GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glnA in Lentibacillus jeotgali Grbi

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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