Alignments for a candidate for glnA in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Shewanella loihica PV-4

Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate 5211138 Shew_3554 glutamine synthetase (RefSeq)

Query= CharProtDB::CH_024014
         (469 letters)



>FitnessBrowser__PV4:5211138
          Length = 469

 Score =  751 bits (1938), Expect = 0.0
 Identities = 363/469 (77%), Positives = 408/469 (86%)

Query: 1   MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60
           MS E VL  L E EVKFVDLRFTDTKGKEQHV+IPAHQV+A+FFE+GKMFDGSSI GWKG
Sbjct: 1   MSVESVLQQLEELEVKFVDLRFTDTKGKEQHVSIPAHQVDADFFEDGKMFDGSSIAGWKG 60

Query: 61  INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTG 120
           INESDMVLMPD +T V+DPF  ++T +IRCDILEPGT+ GYDRDPRSIAK+AE+Y+ STG
Sbjct: 61  INESDMVLMPDPTTFVLDPFTEETTALIRCDILEPGTMTGYDRDPRSIAKKAEEYMVSTG 120

Query: 121 IADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGY 180
           IADTVL GPEPEFFLFDD++FG+ +SG  V +D  E AWNS T YE GN GHRP VKGGY
Sbjct: 121 IADTVLIGPEPEFFLFDDVKFGTDMSGCFVKLDAKEAAWNSGTHYEDGNTGHRPFVKGGY 180

Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240
           FPV PVDS+QD+RS MCLV+E+MG VVEAHHHEVATAGQNE+ATRFN +T+KADEIQI K
Sbjct: 181 FPVAPVDSSQDLRSAMCLVLEEMGQVVEAHHHEVATAGQNEIATRFNKLTEKADEIQILK 240

Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIG 300
           YVVHN+AH +GKTATFMPKP+ GDNGSGMH H SL+K+GVNLF+GDKYAGLSE ALYYIG
Sbjct: 241 YVVHNMAHAYGKTATFMPKPIVGDNGSGMHVHQSLAKDGVNLFSGDKYAGLSETALYYIG 300

Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVR 360
           G+IKHA+A+NA  NP+TNSYKRLVP +EAPVMLAYSARNRSASIRIPVV SPKARRIE R
Sbjct: 301 GIIKHARALNAFTNPSTNSYKRLVPHFEAPVMLAYSARNRSASIRIPVVPSPKARRIETR 360

Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420
           FPDP ANPYL FAALLMAGLDGI+NKIHPGEAMDK+LYDLP EEA EIPQVA SLE AL 
Sbjct: 361 FPDPTANPYLAFAALLMAGLDGIQNKIHPGEAMDKDLYDLPAEEAAEIPQVATSLENALE 420

Query: 421 ELDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
            LD DREFL  GGVF+D+ ID+YIAL+  E ++V  T HP EFELYYS+
Sbjct: 421 NLDADREFLTKGGVFSDDFIDSYIALKTAEAEKVARTTHPAEFELYYSL 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: 783
Number of extensions: 19
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 5211138 Shew_3554 (glutamine synthetase (RefSeq))
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.9567.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   7.8e-211  686.6   0.0   8.9e-211  686.4   0.0    1.0  1  lcl|FitnessBrowser__PV4:5211138  Shew_3554 glutamine synthetase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211138  Shew_3554 glutamine synthetase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.4   0.0  8.9e-211  8.9e-211       2     462 .]       5     468 ..       4     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 686.4 bits;  conditional E-value: 8.9e-211
                        TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvivPfra 79 
                                      +vl+ l+e +vkfvdlrf+D+kGk+++v+ip+++++++++e+g++FDgss+ G+k+i+esD++l+pdp t+v +Pf++
  lcl|FitnessBrowser__PV4:5211138   5 SVLQQLEELEVKFVDLRFTDTKGKEQHVSIPAHQVDADFFEDGKMFDGSSIAGWKGINESDMVLMPDPTTFVLDPFTE 82 
                                      6889999*********************************************************************** PP

                        TIGR00653  80 ekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdseegewn 156
                                      e+++ ++cd+ ep t++ y+rdpRsiak+aee++  t+++d+v +GpE+EFflfd+v+f++ ++  f+++d++e++wn
  lcl|FitnessBrowser__PV4:5211138  83 ETTALIRCDILEPGTMTGYDRDPRSIAKKAEEYMVsTGIADTVLIGPEPEFFLFDDVKFGTDMSGCFVKLDAKEAAWN 160
                                      **********************************99****************************************** PP

                        TIGR00653 157 ..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklvkaaDeivl 231
                                        +++e gn+g+++  kggYf+v+pvD+ +d+r+ ++l+lee+g  ve++HHEvata q+Ei+++f+kl+++aDei++
  lcl|FitnessBrowser__PV4:5211138 161 sgTHYEDGNTGHRPFVKGGYFPVAPVDSSQDLRSAMCLVLEEMGQVVEAHHHEVATAgQNEIATRFNKLTEKADEIQI 238
                                      9999************************************************************************** PP

                        TIGR00653 232 yKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaAltnp 309
                                      +Kyvv+n+a+ +GktatFmpKp++gdngsGmHvh+sl kdg nlf+g++ yagLsetalyyigGi+kHa+al+A+tnp
  lcl|FitnessBrowser__PV4:5211138 239 LKYVVHNMAHAYGKTATFMPKPIVGDNGSGMHVHQSLAKDGVNLFSGDK-YAGLSETALYYIGGIIKHARALNAFTNP 315
                                      *************************************************.**************************** PP

                        TIGR00653 310 tvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepl 387
                                      ++nsYkRLvp +EAPv+laysa+nRsa+iRiP++ +pka+RiE R+pDp+anpYLafaallmAgldGi+nki+pge++
  lcl|FitnessBrowser__PV4:5211138 316 STNSYKRLVPHFEAPVMLAYSARNRSASIRIPVVPSPKARRIETRFPDPTANPYLAFAALLMAGLDGIQNKIHPGEAM 393
                                      ****************************************************************************** PP

                        TIGR00653 388 dknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462
                                      dk+ly+l+ ee++e  i+q+++sLe+al++l++d+  +++++v+++++i+++i+lk++E e++  + hp E+e y++
  lcl|FitnessBrowser__PV4:5211138 394 DKDLYDLPAEEAAE--IPQVATSLENALENLDADRefLTKGGVFSDDFIDSYIALKTAEAEKVARTTHPAEFELYYS 468
                                      **************..*******************888999**********************************95 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.54
//
[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