Alignments for a candidate for glnA in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Shewanella oneidensis MR-1

Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate 203487 SO4410 glutamine synthetase, type I (NCBI ptt file)

Query= CharProtDB::CH_024014
         (469 letters)



>FitnessBrowser__MR1:203487
          Length = 469

 Score =  752 bits (1941), Expect = 0.0
 Identities = 364/469 (77%), Positives = 408/469 (86%)

Query: 1   MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60
           MS E VL  L E EVKFVDLRFTDTKGKEQHV+IP+HQV+A+FFE+GKMFDGSSI GWKG
Sbjct: 1   MSVESVLKQLEELEVKFVDLRFTDTKGKEQHVSIPSHQVDADFFEDGKMFDGSSIAGWKG 60

Query: 61  INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTG 120
           INESDMVLMPD +T V+DPF  ++T +IRCD+LEPGT+ GYDRDPRSIAK+AE+YLRSTG
Sbjct: 61  INESDMVLMPDPTTFVLDPFTEETTALIRCDVLEPGTMTGYDRDPRSIAKKAEEYLRSTG 120

Query: 121 IADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGY 180
           IADTVL GPEPEFFLFDD+RFG+ +SG  V ID  E AWNS T YEGGN GHRP VKGGY
Sbjct: 121 IADTVLVGPEPEFFLFDDVRFGTDMSGCFVKIDAKEAAWNSGTSYEGGNTGHRPFVKGGY 180

Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240
           FPV PVDS+QD+RS MCLV+E+MG VVEAHHHEVATAGQNE+ATRFNT+TKKADEIQI K
Sbjct: 181 FPVAPVDSSQDLRSAMCLVLEEMGQVVEAHHHEVATAGQNEIATRFNTLTKKADEIQILK 240

Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIG 300
           YVVHN+AH +GKTATFMPKP+ GDNGSGMH H SLSK+GVNLFAGDKYAGLSE ALYYIG
Sbjct: 241 YVVHNMAHAYGKTATFMPKPIVGDNGSGMHVHQSLSKDGVNLFAGDKYAGLSETALYYIG 300

Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVR 360
           G+IKHA+A+NA  NP+TNSYKRLVP +EAPVMLAYSARNRSASIRIPVV SPK RRIE R
Sbjct: 301 GIIKHARALNAFTNPSTNSYKRLVPHFEAPVMLAYSARNRSASIRIPVVPSPKGRRIETR 360

Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420
           FPDP ANPYL FAALLMAG+DGI+NKIHPGEAMDK+LYDLP EEA EIPQVA SLE AL 
Sbjct: 361 FPDPHANPYLGFAALLMAGIDGIQNKIHPGEAMDKDLYDLPAEEAAEIPQVATSLENALE 420

Query: 421 ELDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
            L  D EFL  GGVF+++ I +YIAL+  E +RV  T HP+EFE+YYS+
Sbjct: 421 NLQADHEFLTRGGVFSEDFIQSYIALKSAEAERVARTTHPLEFEMYYSL 469


Lambda     K      H
   0.318    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: 771
Number of extensions: 17
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: 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 203487 SO4410 (glutamine synthetase, type I (NCBI ptt file))
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.19357.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.6e-210  684.0   0.0   5.2e-210  683.9   0.0    1.0  1  lcl|FitnessBrowser__MR1:203487  SO4410 glutamine synthetase, typ


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203487  SO4410 glutamine synthetase, type I (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.9   0.0  5.2e-210  5.2e-210       2     462 .]       5     468 ..       4     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 683.9 bits;  conditional E-value: 5.2e-210
                       TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvivPfrae 80 
                                     +vlk l+e +vkfvdlrf+D+kGk+++v+ip ++++++++e+g++FDgss+ G+k+i+esD++l+pdp t+v +Pf++e
  lcl|FitnessBrowser__MR1:203487   5 SVLKQLEELEVKFVDLRFTDTKGKEQHVSIPSHQVDADFFEDGKMFDGSSIAGWKGINESDMVLMPDPTTFVLDPFTEE 83 
                                     6889999************************************************************************ PP

                       TIGR00653  81 kvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdseegewn.. 156
                                     +++ ++cdv ep t++ y+rdpRsiak+aee+l+ t+++d+v +GpE+EFflfd+v+f++ ++  f+++d++e++wn  
  lcl|FitnessBrowser__MR1:203487  84 TTALIRCDVLEPGTMTGYDRDPRSIAKKAEEYLRsTGIADTVLVGPEPEFFLFDDVRFGTDMSGCFVKIDAKEAAWNsg 162
                                     *****************************************************************************99 PP

                       TIGR00653 157 reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklvkaaDeivlyKy 234
                                     +++e+gn+g+++  kggYf+v+pvD+ +d+r+ ++l+lee+g  ve++HHEvata q+Ei+++f++l+k+aDei+++Ky
  lcl|FitnessBrowser__MR1:203487 163 TSYEGGNTGHRPFVKGGYFPVAPVDSSQDLRSAMCLVLEEMGQVVEAHHHEVATAgQNEIATRFNTLTKKADEIQILKY 241
                                     99***************************************************************************** PP

                       TIGR00653 235 vvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaAltnptvns 313
                                     vv+n+a+ +GktatFmpKp++gdngsGmHvh+sl+kdg nlfag++ yagLsetalyyigGi+kHa+al+A+tnp++ns
  lcl|FitnessBrowser__MR1:203487 242 VVHNMAHAYGKTATFMPKPIVGDNGSGMHVHQSLSKDGVNLFAGDK-YAGLSETALYYIGGIIKHARALNAFTNPSTNS 319
                                     **********************************************.******************************** PP

                       TIGR00653 314 YkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknly 392
                                     YkRLvp +EAPv+laysa+nRsa+iRiP++ +pk++RiE R+pDp anpYL faallmAg+dGi+nki+pge++dk+ly
  lcl|FitnessBrowser__MR1:203487 320 YKRLVPHFEAPVMLAYSARNRSASIRIPVVPSPKGRRIETRFPDPHANPYLGFAALLMAGIDGIQNKIHPGEAMDKDLY 398
                                     ******************************************************************************* PP

                       TIGR00653 393 elseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                     +l+ ee++e  i+q+++sLe+al++l++d+  ++ ++v++e++i+++i+lk +E e++  + hp+E+e+y++
  lcl|FitnessBrowser__MR1:203487 399 DLPAEEAAE--IPQVATSLENALENLQADHefLTRGGVFSEDFIQSYIALKSAEAERVARTTHPLEFEMYYS 468
                                     *********..*******************888999**********************************96 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.48
//
[ok]

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

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