Alignments for a candidate for glnA in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Shewanella amazonensis SB2B

Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate 6939323 Sama_3416 glutamine synthetase (RefSeq)

Query= BRENDA::P0A1P6
         (469 letters)



>FitnessBrowser__SB2B:6939323
          Length = 469

 Score =  751 bits (1938), Expect = 0.0
 Identities = 364/469 (77%), Positives = 409/469 (87%)

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

Query: 61  INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATG 120
           INESDMVLMPDA+T V+DPF  ++T IIRCDILEPGT+ GYDRDPRSIAK+AE+YLRATG
Sbjct: 61  INESDMVLMPDATTFVLDPFTEETTAIIRCDILEPGTMTGYDRDPRSIAKKAEEYLRATG 120

Query: 121 IADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGY 180
           IADTVL GPEPEFFLFDD+RFG  +SG+ V ID  E AWNSST YE GN GHRP VKGGY
Sbjct: 121 IADTVLMGPEPEFFLFDDVRFGTDMSGTFVKIDAKEAAWNSSTSYEDGNTGHRPFVKGGY 180

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

Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIG 300
           YVVHN+AH +GKTATFMPKP+ GDNGSGMH H SLAK+G NLF+GDKY GLSE ALYYIG
Sbjct: 241 YVVHNMAHAYGKTATFMPKPIVGDNGSGMHVHQSLAKDGVNLFAGDKYGGLSETALYYIG 300

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

Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420
           FPDP ANPYL FAALLMAGLDGI+NKIHPG+AMDK+LYDLP EEA EIP VA SL+ AL 
Sbjct: 361 FPDPTANPYLGFAALLMAGLDGIQNKIHPGDAMDKDLYDLPAEEAAEIPTVAESLDVALA 420

Query: 421 ALDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469
           ALD DREFL  GGVF+++ ID+YI L+  E +RV  T HP+EFE+YYS+
Sbjct: 421 ALDADREFLTKGGVFSNDFIDSYIRLKTAEAERVNRTTHPLEFEMYYSL 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: 780
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 6939323 Sama_3416 (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.6975.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.3e-209  681.2   0.0   3.8e-209  681.0   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6939323  Sama_3416 glutamine synthetase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939323  Sama_3416 glutamine synthetase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  681.0   0.0  3.8e-209  3.8e-209       1     462 []       4     468 ..       4     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 681.0 bits;  conditional E-value: 3.8e-209
                         TIGR00653   1 eevlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvivPf 77 
                                       e+vlk lk+ +vkfvdlrf+D+kGk+++v+ip ++++++++e+g++FDgss+ G+k+i+esD++l+pd+ t+v +Pf
  lcl|FitnessBrowser__SB2B:6939323   4 ENVLKQLKDLEVKFVDLRFTDTKGKEQHVSIPTHQVDADFFEDGKMFDGSSIAGWKGINESDMVLMPDATTFVLDPF 80 
                                       578999*********************************************************************** PP

                         TIGR00653  78 raekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdseeg 153
                                       ++e++++++cd+ ep t++ y+rdpRsiak+aee+l+ t+++d+v +GpE+EFflfd+v+f++ ++ +f+++d++e+
  lcl|FitnessBrowser__SB2B:6939323  81 TEETTAIIRCDILEPGTMTGYDRDPRSIAKKAEEYLRaTGIADTVLMGPEPEFFLFDDVRFGTDMSGTFVKIDAKEA 157
                                       ***************************************************************************** PP

                         TIGR00653 154 ewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklvkaaD 227
                                       +wn  +++e gn+g+++  kggYf+v+pvD+ +d+r+ ++l+lee+g  ve++HHEvata q+Ei+++f++l+k+aD
  lcl|FitnessBrowser__SB2B:6939323 158 AWNssTSYEDGNTGHRPFVKGGYFPVAPVDSSQDLRSAMCLVLEEMGQVVEAHHHEVATAgQNEIATRFNTLTKKAD 234
                                       ***9999999******************************************************************* PP

                         TIGR00653 228 eivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHakala 304
                                       ei+++Kyvv+n+a+ +GktatFmpKp++gdngsGmHvh+sl kdg nlfag++ y gLsetalyyigGi+kHa+al+
  lcl|FitnessBrowser__SB2B:6939323 235 EIQILKYVVHNMAHAYGKTATFMPKPIVGDNGSGMHVHQSLAKDGVNLFAGDK-YGGLSETALYYIGGIIKHARALN 310
                                       *****************************************************.*********************** PP

                         TIGR00653 305 AltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknki 381
                                       A+tnp++nsYkRLvp +EAPv+laysa+nRsa+iRiP++ +pk++RiE R+pDp+anpYL faallmAgldGi+nki
  lcl|FitnessBrowser__SB2B:6939323 311 AFTNPSTNSYKRLVPHFEAPVMLAYSARNRSASIRIPVVPSPKGRRIETRFPDPTANPYLGFAALLMAGLDGIQNKI 387
                                       ***************************************************************************** PP

                         TIGR00653 382 dpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvE 456
                                       +pg+++dk+ly+l+ ee++e  i++++esL+ al +l++d+  +++++v+++++i+++i lk++E e+++ + hp+E
  lcl|FitnessBrowser__SB2B:6939323 388 HPGDAMDKDLYDLPAEEAAE--IPTVAESLDVALAALDADRefLTKGGVFSNDFIDSYIRLKTAEAERVNRTTHPLE 462
                                       ********************..*******************888999****************************** PP

                         TIGR00653 457 lekyld 462
                                       +e+y++
  lcl|FitnessBrowser__SB2B:6939323 463 FEMYYS 468
                                       ****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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.26
//
[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