Alignments for a candidate for glnA in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Pseudomonas stutzeri RCH2

Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII (uncharacterized)
to candidate GFF2319 Psest_2367 glutamine synthetase, type III

Query= curated2:P31592
         (435 letters)



>FitnessBrowser__psRCH2:GFF2319
          Length = 454

 Score =  303 bits (776), Expect = 7e-87
 Identities = 175/433 (40%), Positives = 248/433 (57%), Gaps = 17/433 (3%)

Query: 10  RDKSIKYFMISYTDLFGGQRAKLVPAEAIADMQKDGAGFAGFATWLDLTP---AHPDLFA 66
           +DK +KY M SY D+ G  + K VP   +  M +    + G A  LD  P   +  ++ A
Sbjct: 17  QDKGVKYAMASYVDIHGVIKGKFVPIAHLGQMLRGSELYTGAA--LDGVPQEISDNEVAA 74

Query: 67  VPDASSVIQLPWKKDVAWVAADCVMDDRPVEQAPRVVLKRLVAEAAKEGLRVKTGVEPEF 126
           +PD ++  Q  W +D+AW A+D  +D +P E   R +LKR    AA+ G     G+E EF
Sbjct: 75  MPDPATGTQCSWNRDLAWFASDLYLDGKPFEACSRGILKRQTEAAAELGYTFNLGIETEF 134

Query: 127 FLI--SADGSV--ISDQFDTAEKPCYDQQAVMRRYDVIAEICDYMLELGWKPYQNDHEDA 182
           FL   + DG    IS++ D A KPCYD + +M    ++ E+   M E+GW  Y  DHEDA
Sbjct: 135 FLFKDTPDGGFAPISERDDMA-KPCYDPRLLMDNLPIVDELVQAMNEMGWGVYSFDHEDA 193

Query: 183 NGQFEMNWEYDDVLKTADKHSFFKFMVKSVAEKHGLRATFMPKPFKGLTGNGCHAHISVW 242
           NGQFE +++Y D L  AD+  FF+ M   +A KHG  ATFMPKP    TG+G H ++S+ 
Sbjct: 194 NGQFETDFKYTDALGMADRFVFFRMMANEIARKHGAFATFMPKPSANRTGSGAHYNMSLA 253

Query: 243 DVDGRVNAF-ADKEMAF--GLSAQGKTFLGGIMKHAPALAAITNPTVNSYKRINAPRTTS 299
           D++   N F  D E  +  G++     F+ G++KHA A+ A+  PTVNSYKR+      S
Sbjct: 254 DIETGKNLFEVDGEDTYGCGVTPLAYHFIAGVLKHAKAICAVIAPTVNSYKRLIRKGAMS 313

Query: 300 GATWSPNTVTWTGNNRTHMVRVPGPG-RFELRLPDGAVNPYLLQAIIIAAGLEGIRSQAD 358
           G+TW+P    +  NNRT+M+R+P  G R E R  D   NPYL  A+I+AAGLEGIR + D
Sbjct: 314 GSTWAPVFCCYGNNNRTNMLRIPSQGARVECRAADIGCNPYLGAAMILAAGLEGIRDELD 373

Query: 359 PGQHYDIDM--YAEGHLVK-DAPRLPLNLLDALRAFDADEGLKAAIGAEFSSAYLKLKHL 415
           PGQ +  +M  Y+E  +V+     LP  L +A+ AF+AD   +   G     A++  K  
Sbjct: 374 PGQPHRENMYHYSEQEVVQMGIETLPRTLSEAIDAFEADPLSRQVFGDAMYQAFVDFKRD 433

