Alignments for a candidate for glnA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Dyella japonica UNC79MFTsu3.2

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate N515DRAFT_3024 N515DRAFT_3024 L-glutamine synthetase (EC 6.3.1.2)

Query= BRENDA::P0A1P6
         (469 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3024
          Length = 469

 Score =  644 bits (1661), Expect = 0.0
 Identities = 306/469 (65%), Positives = 367/469 (78%)

Query: 1   MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60
           M A+ VL ++ EH+V+FVDLRF D  GK  HVT PAH ++   FE+GKMFDGSSI GWKG
Sbjct: 1   MPAQKVLDLIQEHDVEFVDLRFADMLGKHHHVTFPAHTIDESTFEDGKMFDGSSIAGWKG 60

Query: 61  INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATG 120
           INESDM+L+PD  TA +DPF   + L++ CD+LEP T+Q Y RDPRSIAKR E +L++TG
Sbjct: 61  INESDMILLPDPDTAYLDPFSGHTQLVLHCDVLEPSTMQAYGRDPRSIAKRGEAFLKSTG 120

Query: 121 IADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGY 180
           IADT  FGPEPEFF+FD +R+   +      I   E +W+S  KYE  N GHRPGVKGGY
Sbjct: 121 IADTAFFGPEPEFFIFDSVRWQNDMGRVFYEIGSEEASWSSRYKYEDNNTGHRPGVKGGY 180

Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240
           FPV PVDS  D+R++MC V+E +G VVE HHHEVA AGQ E+  +FNT+ +KADE+   K
Sbjct: 181 FPVSPVDSLGDLRADMCKVLESLGQVVEVHHHEVANAGQCEIGVKFNTLVQKADELMTMK 240

Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIG 300
           YV+ NVAH+ GKTATFMPKP+ GDNGSGMH H SLAK+G NLF+GD Y GLS+ AL+YIG
Sbjct: 241 YVIKNVAHQNGKTATFMPKPIVGDNGSGMHVHQSLAKDGKNLFAGDLYGGLSQTALWYIG 300

Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVR 360
           G+ KHAKAINA AN TTNSYKRLVPG+EAPVMLAYSARNRSAS RIP V++PK RRIEVR
Sbjct: 301 GIFKHAKAINAFANSTTNSYKRLVPGFEAPVMLAYSARNRSASCRIPYVSNPKGRRIEVR 360

Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420
           FPDP  + YL F AL+MAGLDGI NKI PG   DK+LYDLPPEE K IPQV  SL++AL 
Sbjct: 361 FPDPMNSGYLVFTALMMAGLDGIINKIDPGAPADKDLYDLPPEEEKNIPQVCSSLDQALE 420

Query: 421 ALDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
           ALD DR+FLKAGGVFTD+ IDAYIAL+ +E  R R + HP+EF++YY++
Sbjct: 421 ALDKDRDFLKAGGVFTDDFIDAYIALKMQEVTRYRASTHPLEFQMYYAL 469


Lambda     K      H
   0.318    0.136    0.401 

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: 748
Number of extensions: 22
Number of successful extensions: 2
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: 469
Length of database: 469
Length adjustment: 33
Effective length of query: 436
Effective length of database: 436
Effective search space:   190096
Effective search space used:   190096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate N515DRAFT_3024 N515DRAFT_3024 (L-glutamine synthetase (EC 6.3.1.2))
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.7832.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.4e-198  644.9   0.0   3.8e-198  644.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3024  N515DRAFT_3024 L-glutamine synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3024  N515DRAFT_3024 L-glutamine synthetase (EC 6.3.1.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  644.8   0.0  3.8e-198  3.8e-198       2     461 ..       5     467 ..       4     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 644.8 bits;  conditional E-value: 3.8e-198
                                    TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkp 67 
                                                  +vl+l++e++v+fvdlrf+D+ Gk ++v++p+++++e+++e+g++FDgss+ G+k+i+esD++l p
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3024   5 KVLDLIQEHDVEFVDLRFADMLGKHHHVTFPAHTIDESTFEDGKMFDGSSIAGWKGINESDMILLP 70 
                                                  78999************************************************************* PP

                                    TIGR00653  68 dpetlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflf 132
                                                  dp+t+  +Pf+ ++ l++ cdv ep t++ y rdpRsiakr e  lk t+++d+++fGpE+EFf+f
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3024  71 DPDTAYLDPFSGHTQLVLHCDVLEPSTMQAYGRDPRSIAKRGEAFLKsTGIADTAFFGPEPEFFIF 136
                                                  ****************************************************************** PP

                                    TIGR00653 133 dkvefkeasnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlalee 196
                                                  d+v+ ++ + + f+e+ see++w+   ++e +n+g+++  kggYf+v pvD++ d+r +++++le+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3024 137 DSVRWQNDMGRVFYEIGSEEASWSsrYKYEDNNTGHRPGVKGGYFPVSPVDSLGDLRADMCKVLES 202
                                                  ************************86678888********************************** PP

                                    TIGR00653 197 lglevevsHHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsG 261
                                                  lg  vev+HHEva+a q Ei++kf++lv++aDe++++Kyv+knva+++GktatFmpKp++gdngsG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3024 203 LGQVVEVHHHEVANAgQCEIGVKFNTLVQKADELMTMKYVIKNVAHQNGKTATFMPKPIVGDNGSG 268
                                                  ****************************************************************** PP

                                    TIGR00653 262 mHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvyl 327
                                                  mHvh+sl kdg+nlfag+  y gLs+tal+yigGi kHaka++A++n+t+nsYkRLvpG+EAPv+l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3024 269 MHVHQSLAKDGKNLFAGDL-YGGLSQTALWYIGGIFKHAKAINAFANSTTNSYKRLVPGFEAPVML 333
                                                  *******************.********************************************** PP

                                    TIGR00653 328 aysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlye 393
                                                  aysa+nRsa+ RiP+++npk++RiEvR+pDp    YL f+al+mAgldGi nkidpg+p dk+ly+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3024 334 AYSARNRSASCRIPYVSNPKGRRIEVRFPDPMNSGYLVFTALMMAGLDGIINKIDPGAPADKDLYD 399
                                                  ****************************************************************** PP

                                    TIGR00653 394 lseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvEl 457
                                                  l++ee k+  i+q+ +sL++al++l++d+  +++++v+++++i+a+i+lk++Ev ++r + hp+E+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3024 400 LPPEEEKN--IPQVCSSLDQALEALDKDRdfLKAGGVFTDDFIDAYIALKMQEVTRYRASTHPLEF 463
                                                  ******99..*******************888999******************************* PP

                                    TIGR00653 458 ekyl 461
                                                  ++y+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3024 464 QMYY 467
                                                  ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (469 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: 00:00:00.02
# Mc/sec: 8.76
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis