1 8 EQIMKRIDEENVRFIRLQFTDMLGNIKNVEIPLSQLD-KALDNKMMFDGSSIEGFVRIEESDMYLQPDLDSFV 79 68999*******************************8.9********************************** PP TIGR00653 74 ivPfraek..vlrvicdvyepvtkepyerdpRsiakraeeelktklgdevyfGpEaEFflfdkvefkeasnss 144 ++P+++ek v+r+icd+y+p +++p+ ++pR+++kr ++++++ + +++G+E+EFflf+ +e+++ NCBI__GCF_000224785.1:WP_010530711.1 80 VFPWTSEKgkVARFICDIYNP-DGTPFAGCPRYNLKRKLQKMEELGFNAFNIGTEPEFFLFKLDEKGQP---- 147 ******9999***********.********************99999999************9999955.... PP TIGR00653 145 flevdseegewnreveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidi 217 +++++++ggYfd++p+D +++rr++vl+lee+g+e+e+sHHE a++q+Eid+ NCBI__GCF_000224785.1:WP_010530711.1 148 --------------------SMELNDHGGYFDLAPTDLGENCRRDIVLELEEMGFEIEASHHEGAPGQHEIDF 200 ....................67899************************************************ PP TIGR00653 218 kfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetal 290 k++++vk+aD+i+++K+vv+++a+kh ++atFmpKplfg ngsGmHv++sl+++gen+f +++g ++Ls+ a NCBI__GCF_000224785.1:WP_010530711.1 201 KYSDAVKHADDIQTFKLVVRTIARKHNLHATFMPKPLFGVNGSGMHVNMSLFRNGENAFFDKDGEMQLSDVAY 273 ****************************************************************999****** PP TIGR00653 291 yyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpY 363 + +G++kHa+ ++A+tnptvnsYkRLvpGyEAP+y+a+s nRs+l+RiP+s+ + ++RiEvRs+Dp+anpY NCBI__GCF_000224785.1:WP_010530711.1 274 QFTAGVIKHATNFTAVTNPTVNSYKRLVPGYEAPCYVAWSGTNRSPLVRIPYSR-GLSTRIEVRSVDPAANPY 345 ******************************************************.****************** PP TIGR00653 364 LafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdkevlkevlgeeliea 436 +a+++ll+ gldG++nk++p+e +d+n+y+++++e++e+G+++lp++L +al+ +++d e++ e+lge+l+e+ NCBI__GCF_000224785.1:WP_010530711.1 346 MAMSVLLASGLDGVENKLTPPESVDQNIYDMDKKEREENGVKDLPATLMDALEVMQQD-ETIVEALGEHLYEH 417 **********************************************************.************** PP TIGR00653 437 fielkrkEveelrlkvhpvElekyl 461 f+e+k+ E++ +r++vhp+E e+yl NCBI__GCF_000224785.1:WP_010530711.1 418 FVEAKTIEWDLFRTTVHPWEREQYL 442 ************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (445 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: 13.39 // [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