Query: 416 EWNAYCSHFTQWE 428
           EWNAY +H + WE
Sbjct: 434 EWNAYHTHVSDWE 446


Lambda     K      H
   0.320    0.135    0.421 

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: 529
Number of extensions: 22
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 435
Length of database: 454
Length adjustment: 32
Effective length of query: 403
Effective length of database: 422
Effective search space:   170066
Effective search space used:   170066
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate GFF2319 Psest_2367 (glutamine synthetase, type III)
to HMM TIGR03105 (glnT: glutamine synthetase, type III (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/TIGR03105.hmm
# target sequence database:        /tmp/gapView.6111.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03105  [M=435]
Accession:   TIGR03105
Description: gln_synth_III: glutamine synthetase, type III
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-178  579.3   0.0   2.2e-178  579.1   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2319  Psest_2367 glutamine synthetase,


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2319  Psest_2367 glutamine synthetase, type III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.1   0.0  2.2e-178  2.2e-178       2     434 ..      13     451 ..      12     452 .. 0.98

  Alignments for each domain:
  == domain 1  score: 579.1 bits;  conditional E-value: 2.2e-178
                           TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlPwk 76 
                                         k+ l++kgvky +a++vd++Gv k+k+vP+ +l +++++++ ++G a++g+ +e +d++++a+pd+++ +q  w+
  lcl|FitnessBrowser__psRCH2:GFF2319  13 KQQLQDKGVKYAMASYVDIHGVIKGKFVPIAHLGQMLRGSELYTGAALDGVPQEISDNEVAAMPDPATGTQCSWN 87 
                                         7899*********************************************************************** PP

                           TIGR03105  77 pevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpcYDqr 151
                                         +++aw a+dl+++gkp+e  +R +lk++ + aae g+t+++G+e+effl++++ dg+ ++  ++D +akpcYD r
  lcl|FitnessBrowser__psRCH2:GFF2319  88 RDLAWFASDLYLDGKPFEACSRGILKRQTEAAAELGYTFNLGIETEFFLFKDTPDGGFAPISERDDMAKPCYDPR 162
                                         *************************************************************************** PP

                           TIGR03105 152 almrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeegllatfmPkP 226
                                          lm +  +++e+++a+ne+Gw++Y++DheDanGqfe +f+y+Dal +aDr++ff+++++eia+++g  atfmPkP
  lcl|FitnessBrowser__psRCH2:GFF2319 163 LLMDNLPIVDELVQAMNEMGWGVYSFDHEDANGQFETDFKYTDALGMADRFVFFRMMANEIARKHGAFATFMPKP 237
                                         *************************************************************************** PP

                           TIGR03105 227 fadrtGnGlhlhlslld.edgknlfaddad.eeglglsklayhfiaGilkhakaLaallaPtvnsYkRlvakrtl 299
                                          a+rtG+G+h+++sl+d e+gknlf+ d + + g g++ layhfiaG+lkhaka++a++aPtvnsYkRl++k+++
  lcl|FitnessBrowser__psRCH2:GFF2319 238 SANRTGSGAHYNMSLADiETGKNLFEVDGEdTYGCGVTPLAYHFIAGVLKHAKAICAVIAPTVNSYKRLIRKGAM 312
                                         *****************9999****98865489****************************************** PP

                           TIGR03105 300 sgatWaPalisyggnnRthmvRiP.dagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkdenlya... 370
                                         sg tWaP++  yg+nnRt+m+RiP ++ R+e R aD ++npYl +a++laaGL+Gi+++ldpg+++ en+y+   
  lcl|FitnessBrowser__psRCH2:GFF2319 313 SGSTWAPVFCCYGNNNRTNMLRIPsQGARVECRAADIGCNPYLGAAMILAAGLEGIRDELDPGQPHRENMYHyse 387
                                         ************************7778*******************************************9988 PP

                           TIGR03105 371 eelaekgvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryl 434
                                         +e+ ++g+etLP+tL+ea++a+ead+l ++++G+++ ++f+++kr ew++yh++vsdWei+ryl
  lcl|FitnessBrowser__psRCH2:GFF2319 388 QEVVQMGIETLPRTLSEAIDAFEADPLSRQVFGDAMYQAFVDFKRDEWNAYHTHVSDWEIQRYL 451
                                         9999***********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (454 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: 6.94
//
[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