Alignments for a candidate for glnA in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Trichormus variabilis ATCC 29413

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate WP_011317041.1 AVA_RS00740 type I glutamate--ammonia ligase

Query= SwissProt::P00964
         (474 letters)



>NCBI__GCF_000204075.1:WP_011317041.1
          Length = 474

 Score =  971 bits (2511), Expect = 0.0
 Identities = 469/474 (98%), Positives = 472/474 (99%)

Query: 1   MTTPQEVLKRIQDEKIELIDLKFIDTVGTWQHLTLYQNQIDESSFSDGVPFDGSSIRGWK 60
           MTT QEVLKRIQDEKIELIDLKFIDTVGTWQHLTLYQNQIDESSF+DGVPFDGSSIRGWK
Sbjct: 1   MTTSQEVLKRIQDEKIELIDLKFIDTVGTWQHLTLYQNQIDESSFTDGVPFDGSSIRGWK 60

Query: 61  AINESDMTMVLDPNTAWIDPFMEVPTLSIVCSIKEPRTGEWYNRCPRVIAQKAIDYLVST 120
           AINESDMTMVLDPNTAWIDPFMEVPTLSIVCSIKEPRTGEWYNRCPRVIAQKA+DYLV+T
Sbjct: 61  AINESDMTMVLDPNTAWIDPFMEVPTLSIVCSIKEPRTGEWYNRCPRVIAQKAVDYLVAT 120

Query: 121 GIGDTAFFGPEAEFFIFDSARFAQNANEGYYFLDSVEGAWNSGKEGTADKPNLAYKPRFK 180
           GIGDTAFFGPEAEFFIFDSARFAQ ANEGYYFLDSVEGAWNSGKEGTADKPNLAYKPRFK
Sbjct: 121 GIGDTAFFGPEAEFFIFDSARFAQTANEGYYFLDSVEGAWNSGKEGTADKPNLAYKPRFK 180

Query: 181 EGYFPVSPTDSFQDIRTEMLLTMAKLGVPIEKHHHEVATGGQCELGFRFGKLIEAADWLM 240
           EGYFPVSPTDSFQDIRTEMLLTMAKLGVPIEKHHHEVATGGQCELGFRFGKLIEAADWLM
Sbjct: 181 EGYFPVSPTDSFQDIRTEMLLTMAKLGVPIEKHHHEVATGGQCELGFRFGKLIEAADWLM 240

Query: 241 IYKYVIKNVAKKYGKTVTFMPKPIFGDNGSGMHCHQSIWKDGKPLFAGDQYAGLSEMGLY 300
           IYKYVIKNVAKKYGKTVTFMPKPIFGDNGSGMHCHQSIWKDGKPLFAGDQYAGLSEMGLY
Sbjct: 241 IYKYVIKNVAKKYGKTVTFMPKPIFGDNGSGMHCHQSIWKDGKPLFAGDQYAGLSEMGLY 300

Query: 301 YIGGLLKHAPALLAITNPSTNSYKRLVPGYEAPVNLAYSQGNRSASIRIPLSGTNPKAKR 360
           YIGGLLKHAPALLAITNPSTNSYKRLVPGYEAPVNLAYSQGNRSASIRIPLSGTNPKAKR
Sbjct: 301 YIGGLLKHAPALLAITNPSTNSYKRLVPGYEAPVNLAYSQGNRSASIRIPLSGTNPKAKR 360

Query: 361 LEFRCPDATSNPYLAFAAMLCAGIDGIKNKIHPGEPLDKNIYELSPEELAKVPSTPGSLE 420
           LEFRCPDATSNPYLAFAAMLCAGIDGIKNKIHPGEPLDKNIYELSPEELAKVPSTPGSLE
Sbjct: 361 LEFRCPDATSNPYLAFAAMLCAGIDGIKNKIHPGEPLDKNIYELSPEELAKVPSTPGSLE 420

Query: 421 LALEALENDHAFLTDTGVFTEDFIQNWIDYKLANEVKQMQLRPHPYEFSIYYDV 474
           LALEALENDHAFLTDTGVFTEDFIQNWIDYKLANEVKQMQLRPHPYEFSIYYDV
Sbjct: 421 LALEALENDHAFLTDTGVFTEDFIQNWIDYKLANEVKQMQLRPHPYEFSIYYDV 474


