GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glnA in Phyllobacterium brassicacearum STM 196

Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase III; GSIII; EC 6.3.1.2 (characterized)
to candidate WP_106712819.1 CU102_RS19800 type III glutamate--ammonia ligase

Query= SwissProt::O87393
         (435 letters)



>NCBI__GCF_003010955.1:WP_106712819.1
          Length = 435

 Score =  802 bits (2071), Expect = 0.0
 Identities = 379/435 (87%), Positives = 403/435 (92%)

Query: 1   MTLDLSTFAREKGVKYFMISYTDLFGGQRAKLVPAEAIADMQKGGAGFAGFATWFDLTPA 60
           MTLDLSTFA E GVKYFMISYTDL GGQRAKLVPA+AIADMQ+ GAGFAGFATW DLTPA
Sbjct: 1   MTLDLSTFAAENGVKYFMISYTDLCGGQRAKLVPAQAIADMQRDGAGFAGFATWLDLTPA 60

Query: 61  HPDLFALPDASAVIQLPWKKDVAWVAADCIMDDAPVEQAPRVVLKKLVAEAAQEGLRVKT 120
           HPDLFA+PDA +VIQLPWK+DVAWVAADC+M+DAPV+QAPRV+LK+LV EA Q+GLRVKT
Sbjct: 61  HPDLFAVPDAGSVIQLPWKRDVAWVAADCMMEDAPVQQAPRVLLKRLVGEARQQGLRVKT 120

Query: 121 GVEPEFFLISPDGSKISDTFDTAEKPCYDQQAIMRRYDVIAEICDYMLELGWKPYQNDHE 180
           GVEPEFFL++PDGS+ISD  D+ EKPCYDQQA+MRRYDVIAEICD MLELGWKPYQNDHE
Sbjct: 121 GVEPEFFLVTPDGSQISDQRDSGEKPCYDQQAVMRRYDVIAEICDCMLELGWKPYQNDHE 180

Query: 181 DANGQFEMNWEYDDALRTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS 240
           DANGQFEMNWEYDDAL TADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS
Sbjct: 181 DANGQFEMNWEYDDALNTADKHSFFKFMVKSIAEKHGLRATFMPKPFKGLTGNGCHCHIS 240

Query: 241 VWDLAGEVNAFADNKAEFGLSAEGRHFLGGIMKHASALAAVTNPTVNSYKRINAPRTISG 300
           VWD+ G  NAFAD +  FGLS  G+ FLGGIMKHASALAAVTNPTVNSYKRINAPRT+SG
Sbjct: 241 VWDVEGRTNAFADKRMPFGLSENGKTFLGGIMKHASALAAVTNPTVNSYKRINAPRTVSG 300

Query: 301 ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGVRSKADPG 360
           ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSG+R+ ADPG
Sbjct: 301 ATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGLRTNADPG 360

Query: 361 RHYDIDMYKDGHKVTDAPKLPLNLLDALREYNRDEELQEALGREFSAAYLKLKQGEWNTY 420
           RHYDIDMYKDGH VTDAPKLPLNLLDALR Y  DEELQ ALG EFS+AYLKLK  EWN Y
Sbjct: 361 RHYDIDMYKDGHTVTDAPKLPLNLLDALRAYESDEELQVALGTEFSSAYLKLKHSEWNAY 420

Query: 421 CSQFTEWEHQTTLDV 435
           CSQFTEWEHQTTLD+
Sbjct: 421 CSQFTEWEHQTTLDI 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: 788
Number of extensions: 27
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 WP_106712819.1 CU102_RS19800 (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.2550268.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     5e-205  666.9   0.0   5.6e-205  666.8   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106712819.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106712819.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.8   0.0  5.6e-205  5.6e-205       2     435 .]       6     434 ..       5     434 .. 0.99

  Alignments for each domain:
  == domain 1  score: 666.8 bits;  conditional E-value: 5.6e-205
                             TIGR03105   2 kklleekgvkyvlaafvdllGvakaklvPvealdalakegagfaGfavsglglePadadllavpdldsliqlP 74 
                                           +++++e+gvky++++++dl G ++aklvP++a+++++++gagfaGfa++ l+l+Pa++dl+avpd+ s+iqlP
  NCBI__GCF_003010955.1:WP_106712819.1   6 STFAAENGVKYFMISYTDLCGGQRAKLVPAQAIADMQRDGAGFAGFATW-LDLTPAHPDLFAVPDAGSVIQLP 77 
                                           67899********************************************.*********************** PP

                             TIGR03105  75 wkpevawvaadlvvegkpvelapRvvlkkllaeaaekgftlktGveceffllrreedgklsvaDkaDklakpc 147
                                           wk++vawvaad+++e++pv++apRv+lk+l+ ea ++g+++ktGve+effl++ +   +++++D++D+ +kpc
  NCBI__GCF_003010955.1:WP_106712819.1  78 WKRDVAWVAADCMMEDAPVQQAPRVLLKRLVGEARQQGLRVKTGVEPEFFLVTPD---GSQISDQRDSGEKPC 147
                                           ******************************************************9...899************ PP

                             TIGR03105 148 YDqralmrrydvleeisealnelGwdlYqiDheDanGqfelnfeyaDalttaDrvaffkylvkeiaeeeglla 220
                                           YDq+a+mrrydv++ei++++ elGw++Yq+DheDanGqfe+n+ey+Dal taD+++ffk++vk+iae++gl+a
  NCBI__GCF_003010955.1:WP_106712819.1 148 YDQQAVMRRYDVIAEICDCMLELGWKPYQNDHEDANGQFEMNWEYDDALNTADKHSFFKFMVKSIAEKHGLRA 220
                                           ************************************************************************* PP

                             TIGR03105 221 tfmPkPfadrtGnGlhlhlslldedg.knlfaddadeeglglsklayhfiaGilkhakaLaallaPtvnsYkR 292
                                           tfmPkPf+ +tGnG+h+h+s++d +g +n+fad+  ++ +gls+ +++f++Gi+kha+aLaa+++PtvnsYkR
  NCBI__GCF_003010955.1:WP_106712819.1 221 TFMPKPFKGLTGNGCHCHISVWDVEGrTNAFADK--RMPFGLSENGKTFLGGIMKHASALAAVTNPTVNSYKR 291
                                           *************************989*****9..9************************************ PP

                             TIGR03105 293 lvakrtlsgatWaPalisyggnnRthmvRiPdagRlelRlaDgaanpYlvsaavlaaGLdGierkldpgkrkd 365
                                           ++a+rt+sgatWaP+ ++++gnnRthmvR+P++gR+elRl+Dga+npYl++a+++aaGL G++ ++dpg+++d
  NCBI__GCF_003010955.1:WP_106712819.1 292 INAPRTVSGATWAPNSVTWTGNNRTHMVRVPGPGRFELRLPDGAVNPYLLQAIIIAAGLSGLRTNADPGRHYD 364
                                           ************************************************************************* PP

                             TIGR03105 366 enlyaeelaekgvetLPqtLlealraleadelleealGkelveeflklkreeweeyhrtvsdWeidryle 435
                                           +++y+++++++++ +LP +Ll+alra+e+de l+ alG+e+++++lklk++ew++y++++++We +++l+
  NCBI__GCF_003010955.1:WP_106712819.1 365 IDMYKDGHTVTDAPKLPLNLLDALRAYESDEELQVALGTEFSSAYLKLKHSEWNAYCSQFTEWEHQTTLD 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.98
//
[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:

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:

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:

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:

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