Alignments for a candidate for glnA in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Marinobacter adhaerens HP15

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII; EC 6.3.1.2 (characterized)
to candidate GFF3214 HP15_3156 glutamate-ammonia ligase

Query= SwissProt::O87393
         (435 letters)



>FitnessBrowser__Marino:GFF3214
          Length = 452

 Score =  301 bits (771), Expect = 3e-86
 Identities = 168/432 (38%), Positives = 244/432 (56%), Gaps = 17/432 (3%)

Query: 11  EKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATWFDLTP---AHPDLFAL 67
           E+GVKY + SY D+ G  + K VP   +  M +G   + G A   D  P   +  ++ ++
Sbjct: 16  EEGVKYAIASYVDIHGVTKGKFVPVAHLGQMMEGSELYTGAA--LDGVPQDISDDEVASM 73

Query: 68  PDASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKTGVEPEFF 127
           PDA  +   PW + +AW   +  ++  P E   R +L++ ++ AA  G R   G+E EFF
Sbjct: 74  PDADGLAICPWNRQLAWFPGNLFLNGTPFEACSRNILRRQLSAAADMGYRFNLGIETEFF 133

Query: 128 LI--SPDG--SKISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHEDAN 183
           L   + DG  + +SD  D   KPCYD + +M    ++ E+ D M ELGW  Y  DHEDAN
Sbjct: 134 LFRDTEDGGFAPLSDR-DNLGKPCYDPRTLMDNLPIMDELVDAMNELGWDVYSFDHEDAN 192

Query: 184 GQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHISVWD 243
           GQFE +++Y DAL  +D+  FF+ M   IA KHG  A+FMPKPF   TG+G H ++S+ D
Sbjct: 193 GQFETDFKYADALTMSDRLVFFRMMANEIARKHGAFASFMPKPFADRTGSGAHYNMSLAD 252

Query: 244 LAGEVNAF---ADNKAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPRTISG 300
           L    N F    D+    G+S    HF  G++KH +A++AV  PTVNSYKR+    ++SG
Sbjct: 253 LKTGENLFEPRGDDLHNCGISKIAYHFTAGVLKHGAAISAVIAPTVNSYKRLVRQGSMSG 312

Query: 301 ATWAPNSVTWTGNNRTHMVRVPG-PGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSKADP 359
           +TWAP  + +  NNRT+M+R+PG  GR E R  D A NPYL  A+I+AAGL G+R   D 
Sbjct: 313 STWAPVFMCYGSNNRTNMIRIPGMGGRIECRAADIACNPYLGSALILAAGLEGIREGLDA 372

Query: 360 G--RHYDIDMYKDGHKVTDAPK-LPLNLLDALREYNRDEELQEALGREFSAAYLKLKQGE 416
           G   H ++  Y D        + LP NL +A+  +  D   +E  G     +++  K+GE
Sbjct: 373 GAPHHENMYNYSDAEIAEQGIEYLPRNLGEAVEAFEADPLAKEVFGEAMFNSFIDFKKGE 432

Query: 417 WNTYCSQFTEWE 428
           W +Y +  + WE
Sbjct: 433 WESYQNHVSSWE 444


Lambda     K      H
   0.319    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: 502
Number of extensions: 25
Number of successful extensions: 6
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: 435
Length of database: 452
Length adjustment: 32
Effective length of query: 403
Effective length of database: 420
Effective search space:   169260
Effective search space used:   169260
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 GFF3214 HP15_3156 (glutamate-ammonia ligase)
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.9072.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.3e-179  581.9   0.0   3.8e-179  581.7   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3214  HP15_3156 glutamate-ammonia liga


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3214  HP15_3156 glutamate-ammonia ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.7   0.0  3.8e-179  3.8e-179       2     434 ..      11     449 ..      10     450 .. 0.98

  Alignments for each domain:
  == domain 1  score: 581.7 bits;  conditional E-value: 3.8e-179
                           TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlPwk 76 
                                         k+ l e+gvky +a++vd++Gv+k+k+vPv +l +++++++ ++G a++g+ +  +d++++++pd+d l   Pw+
  lcl|FitnessBrowser__Marino:GFF3214  11 KEKLTEEGVKYAIASYVDIHGVTKGKFVPVAHLGQMMEGSELYTGAALDGVPQDISDDEVASMPDADGLAICPWN 85 
                                         678899********************************************************************* PP

                           TIGR03105  77 pevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpcYDqr 151
                                         +++aw +++l+++g+p+e  +R++l+++l+ aa++g+++++G+e+effl+r++edg+ ++  ++D+l kpcYD r
  lcl|FitnessBrowser__Marino:GFF3214  86 RQLAWFPGNLFLNGTPFEACSRNILRRQLSAAADMGYRFNLGIETEFFLFRDTEDGGFAPLSDRDNLGKPCYDPR 160
                                         *************************************************************************** PP

                           TIGR03105 152 almrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeegllatfmPkP 226
                                         +lm +  +++e+++a+nelGwd+Y++DheDanGqfe +f+yaDalt++Dr++ff+++++eia+++g  a+fmPkP
  lcl|FitnessBrowser__Marino:GFF3214 161 TLMDNLPIMDELVDAMNELGWDVYSFDHEDANGQFETDFKYADALTMSDRLVFFRMMANEIARKHGAFASFMPKP 235
                                         *************************************************************************** PP

                           TIGR03105 227 fadrtGnGlhlhlslld.edgknlfaddad.eeglglsklayhfiaGilkhakaLaallaPtvnsYkRlvakrtl 299
                                         fadrtG+G+h+++sl+d ++g+nlf+ + d  ++ g+sk+ayhf aG+lkh++a++a++aPtvnsYkRlv+++++
  lcl|FitnessBrowser__Marino:GFF3214 236 FADRTGSGAHYNMSLADlKTGENLFEPRGDdLHNCGISKIAYHFTAGVLKHGAAISAVIAPTVNSYKRLVRQGSM 310
                                         *****************999******99875899***************************************** PP

                           TIGR03105 300 sgatWaPalisyggnnRthmvRiP.dagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkdenlya... 370
                                         sg tWaP+++ yg+nnRt+m+RiP  +gR+e R aD a+npYl sa++laaGL+Gi++ ld+g++++en+y+   
  lcl|FitnessBrowser__Marino:GFF3214 311 SGSTWAPVFMCYGSNNRTNMIRIPgMGGRIECRAADIACNPYLGSALILAAGLEGIREGLDAGAPHHENMYNysd 385
                                         ************************5579*******************************************9998 PP

                           TIGR03105 371 eelaekgvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryl 434
                                         +e+ae+g+e LP++L ea++a+ead+l +e++G+++ ++f+++k+ ewe+y+++vs+We+dryl
  lcl|FitnessBrowser__Marino:GFF3214 386 AEIAEQGIEYLPRNLGEAVEAFEADPLAKEVFGEAMFNSFIDFKKGEWESYQNHVSSWEVDRYL 449
                                         99*************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (452 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: 00:00:00.01
# Mc/sec: 11.02
//
[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