Lambda     K      H
   0.318    0.137    0.420 

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: 949
Number of extensions: 29
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: 474
Length of database: 474
Length adjustment: 33
Effective length of query: 441
Effective length of database: 441
Effective search space:   194481
Effective search space used:   194481
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 WP_011317041.1 AVA_RS00740 (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.2081303.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-208  679.5   0.0   1.3e-208  679.3   0.0    1.0  1  NCBI__GCF_000204075.1:WP_011317041.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011317041.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  679.3   0.0  1.3e-208  1.3e-208       2     462 .]       6     473 ..       5     473 .. 0.98

  Alignments for each domain:
  == domain 1  score: 679.3 bits;  conditional E-value: 1.3e-208
                             TIGR00653   2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvi 74 
                                           evlk +++e+++ +dl+f+D+ G++++++++ ++++e+ +++g+ FDgss++G+k+i+esD+ ++ dp+t+ i
  NCBI__GCF_000204075.1:WP_011317041.1   6 EVLKRIQDEKIELIDLKFIDTVGTWQHLTLYQNQIDESSFTDGVPFDGSSIRGWKAINESDMTMVLDPNTAWI 78 
                                           7899********************************************************************* PP

                             TIGR00653  75 vPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssfl 146
                                           +Pf++ ++l+++c+++ep t+e+y+r+pR ia++a ++l  t++gd+++fGpEaEFf+fd+ +f +++n+ ++
  NCBI__GCF_000204075.1:WP_011317041.1  79 DPFMEVPTLSIVCSIKEPRTGEWYNRCPRVIAQKAVDYLVaTGIGDTAFFGPEAEFFIFDSARFAQTANEGYY 151
                                           ***************************************99******************************** PP

                             TIGR00653 147 evdseegewn..reveeg..nkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaE 214
                                            +ds+eg+wn  +e  ++  n +yk++ k+gYf+v p+D+ +dir+e++l++++lg+ +e++HHEvat+ q E
  NCBI__GCF_000204075.1:WP_011317041.1 152 FLDSVEGAWNsgKEGTADkpNLAYKPRFKEGYFPVSPTDSFQDIRTEMLLTMAKLGVPIEKHHHEVATGgQCE 224
                                           **********664433336799*************************************************** PP

                             TIGR00653 215 idikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLse 287
                                           ++++f kl++aaD +++yKyv+knvakk+Gkt+tFmpKp+fgdngsGmH+h+s+wkdg++lfag++ yagLse
  NCBI__GCF_000204075.1:WP_011317041.1 225 LGFRFGKLIEAADWLMIYKYVIKNVAKKYGKTVTFMPKPIFGDNGSGMHCHQSIWKDGKPLFAGDQ-YAGLSE 296
                                           ******************************************************************.****** PP

                             TIGR00653 288 talyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasa.npkakRiEvRspDps 359
                                           ++lyyigG+lkHa+al A+tnp++nsYkRLvpGyEAPv+lays+ nRsa+iRiP+s  npkakR+E+R+pD++
  NCBI__GCF_000204075.1:WP_011317041.1 297 MGLYYIGGLLKHAPALLAITNPSTNSYKRLVPGYEAPVNLAYSQGNRSASIRIPLSGtNPKAKRLEFRCPDAT 369
                                           ********************************************************99*************** PP

                             TIGR00653 360 anpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlg 430
                                           +npYLafaa+l+Ag+dGiknki+pgepldkn+yels+eel++  ++++p sLe al++le+d+  ++ ++v++
  NCBI__GCF_000204075.1:WP_011317041.1 370 SNPYLAFAAMLCAGIDGIKNKIHPGEPLDKNIYELSPEELAK--VPSTPGSLELALEALENDHafLTDTGVFT 440
                                           ******************************************..*******************99999***** PP

                             TIGR00653 431 eelieafielkr.kEveelrlkvhpvElekyld 462
                                           e++i+++i++k  +Ev++++l++hp+E++ y+d
  NCBI__GCF_000204075.1:WP_011317041.1 441 EDFIQNWIDYKLaNEVKQMQLRPHPYEFSIYYD 473
                                           ***********999*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (462 nodes)
Target sequences:                          1  (474 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: 16.75
//
[ok]

This GapMind analysis is from Jul 25 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:

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