Alignments for a candidate for glnA in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for glnA in Sinorhizobium meliloti 1021

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII; EC 6.3.1.2 (characterized)
to candidate SMc02613 SMc02613 glutamine synthetase

Query= SwissProt::O87393
         (435 letters)



>FitnessBrowser__Smeli:SMc02613
          Length = 435

 Score =  900 bits (2325), Expect = 0.0
 Identities = 435/435 (100%), Positives = 435/435 (100%)

Query: 1   MTLDLSTFAREKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATWFDLTPA 60
           MTLDLSTFAREKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATWFDLTPA
Sbjct: 1   MTLDLSTFAREKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATWFDLTPA 60

Query: 61  HPDLFALPDASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKT 120
           HPDLFALPDASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKT
Sbjct: 61  HPDLFALPDASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKT 120

Query: 121 GVEPEFFLISPDGSKISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHE 180
           GVEPEFFLISPDGSKISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHE
Sbjct: 121 GVEPEFFLISPDGSKISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHE 180

Query: 181 DANGQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS 240
           DANGQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS
Sbjct: 181 DANGQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS 240

Query: 241 VWDLAGEVNAFADNKAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPRTISG 300
           VWDLAGEVNAFADNKAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPRTISG
Sbjct: 241 VWDLAGEVNAFADNKAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPRTISG 300

Query: 301 ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSKADPG 360
           ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSKADPG
Sbjct: 301 ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSKADPG 360

Query: 361 RHYDIDMYKDGHKVTDAPKLPLNLLDALREYNRDEELQEALGREFSAAYLKLKQGEWNTY 420
           RHYDIDMYKDGHKVTDAPKLPLNLLDALREYNRDEELQEALGREFSAAYLKLKQGEWNTY
Sbjct: 361 RHYDIDMYKDGHKVTDAPKLPLNLLDALREYNRDEELQEALGREFSAAYLKLKQGEWNTY 420

Query: 421 CSQFTEWEHQTTLDV 435
           CSQFTEWEHQTTLDV
Sbjct: 421 CSQFTEWEHQTTLDV 435


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: 850
Number of extensions: 24
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: 435
Length of database: 435
Length adjustment: 32
Effective length of query: 403
Effective length of database: 403
Effective search space:   162409
Effective search space used:   162409
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 SMc02613 SMc02613 (glutamine synthetase)
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.7728.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.3e-206  672.2   0.0   1.5e-206  672.0   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc02613  SMc02613 glutamine synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02613  SMc02613 glutamine synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.0   0.0  1.5e-206  1.5e-206       2     435 .]       6     434 ..       5     434 .. 0.99

  Alignments for each domain:
  == domain 1  score: 672.0 bits;  conditional E-value: 1.5e-206
                           TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlPwk 76 
                                         +++++ekgvky++++++dl+G ++aklvP+ea+++++k+gagfaGfa++ ++l+Pa++dl+a+pd++++iqlPwk
  lcl|FitnessBrowser__Smeli:SMc02613   6 STFAREKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATW-FDLTPAHPDLFALPDASAVIQLPWK 79 
                                         6799*********************************************.************************* PP

                           TIGR03105  77 pevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpcYDqr 151
                                         ++vawvaad++++++pve+apRvvlkkl+aeaa++g+++ktGve+effl++ +   +++++D+ D+++kpcYDq+
  lcl|FitnessBrowser__Smeli:SMc02613  80 KDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKTGVEPEFFLISPD---GSKISDTFDTAEKPCYDQQ 151
                                         ****************************************************9...899**************** PP

                           TIGR03105 152 almrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeegllatfmPkP 226
                                         a+mrrydv++ei++++ elGw++Yq+DheDanGqfe+n+ey+Dal taD+++ffk++vk+iae++gl+atfmPkP
  lcl|FitnessBrowser__Smeli:SMc02613 152 AIMRRYDVIAEICDYMLELGWKPYQNDHEDANGQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKP 226
                                         *************************************************************************** PP

                           TIGR03105 227 fadrtGnGlhlhlslldedg.knlfaddadeeglglsklayhfiaGilkhakaLaallaPtvnsYkRlvakrtls 300
                                         f+ +tGnG+h+h+s++d  g  n+fad+  ++++gls+ + hf++Gi+kha+aLaa+++PtvnsYkR++a+rt+s
  lcl|FitnessBrowser__Smeli:SMc02613 227 FKGLTGNGCHCHISVWDLAGeVNAFADN--KAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPRTIS 299
                                         *****************99989*****9..9******************************************** PP

                           TIGR03105 301 gatWaPalisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkdenlyaeelae 375
                                         gatWaP+ ++++gnnRthmvR+P++gR+elRl+Dga+npYl++a+++aaGL G+++k+dpg+++d+++y++++++
  lcl|FitnessBrowser__Smeli:SMc02613 300 GATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSKADPGRHYDIDMYKDGHKV 374
                                         *************************************************************************** PP

                           TIGR03105 376 kgvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryle 435
                                         +++ +LP +Ll+alr++++de l+ealG+e+++++lklk+ ew++y++++++We +++l+
  lcl|FitnessBrowser__Smeli:SMc02613 375 TDAPKLPLNLLDALREYNRDEELQEALGREFSAAYLKLKQGEWNTYCSQFTEWEHQTTLD 434
                                         ********************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (435 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: 11.29
//
[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