Alignments for a candidate for glnA in Thiomicrorhabdus arctica DSM 13458

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Thiomicrorhabdus arctica DSM 13458

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII; EC 6.3.1.2 (characterized)
to candidate WP_019556640.1 F612_RS0104905 type III glutamate--ammonia ligase

Query= SwissProt::O87393
         (435 letters)



>NCBI__GCF_000381085.1:WP_019556640.1
          Length = 453

 Score =  325 bits (834), Expect = 1e-93
 Identities = 177/435 (40%), Positives = 258/435 (59%), Gaps = 20/435 (4%)

Query: 10  REKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFAT-WFDLTPAHPDLFALP 68
           + KGVKY + +Y D+ G  + K VP +    M KG   + G+A       P   ++ ++P
Sbjct: 15  KAKGVKYCLGAYVDIHGIPKGKFVPIDHFPQMVKGSELYTGYAVDGLGQKPNEDEIASVP 74

Query: 69  DASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKTGVEPEFFL 128
           D +++IQLPW+ +VAW+AAD  +   P +   RV LKK++AEAA+ G     G+E E F+
Sbjct: 75  DLNSLIQLPWQPEVAWMAADNTLHGEPYDINTRVALKKVLAEAAEMGFGFNLGIECELFV 134

Query: 129 ISP--DGS-KISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHEDANGQ 185
           +    DGS  I D  D   KPCYD  + M R+  I ++   + +LGW  Y  DHEDANGQ
Sbjct: 135 VKEEADGSLSIPDKNDNLTKPCYDVSSFMNRFTWIDKMATTIDDLGWDLYSLDHEDANGQ 194

Query: 186 FEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHISVWDLA 245
           +E +++Y DAL   D+  FF++M K  A + GL AT MPKPF   TGNG H ++S++DL 
Sbjct: 195 YEFDFKYSDALTMCDRFIFFRYMAKHYAAEEGLLATMMPKPFADKTGNGAHFNMSLFDLE 254

Query: 246 GEVNAF----ADNKAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPRTISGA 301
            + N F     D+    GL+  G HF+ G++KH  AL AV +PTVNSYKR+     ++  
Sbjct: 255 SKENLFEYDPKDDPRGLGLTEIGYHFIAGVLKHGPALCAVFSPTVNSYKRLVRQGDMATF 314

Query: 302 TWAPNSVTWTGNNRTHMVRVP-GPGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSKADPG 360
           +WAP   ++  NNRT+ VR+P G GRFE R  DGAVNPYL   +++AAGL G+R K DPG
Sbjct: 315 SWAPVFNSFGSNNRTNSVRIPLGGGRFENRNADGAVNPYLAATLVLAAGLEGIREKLDPG 374

Query: 361 RHYDIDMYKDGHKVTDAPK-------LPLNLLDALREYNRDEELQEALGREFSAAYLKLK 413
           +  + ++Y     +T+A +       LP NL DA++ +  D  +++ LG+  S  ++K K
Sbjct: 375 KAQEDNLY----DLTEAERTARGIEFLPQNLNDAVQAFADDPFVEKVLGKGLSDEFIKYK 430

Query: 414 QGEWNTYCSQFTEWE 428
           + EWN Y    + WE
Sbjct: 431 RAEWNDYHQTVSAWE 445


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: 567
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: 453
Length adjustment: 32
Effective length of query: 403
Effective length of database: 421
Effective search space:   169663
Effective search space used:   169663
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 WP_019556640.1 F612_RS0104905 (type III 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.3819803.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-203  662.0   0.0   1.8e-203  661.8   0.0    1.0  1  NCBI__GCF_000381085.1:WP_019556640.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381085.1:WP_019556640.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  661.8   0.0  1.8e-203  1.8e-203       2     434 ..      11     450 ..      10     451 .. 0.98

  Alignments for each domain:
  == domain 1  score: 661.8 bits;  conditional E-value: 1.8e-203
                             TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlP 74 
                                           ++ l++kgvky+l a+vd++G++k+k+vP+++  +++k+++ ++G+av+glg++P+++++++vpdl+sliqlP
  NCBI__GCF_000381085.1:WP_019556640.1  11 QADLKAKGVKYCLGAYVDIHGIPKGKFVPIDHFPQMVKGSELYTGYAVDGLGQKPNEDEIASVPDLNSLIQLP 83 
                                           567899******************************************************************* PP

                             TIGR03105  75 wkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpc 147
                                           w+pevaw+aad++++g+p+++++Rv+lkk+laeaae+gf +++G+ece+f++++e+dg+ls++Dk+D+l+kpc
  NCBI__GCF_000381085.1:WP_019556640.1  84 WQPEVAWMAADNTLHGEPYDINTRVALKKVLAEAAEMGFGFNLGIECELFVVKEEADGSLSIPDKNDNLTKPC 156
                                           ************************************************************************* PP

                             TIGR03105 148 YDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeeglla 220
                                           YD++++m+r+++++++++++ +lGwdlY+ DheDanGq+e++f+y+Dalt++Dr++ff+y++k++a+eeglla
  NCBI__GCF_000381085.1:WP_019556640.1 157 YDVSSFMNRFTWIDKMATTIDDLGWDLYSLDHEDANGQYEFDFKYSDALTMCDRFIFFRYMAKHYAAEEGLLA 229
                                           ************************************************************************* PP

                             TIGR03105 221 tfmPkPfadrtGnGlhlhlslldedg.knlfaddad..eeglglsklayhfiaGilkhakaLaallaPtvnsY 290
                                           t+mPkPfad+tGnG+h+++sl+d ++ +nlf+ d++  ++glgl++++yhfiaG+lkh++aL+a+++PtvnsY
  NCBI__GCF_000381085.1:WP_019556640.1 230 TMMPKPFADKTGNGAHFNMSLFDLESkENLFEYDPKddPRGLGLTEIGYHFIAGVLKHGPALCAVFSPTVNSY 302
                                           ***********************66659***98876569********************************** PP

                             TIGR03105 291 kRlvakrtlsgatWaPalisyggnnRthmvRiP.dagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgk 362
                                           kRlv+++ +++++WaP+++s+g+nnRt++vRiP ++gR+e R+aDga+npYl++++vlaaGL+Gi++kldpgk
  NCBI__GCF_000381085.1:WP_019556640.1 303 KRLVRQGDMATFSWAPVFNSFGSNNRTNSVRIPlGGGRFENRNADGAVNPYLAATLVLAAGLEGIREKLDPGK 375
                                           *********************************99************************************** PP

                             TIGR03105 363 rkdenlya...eelaekgvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidr 432
                                           ++++nly+   +e++++g+e+LPq+L++a++a+++d+++e++lGk+l++ef+k+kr ew++yh+tvs+Wei+r
  NCBI__GCF_000381085.1:WP_019556640.1 376 AQEDNLYDlteAERTARGIEFLPQNLNDAVQAFADDPFVEKVLGKGLSDEFIKYKRAEWNDYHQTVSAWEIKR 448
                                           *******9998899*********************************************************** PP

                             TIGR03105 433 yl 434
                                           y+
  NCBI__GCF_000381085.1:WP_019556640.1 449 YS 450
                                           97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (453 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: 00:00:00.01
# Mc/sec: 17.68
//
[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