Alignments for a candidate for glnA in Ruegeria conchae TW15

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Ruegeria conchae TW15

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII; EC 6.3.1.2 (characterized)
to candidate WP_010437776.1 G7G_RS0101980 type III glutamate--ammonia ligase

Query= SwissProt::O87393
         (435 letters)



>NCBI__GCF_000192475.1:WP_010437776.1
          Length = 442

 Score =  710 bits (1832), Expect = 0.0
 Identities = 330/442 (74%), Positives = 381/442 (86%), Gaps = 7/442 (1%)

Query: 1   MTLDLSTFAREKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATWFDLTPA 60
           MT DL+ FA+EKGVKYFMIS+TDLFGGQRAKLVPA+AIA+MQ+ GAGFAGFATW D+TPA
Sbjct: 1   MTTDLAAFAKEKGVKYFMISFTDLFGGQRAKLVPAQAIAEMQEDGAGFAGFATWLDMTPA 60

Query: 61  HPDLFALPDASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKT 120
           HPD+ A+PD S+VIQLPWK +VAWVA +C+M+   V QAPR VL++L+ EAA+ G+ VKT
Sbjct: 61  HPDMLAVPDPSSVIQLPWKPEVAWVAGNCVMEGKDVAQAPRNVLRRLIGEAAEMGMHVKT 120

Query: 121 GVEPEFFLISPDGSKISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHE 180
           G+E EFFL++PDG +ISD FDTAEKPCYDQQA+MRRYDV+ EICDYMLELGW PYQNDHE
Sbjct: 121 GIEAEFFLLTPDGEQISDPFDTAEKPCYDQQAVMRRYDVVREICDYMLELGWGPYQNDHE 180

Query: 181 DANGQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS 240
           DANGQFEMNWE+DD L+TADKHSFFKFM KS+AEKHGLRATFMPKP +GLTGNGCH HIS
Sbjct: 181 DANGQFEMNWEFDDVLKTADKHSFFKFMTKSVAEKHGLRATFMPKPVEGLTGNGCHAHIS 240

Query: 241 VWDLAG---EVNAFADN----KAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRIN 293
           VWD  G   + N FA        E GL  +G+HFLGGIMKHASALAA+TNPTVNSYKRIN
Sbjct: 241 VWDAPGADAKTNVFAGEGDGPTGEVGLGEQGKHFLGGIMKHASALAAITNPTVNSYKRIN 300

Query: 294 APRTISGATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGV 353
           APRT+SGATWAPN+VTWTGNNRTHMVRVPGPGRFELRL DGA NPYLLQA+IIAAGLSG+
Sbjct: 301 APRTMSGATWAPNTVTWTGNNRTHMVRVPGPGRFELRLADGATNPYLLQAVIIAAGLSGI 360

Query: 354 RSKADPGRHYDIDMYKDGHKVTDAPKLPLNLLDALREYNRDEELQEALGREFSAAYLKLK 413
           RSKADPGR +DIDMY +GH VTDAPKLPLN+LD LREY+ D EL+  +G+EFS+A+LK+K
Sbjct: 361 RSKADPGRRWDIDMYAEGHTVTDAPKLPLNMLDGLREYDNDTELKAMMGQEFSSAFLKMK 420

Query: 414 QGEWNTYCSQFTEWEHQTTLDV 435
             EWN++ S F+ WE   TLD+
Sbjct: 421 HQEWNSFVSHFSRWEKDHTLDI 442


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: 767
Number of extensions: 26
Number of successful extensions: 2
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: 442
Length adjustment: 32
Effective length of query: 403
Effective length of database: 410
Effective search space:   165230
Effective search space used:   165230
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_010437776.1 G7G_RS0101980 (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.3088173.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.6e-201  653.4   0.0   7.5e-201  653.2   0.0    1.0  1  NCBI__GCF_000192475.1:WP_010437776.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010437776.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  653.2   0.0  7.5e-201  7.5e-201       2     435 .]       6     441 ..       5     441 .. 0.98

  Alignments for each domain:
  == domain 1  score: 653.2 bits;  conditional E-value: 7.5e-201
                             TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlP 74 
                                           +++++ekgvky++++f+dl+G ++aklvP++a+++++++gagfaGfa++ l+++Pa++d+lavpd++s+iqlP
  NCBI__GCF_000192475.1:WP_010437776.1   6 AAFAKEKGVKYFMISFTDLFGGQRAKLVPAQAIAEMQEDGAGFAGFATW-LDMTPAHPDMLAVPDPSSVIQLP 77 
                                           6799*********************************************.*********************** PP

                             TIGR03105  75 wkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpc 147
                                           wkpevawva+++v+egk v++apR+vl++l+ eaae+g+++ktG+e+effll+ +   + +++D  D+++kpc
  NCBI__GCF_000192475.1:WP_010437776.1  78 WKPEVAWVAGNCVMEGKDVAQAPRNVLRRLIGEAAEMGMHVKTGIEAEFFLLTPD---GEQISDPFDTAEKPC 147
                                           ******************************************************9...789************ PP

                             TIGR03105 148 YDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeeglla 220
                                           YDq+a+mrrydv++ei++++ elGw++Yq+DheDanGqfe+n+e++D+l+taD+++ffk+++k++ae++gl+a
  NCBI__GCF_000192475.1:WP_010437776.1 148 YDQQAVMRRYDVVREICDYMLELGWGPYQNDHEDANGQFEMNWEFDDVLKTADKHSFFKFMTKSVAEKHGLRA 220
                                           ************************************************************************* PP

                             TIGR03105 221 tfmPkPfadrtGnGlhlhlslldedg....knlfaddad..eeglglsklayhfiaGilkhakaLaallaPtv 287
                                           tfmPkP + +tGnG+h+h+s++d+ g    +n+fa + d  + ++gl ++++hf++Gi+kha+aLaa+++Ptv
  NCBI__GCF_000192475.1:WP_010437776.1 221 TFMPKPVEGLTGNGCHAHISVWDAPGadakTNVFAGEGDgpTGEVGLGEQGKHFLGGIMKHASALAAITNPTV 293
                                           ***********************665444689****99987899***************************** PP

                             TIGR03105 288 nsYkRlvakrtlsgatWaPalisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaavlaaGLdGierkldp 360
                                           nsYkR++a+rt+sgatWaP++++++gnnRthmvR+P++gR+elRlaDga+npYl++a+++aaGL Gi++k+dp
  NCBI__GCF_000192475.1:WP_010437776.1 294 NSYKRINAPRTMSGATWAPNTVTWTGNNRTHMVRVPGPGRFELRLADGATNPYLLQAVIIAAGLSGIRSKADP 366
                                           ************************************************************************* PP

                             TIGR03105 361 gkrkdenlyaeelaekgvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidry 433
                                           g+r d+++yae+++++++ +LP ++l+ lr++++d+ l++ +G+e++++flk+k++ew+++ +++s We d++
  NCBI__GCF_000192475.1:WP_010437776.1 367 GRRWDIDMYAEGHTVTDAPKLPLNMLDGLREYDNDTELKAMMGQEFSSAFLKMKHQEWNSFVSHFSRWEKDHT 439
                                           ************************************************************************9 PP

                             TIGR03105 434 le 435
                                           l+
  NCBI__GCF_000192475.1:WP_010437776.1 440 LD 441
                                           85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (442 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.01
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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